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	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	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
Unknown	0	broad.mit.edu	37	1	726626	726630	+	IGR	DEL	GACTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:726626_726630delGACTC								LOC100133331 (46890 upstream) : NCRNA00115 (34957 downstream)																																			---	---	---	---
CDK11B	984	broad.mit.edu	37	1	1650497	1650498	+	Intron	INS	-	AG	AG	rs111891151		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1650497_1650498insAG	uc001agv.1	-						CDK11B_uc001ags.1_5'Flank|CDK11B_uc001agt.1_5'Flank|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc009vkr.2_Intron|CDK11A_uc009vks.2_Intron|CDK11A_uc010nys.1_Intron|CDK11A_uc010nyt.1_Intron|CDK11A_uc010nyu.1_Intron|CDK11A_uc009vkt.1_Intron|CDK11A_uc009vku.1_Intron|CDK11A_uc009vkv.1_Intron|CDK11A_uc001aht.1_Intron|CDK11B_uc001ahu.1_Intron|CDK11B_uc001ahv.1_Intron|CDK11B_uc001ahw.1_Intron	NM_033486	NP_277021			cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1																		---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2021925	2021925	+	Intron	DEL	C	-	-	rs138250449		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2021925delC	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
MORN1	79906	broad.mit.edu	37	1	2283628	2283628	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2283628delA	uc001ajb.1	-						MORN1_uc009vld.2_Intron|LOC100129534_uc001ajc.3_RNA	NM_024848	NP_079124			MORN repeat containing 1											ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-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;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5727060	5727060	+	Intron	DEL	T	-	-	rs35495212		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5727060delT	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5768292	5768292	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5768292delC								AJAP1 (924442 upstream) : NPHP4 (154578 downstream)																																			---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	6051166	6051166	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6051166delT	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron|KCNAB2_uc009vlv.1_5'Flank	NM_015102	NP_055917			nephroretinin						actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6257785delT	uc001amd.2	-	2	90	c.44delA	c.(43-45)AAGfs	p.K15fs	RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs	NM_000983	NP_000974	P35268	RL22_HUMAN	ribosomal protein L22 proprotein	15					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|RNA binding|structural constituent of ribosome				0	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)				T	RUNX1	AML|CML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	6833551	6833551	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6833551delG								DNAJC11 (71585 upstream) : CAMTA1 (11833 downstream)																																			---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	6986745	6986746	+	Intron	INS	-	TCCTTCCC	TCCTTCCC	rs145722380	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6986745_6986746insTCCTTCCC	uc001aoi.2	+							NM_015215	NP_056030			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8069679	8069679	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8069679delA								PARK7 (24338 upstream) : ERRFI1 (2101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8187396	8187396	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8187396delC								ERRFI1 (101003 upstream) : SLC45A1 (196994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8318160	8318160	+	IGR	DEL	T	-	-	rs113834861		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8318160delT								ERRFI1 (231767 upstream) : SLC45A1 (66230 downstream)																																			---	---	---	---
RERE	473	broad.mit.edu	37	1	8616683	8616683	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8616683delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234			atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
SLC25A33	84275	broad.mit.edu	37	1	9601046	9601048	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9601046_9601048delTTT	uc001apw.2	+						SLC25A33_uc001apx.2_Intron	NM_032315	NP_115691			mitochondrial carrier protein MGC4399						transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PGD	5226	broad.mit.edu	37	1	10477770	10477770	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10477770delT	uc001arc.2	+						PGD_uc001ard.2_Intron|PGD_uc010oak.1_Intron|PGD_uc010oal.1_Intron	NM_002631	NP_002622			phosphogluconate dehydrogenase						pentose-phosphate shunt, oxidative branch	cytosol	NADP binding|phosphogluconate dehydrogenase (decarboxylating) activity|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
APITD1	378708	broad.mit.edu	37	1	10499798	10499798	+	Intron	DEL	A	-	-	rs77332195		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10499798delA	uc001are.2	+						APITD1_uc001arf.2_Intron|APITD1_uc001arg.2_Intron|APITD1_uc001arh.2_Intron	NM_199294	NP_954988			apoptosis-inducing, TAF9-like domain 1 isoform						DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10835419	10835420	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10835419_10835420delTT	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312			castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10977845	10977846	+	IGR	INS	-	AAAATTGTCAAC	AAAATTGTCAAC	rs144185712	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10977845_10977846insAAAATTGTCAAC								CASZ1 (121138 upstream) : C1orf127 (28687 downstream)																																			---	---	---	---
EXOSC10	5394	broad.mit.edu	37	1	11142385	11142386	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11142385_11142386delCA	uc001asa.2	-						EXOSC10_uc001asb.2_Intron|EXOSC10_uc009vmy.1_Intron	NM_001001998	NP_001001998			exosome component 10 isoform 1						CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)														---	---	---	---
EXOSC10	5394	broad.mit.edu	37	1	11158219	11158219	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11158219delA	uc001asa.2	-						EXOSC10_uc001asb.2_Intron|EXOSC10_uc009vmy.1_Intron	NM_001001998	NP_001001998			exosome component 10 isoform 1						CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11618033	11618033	+	IGR	DEL	G	-	-	rs57064183		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11618033delG								PTCHD2 (20394 upstream) : FBXO2 (90417 downstream)																																			---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12385320	12385320	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12385320delT	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc001aty.1_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	13218513	13218513	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13218513delA								LOC440563 (34546 upstream) : PRAMEF3 (110320 downstream)																																			---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13719052	13719052	+	3'UTR	DEL	T	-	-	rs141370897	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13719052delT	uc009vnz.1	+	3						NM_001099851	NP_001093321			PRAME family member 17												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14194397	14194397	+	IGR	DEL	A	-	-	rs35375614		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14194397delA								PRDM2 (42825 upstream) : KAZ (730816 downstream)																																			---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16186937	16186938	+	Intron	INS	-	GT	GT	rs141891929	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16186937_16186938insGT	uc001axk.1	+							NM_015001	NP_055816			spen homolog, transcriptional regulator						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
CROCCL1	84809	broad.mit.edu	37	1	16960418	16960418	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16960418delA	uc001azg.1	-						CROCCL1_uc009vov.1_5'Flank|CROCCL1_uc001aze.2_5'Flank|CROCCL1_uc001azf.2_5'Flank|CROCCL1_uc001azi.1_Intron|uc001azj.1_Intron					Homo sapiens mRNA for FLJ00313 protein.												0																		---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17106515	17106516	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17106515_17106516delAC	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17195763	17195763	+	Intron	DEL	A	-	-	rs68102505		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17195763delA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17202568	17202568	+	Intron	DEL	T	-	-	rs68120347		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17202568delT	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17229591	17229592	+	Intron	INS	-	TT	TT	rs112049170		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229591_17229592insTT	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19349591	19349591	+	IGR	DEL	C	-	-	rs28437983	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19349591delC								IFFO2 (66765 upstream) : UBR4 (49013 downstream)																																			---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19557064	19557064	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19557064delA	uc001bbo.2	-						KIAA0090_uc001bbp.2_Intron|KIAA0090_uc001bbq.2_Intron|KIAA0090_uc001bbr.2_Intron	NM_015047	NP_055862			hypothetical protein LOC23065 precursor							integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20066382	20066382	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20066382delC	uc001bcn.2	-	12	1356	c.1114delG	c.(1114-1116)GTGfs	p.V372fs	TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Frame_Shift_Del_p.V372fs|TMCO4_uc001bcp.1_Frame_Shift_Del_p.V332fs	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	372						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20075854	20075854	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20075854delT	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Intron|TMCO4_uc001bcq.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20152172	20152172	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20152172delT								RNF186 (10401 upstream) : OTUD3 (56716 downstream)																																			---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21793229	21793229	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21793229delA	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640			neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
ALPL	249	broad.mit.edu	37	1	21901025	21901026	+	Intron	INS	-	AC	AC	rs143241632	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21901025_21901026insAC	uc001bet.2	+						ALPL_uc010odn.1_Intron|ALPL_uc010odo.1_Intron|ALPL_uc010odp.1_Intron|ALPL_uc001beu.3_Intron	NM_000478	NP_000469			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)											OREG0013206	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
USP48	84196	broad.mit.edu	37	1	22030892	22030892	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22030892delA	uc001bfb.2	-						USP48_uc001bfa.2_Intron|USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron|USP48_uc001bfd.1_5'UTR	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22222627	22222627	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22222627delC	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron|HSPG2_uc009vqe.1_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22235083	22235084	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22235083_22235084delAA	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	22557632	22557635	+	IGR	DEL	CATC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22557632_22557635delCATC								WNT4 (87247 upstream) : ZBTB40 (220709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22591829	22591836	+	IGR	DEL	TGTGTGTG	-	-	rs72131998		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22591829_22591836delTGTGTGTG								WNT4 (121444 upstream) : ZBTB40 (186508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22881578	22881583	+	IGR	DEL	CACGCG	-	-	rs5012140	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22881578_22881583delCACGCG								ZBTB40 (23928 upstream) : EPHA8 (8421 downstream)																																			---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23762668	23762668	+	Intron	DEL	T	-	-	rs77206819		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23762668delT	uc001bha.2	-						ASAP3_uc001bgy.1_Intron|ASAP3_uc001bgz.1_Intron|ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhb.2_Intron	NM_017707	NP_060177			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
HMGCL	3155	broad.mit.edu	37	1	24141978	24141978	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24141978delT	uc001bib.2	-						HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Intron|HMGCL_uc009vqs.1_Intron|HMGCL_uc001bid.1_Intron	NM_000191	NP_000182			3-hydroxy-3-methylglutaryl CoA lyase isoform 1						acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)														---	---	---	---
FUCA1	2517	broad.mit.edu	37	1	24175456	24175457	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24175456_24175457delTT	uc001bie.2	-							NM_000147	NP_000138			fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)														---	---	---	---
SRRM1	10250	broad.mit.edu	37	1	24996096	24996096	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24996096delT	uc001bjm.2	+						SRRM1_uc010oel.1_Intron|SRRM1_uc009vri.1_Intron	NM_005839	NP_005830			serine/arginine repetitive matrix 1						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)														---	---	---	---
CLIC4	25932	broad.mit.edu	37	1	25166334	25166334	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25166334delT	uc001bjo.2	+						CLIC4_uc001bjn.2_Intron|CLIC4_uc001bjp.1_Intron	NM_013943	NP_039234			chloride intracellular channel 4						cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)														---	---	---	---
RHCE	6006	broad.mit.edu	37	1	25698581	25698581	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25698581delA	uc001bkf.2	-						RHCE_uc001bkg.2_Intron|RHCE_uc001bkh.2_Intron|RHCE_uc001bki.2_Intron|RHCE_uc001bkj.2_Intron	NM_020485	NP_065231			Rhesus blood group, CcEe antigens isoform 1							integral to plasma membrane					0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ZDHHC18	84243	broad.mit.edu	37	1	27164491	27164493	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27164491_27164493delTTT	uc001bnb.2	+						ZDHHC18_uc010ofh.1_Intron	NM_032283	NP_115659			zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)														---	---	---	---
FAM76A	199870	broad.mit.edu	37	1	28086990	28086990	+	Intron	DEL	T	-	-	rs111588196		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28086990delT	uc001boq.2	+						FAM76A_uc001bor.2_Intron|FAM76A_uc001bos.2_Intron|FAM76A_uc001bot.2_Intron|FAM76A_uc010ofm.1_Intron	NM_152660	NP_689873			hypothetical protein LOC199870 isoform 3												0		Colorectal(325;0.000147)|all_lung(284;0.00181)|Lung NSC(340;0.00278)|Renal(390;0.00357)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00253)|KIRC - Kidney renal clear cell carcinoma(1967;0.00292)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SESN2	83667	broad.mit.edu	37	1	28601040	28601042	+	Intron	DEL	AAA	-	-	rs111581518		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28601040_28601042delAAA	uc001bps.2	+							NM_031459	NP_113647			sestrin 2						cell cycle arrest	cytoplasm|nucleus				skin(3)|ovary(2)|pancreas(1)|lung(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28780269	28780269	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28780269delA	uc001bpw.2	+						PHACTR4_uc001bpu.2_Intron|PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28788202	28788202	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28788202delT	uc001bpw.2	+						PHACTR4_uc001bpu.2_Intron|PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SNHG3-RCC1	751867	broad.mit.edu	37	1	28833749	28833749	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28833749delT	uc001bqa.1	+						SNHG3-RCC1_uc001bqb.1_Intron|SNHG3-RCC1_uc001bqc.1_Intron	NM_001048197	NP_001041662			regulator of chromosome condensation 1												0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	29654642	29654643	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29654642_29654643delTT								PTPRU (1327 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	31177017	31177018	+	IGR	INS	-	GTCT	GTCT	rs148925760	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31177017_31177018insGTCT								None (None upstream) : MATN1 (7108 downstream)																																			---	---	---	---
MATN1	4146	broad.mit.edu	37	1	31192946	31192947	+	Intron	DEL	TA	-	-	rs10553997		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31192946_31192947delTA	uc001brz.2	-						uc001bsb.1_Intron|MATN1_uc001bsa.1_5'Flank	NM_002379	NP_002370			matrilin 1, cartilage matrix protein precursor						protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)												OREG0013305	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	31400478	31400478	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31400478delT								SDC3 (18998 upstream) : PUM1 (3875 downstream)																																			---	---	---	---
SYNC	81493	broad.mit.edu	37	1	33146114	33146114	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33146114delT	uc001bvt.2	-	5					SYNC_uc010ohl.1_3'UTR|RBBP4_uc001bvr.2_3'UTR|RBBP4_uc001bvs.2_3'UTR|RBBP4_uc010ohj.1_3'UTR|RBBP4_uc010ohk.1_3'UTR	NM_030786	NP_110413			syncoilin, intermediate filament 1 isoform 1							intermediate filament|perinuclear region of cytoplasm	structural molecule activity			ovary(1)	1																		---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34027548	34027548	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34027548delA	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34579964	34579964	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34579964delA	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
SFPQ	6421	broad.mit.edu	37	1	35658910	35658910	+	5'Flank	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35658910delG	uc001bys.2	-						SFPQ_uc001byr.2_5'Flank	NM_005066	NP_005057			splicing factor proline/glutamine rich						alternative nuclear mRNA splicing, via spliceosome|DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|nucleotide binding|protein binding|protein binding|RNA binding		SFPQ/TFE3(6)	kidney(4)|soft_tissue(2)|ovary(1)|skin(1)	8		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)						T	TFE3	papillary renal cell								---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35879694	35879695	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35879694_35879695delTT	uc001byt.2	+						ZMYM4_uc009vuu.2_Intron|ZMYM4_uc001byu.2_Intron|ZMYM4_uc009vuv.2_Intron	NM_005095	NP_005086			zinc finger protein 262						multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	35969805	35969805	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35969805delT	uc001byx.2	-						KIAA0319L_uc010ohw.1_Intron|KIAA0319L_uc001byz.2_Intron|KIAA0319L_uc010ohx.1_Intron	NM_024874	NP_079150			dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
PSMB2	5690	broad.mit.edu	37	1	36091363	36091363	+	Intron	DEL	A	-	-	rs77907092		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36091363delA	uc001bzf.1	-						PSMB2_uc001bzd.1_Intron|PSMB2_uc010ohz.1_Intron|PSMB2_uc001bzg.1_Intron	NM_002794	NP_002785			proteasome beta 2 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	37636503	37636504	+	IGR	INS	-	A	A	rs138774341	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37636503_37636504insA								GRIK3 (136659 upstream) : ZC3H12A (303615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37670571	37670571	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37670571delA								GRIK3 (170727 upstream) : ZC3H12A (269548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38552625	38552626	+	IGR	INS	-	C	C	rs145782991	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38552625_38552626insC								POU3F1 (40175 upstream) : RRAGC (752389 downstream)																																			---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39575120	39575120	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39575120delT	uc010ois.1	+							NM_012090	NP_036222			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40110528	40110528	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40110528delA								HEYL (5180 upstream) : NT5C1A (14265 downstream)																																			---	---	---	---
ZMPSTE24	10269	broad.mit.edu	37	1	40724004	40724004	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40724004delG	uc001cfg.2	+	1	272	c.61delG	c.(61-63)GGGfs	p.G21fs	uc001cff.2_5'Flank	NM_005857	NP_005848	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	21	Helical; (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	metal ion binding|metalloexopeptidase activity				0	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)															---	---	---	---
YBX1	4904	broad.mit.edu	37	1	43162183	43162183	+	Intron	DEL	C	-	-	rs113762321		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43162183delC	uc001chs.2	+							NM_004559	NP_004550			nuclease sensitive element binding protein 1						CRD-mediated mRNA stabilization|negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|positive regulation of cell division|transcription from RNA polymerase II promoter	CRD-mediated mRNA stability complex|extracellular region|histone pre-mRNA 3'end processing complex|nucleoplasm|stress granule|U12-type spliceosomal complex	double-stranded DNA binding|protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			ovary(4)|upper_aerodigestive_tract(1)	5	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
WDR65	149465	broad.mit.edu	37	1	43664440	43664440	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43664440delA	uc001cip.1	+						EBNA1BP2_uc001cio.2_Intron|WDR65_uc010ojz.1_Intron|WDR65_uc001ciq.1_Intron	NM_152498	NP_689711			WD repeat domain 65											skin(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
KDM4A	9682	broad.mit.edu	37	1	44137863	44137864	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44137863_44137864delTT	uc001cjx.2	+						KDM4A_uc010oki.1_Intron	NM_014663	NP_055478			jumonji domain containing 2A						interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44218175	44218178	+	Intron	DEL	TTTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44218175_44218178delTTTG	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44278549	44278550	+	Intron	DEL	GT	-	-	rs140530298	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44278549_44278550delGT	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
PTCH2	8643	broad.mit.edu	37	1	45299111	45299113	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45299111_45299113delTTT	uc010olf.1	-						PTCH2_uc010olg.1_Intron	NM_003738	NP_003729			patched 2						protein complex assembly|spermatogenesis	integral to plasma membrane	hedgehog receptor activity			lung(6)|breast(6)|central_nervous_system(3)|skin(2)|ovary(1)	18	Acute lymphoblastic leukemia(166;0.155)													Basal_Cell_Nevus_syndrome				---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46531596	46531597	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46531596_46531597delAA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46543166	46543166	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46543166delA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46937122	46937123	+	IGR	DEL	TT	-	-	rs113348840		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46937122_46937123delTT								FAAH (57602 upstream) : DMBX1 (35545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	46961656	46961656	+	IGR	DEL	T	-	-	rs61646546		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46961656delT								FAAH (82136 upstream) : DMBX1 (11012 downstream)																																			---	---	---	---
STIL	6491	broad.mit.edu	37	1	47735262	47735262	+	Intron	DEL	T	-	-	rs72192224		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47735262delT	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crf.1_Intron|STIL_uc001crg.1_Intron	NM_003035	NP_003026			SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51174194	51174195	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51174194_51174195delAA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	p.0?(1)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51511883	51511883	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51511883delT								CDKN2C (71576 upstream) : C1orf185 (56023 downstream)																																			---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52308324	52308324	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52308324delA	uc001ctc.3	-						NRD1_uc009vzb.2_5'Flank|NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.1_Intron|NRD1_uc009vzc.1_Intron|NRD1_uc001ctg.1_5'Flank	NM_002525	NP_002516			nardilysin isoform a						cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52338842	52338842	+	Intron	DEL	A	-	-	rs111616092		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52338842delA	uc001ctc.3	-						NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.1_Intron|NRD1_uc009vzc.1_Intron	NM_002525	NP_002516			nardilysin isoform a						cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53238351	53238352	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53238351_53238352delTT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
TMEM48	55706	broad.mit.edu	37	1	54269247	54269247	+	Intron	DEL	T	-	-	rs72154884		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54269247delT	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557			transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54919189	54919190	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54919189_54919190delTC								SSBP3 (47097 upstream) : ACOT11 (88740 downstream)																																			---	---	---	---
USP24	23358	broad.mit.edu	37	1	55609729	55609729	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55609729delT	uc001cyg.3	-							NM_015306	NP_056121			ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55637157	55637157	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55637157delT	uc001cyg.3	-							NM_015306	NP_056121			ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
PRKAA2	5563	broad.mit.edu	37	1	57158313	57158313	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57158313delT	uc001cyk.3	+							NM_006252	NP_006243			AMP-activated protein kinase alpha 2 catalytic						carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleoplasm	ATP binding|metal ion binding			breast(4)|ovary(1)|stomach(1)	6																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58490790	58490791	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58490790_58490791delCA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59707293	59707293	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59707293delT								LOC729467 (94814 upstream) : FGGY (55332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61519257	61519259	+	IGR	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61519257_61519259delAAA								C1orf87 (979831 upstream) : NFIA (23687 downstream)																																			---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62941104	62941104	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62941104delA	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron|DOCK7_uc001dar.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65313079	65313079	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65313079delA	uc001dbu.1	-						JAK1_uc009wam.1_Intron|JAK1_uc009wal.1_5'Flank	NM_002227	NP_002218			janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)				Mis		ALL								---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67099769	67099769	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67099769delA	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
IL12RB2	3595	broad.mit.edu	37	1	67775463	67775463	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67775463delG	uc001ddu.2	+						IL12RB2_uc010oqi.1_Intron|IL12RB2_uc010oqj.1_Intron	NM_001559	NP_001550			interleukin 12 receptor, beta 2 precursor						positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70555398	70555398	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70555398delT	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_Intron	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	70930332	70930335	+	IGR	DEL	AAAG	-	-	rs67323841		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70930332_70930335delAAAG								CTH (25080 upstream) : PTGER3 (387701 downstream)																																			---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72501543	72501543	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72501543delA	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	73077427	73077428	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73077427_73077428delAC								NEGR1 (329022 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74058445	74058445	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74058445delA								None (None upstream) : LRRIQ3 (433259 downstream)																																			---	---	---	---
FPGT	8790	broad.mit.edu	37	1	74670596	74670597	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74670596_74670597insA	uc001dgb.1	+	4	902_903	c.865_866insA	c.(865-867)GAAfs	p.E289fs	TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron|FPGT_uc010oqt.1_Intron|FPGT_uc010oqu.1_Intron|FPGT_uc010oqv.1_Intron	NM_003838	NP_003829	O14772	FPGT_HUMAN	fucose-1-phosphate guanyltransferase	289					fucose metabolic process	cytoplasm	fucose-1-phosphate guanylyltransferase activity|GTP binding			skin(1)	1																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74853970	74853970	+	Intron	DEL	T	-	-	rs6424588	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74853970delT	uc001dgf.1	+						TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							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																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78162897	78162897	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78162897delA	uc001dht.2	-	25					USP33_uc009wca.1_RNA|USP33_uc001dhs.2_3'UTR|USP33_uc001dhu.2_3'UTR	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78204970	78204970	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78204970delT	uc001dht.2	-	6	771	c.424delA	c.(424-426)ATAfs	p.I142fs	USP33_uc001dhu.2_Frame_Shift_Del_p.I111fs|USP33_uc001dhv.2_5'UTR|USP33_uc001dhw.2_Frame_Shift_Del_p.I142fs	NM_015017	NP_055832	Q8TEY7	UBP33_HUMAN	ubiquitin specific protease 33 isoform 1	142					axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
RPF1	80135	broad.mit.edu	37	1	84948418	84948419	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84948418_84948419delAA	uc001djv.3	+							NM_025065	NP_079341			RNA processing factor 1						rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding				0																		---	---	---	---
MCOLN2	255231	broad.mit.edu	37	1	85433447	85433449	+	Intron	DEL	AGG	-	-	rs72431763		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85433447_85433449delAGG	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991			mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)														---	---	---	---
WDR63	126820	broad.mit.edu	37	1	85528488	85528491	+	Intron	DEL	AATG	-	-	rs67150410		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85528488_85528491delAATG	uc001dkt.2	+						WDR63_uc009wcl.2_Intron	NM_145172	NP_660155			WD repeat domain 63											upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)														---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624983	85624983	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85624983delA	uc009wcm.2	-							NM_032184	NP_115560			synapse defective 1, Rho GTPase, homolog 2						activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85988468	85988469	+	Intron	INS	-	TA	TA	rs138199506	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85988468_85988469insTA	uc001dlc.2	-							NM_001134445	NP_001127917			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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	86177354	86177354	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86177354delT								ZNHIT6 (3238 upstream) : COL24A1 (17564 downstream)																																			---	---	---	---
ODF2L	57489	broad.mit.edu	37	1	86820550	86820550	+	Intron	DEL	A	-	-	rs76785175		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86820550delA	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron	NM_020729	NP_065780			outer dense fiber of sperm tails 2-like isoform							centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)														---	---	---	---
CLCA1	1179	broad.mit.edu	37	1	86965770	86965770	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86965770delT	uc001dlt.2	+	14						NM_001285	NP_001276			chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	88450561	88450561	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88450561delA								LMO4 (635958 upstream) : PKN2 (699361 downstream)																																			---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89220133	89220133	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89220133delG	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron	NM_006256	NP_006247			protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
GBP4	115361	broad.mit.edu	37	1	89655543	89655544	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89655543_89655544delAA	uc001dnb.2	-							NM_052941	NP_443173			guanylate binding protein 4							cytoplasm	GTP binding|GTPase activity				0				all cancers(265;0.00723)|Epithelial(280;0.0291)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	91252142	91252143	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91252142_91252143delAG								BARHL2 (69348 upstream) : ZNF644 (128717 downstream)																																			---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91817091	91817091	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91817091delT	uc001doa.3	-						HFM1_uc009wdb.2_Intron|HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron	NM_001017975	NP_001017975			HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92066062	92066063	+	IGR	DEL	AA	-	-	rs144829580		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92066062_92066063delAA								CDC7 (74742 upstream) : HSP90B3P (34505 downstream)																																			---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93198614	93198614	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93198614delA	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93602676	93602676	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93602676delA	uc009wdj.2	+	15					MTF2_uc010oth.1_3'UTR|MTF2_uc009wdk.2_3'UTR|MTF2_uc001dpi.3_3'UTR|MTF2_uc010oti.1_3'UTR|MTF2_uc001dpj.3_3'UTR|MTF2_uc001dpl.3_3'UTR|MTF2_uc001dpm.3_3'UTR	NM_007358	NP_031384			metal response element binding transcription							nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94165382	94165383	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94165382_94165383delCA	uc001dqb.2	-							NM_003567	NP_003558			breast cancer antiestrogen resistance 3						response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94664795	94664795	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94664795delA	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron	NM_004815	NP_004806			PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	95150014	95150014	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95150014delC	uc001dqu.2	-											Homo sapiens cDNA clone IMAGE:4795773.																														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97700330	97700330	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97700330delT	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	99693798	99693799	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99693798_99693799insA								LPPR5 (223349 upstream) : LPPR4 (36101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	99951416	99951416	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99951416delA								LPPR4 (176280 upstream) : PALMD (160015 downstream)																																			---	---	---	---
DBT	1629	broad.mit.edu	37	1	100703972	100703975	+	Intron	DEL	TTCT	-	-	rs75373528		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100703972_100703975delTTCT	uc001dta.2	-						DBT_uc010oug.1_Intron	NM_001918	NP_001909			dihydrolipoamide branched chain transacylase						branched chain family amino acid catabolic process|fatty-acyl-CoA biosynthetic process	microtubule cytoskeleton|mitochondrial alpha-ketoglutarate dehydrogenase complex|mitochondrial nucleoid	acyltransferase activity|cofactor binding|dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity|protein binding			pancreas(1)	1		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103473926	103473926	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103473926delA	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103577988	103577988	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103577988delA								COL11A1 (3936 upstream) : RNPC3 (490590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107081130	107081132	+	IGR	DEL	CGA	-	-	rs79236640		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107081130_107081132delCGA								None (None upstream) : PRMT6 (518135 downstream)																																			---	---	---	---
FAM102B	284611	broad.mit.edu	37	1	109159085	109159085	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109159085delA	uc010ouy.1	+							NM_001010883	NP_001010883			hypothetical protein LOC284611											large_intestine(1)	1		all_epithelial(167;5.52e-05)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0217)|Lung(183;0.109)|COAD - Colon adenocarcinoma(174;0.141)|Epithelial(280;0.182)														---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109559412	109559412	+	Intron	DEL	A	-	-	rs139039697		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109559412delA	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_Intron	NM_001142551	NP_001136023			WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)														---	---	---	---
SLC16A4	9122	broad.mit.edu	37	1	110914797	110914797	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110914797delT	uc001dzo.1	-						SLC16A4_uc009wfs.1_Intron|SLC16A4_uc001dzp.1_Intron|SLC16A4_uc010ovy.1_Intron|SLC16A4_uc001dzq.1_Intron|SLC16A4_uc010ovz.1_Intron	NM_004696	NP_004687			solute carrier family 16, member 4							integral to plasma membrane|membrane fraction	monocarboxylic acid transmembrane transporter activity|symporter activity			ovary(3)	3		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)													---	---	---	---
DDX20	11218	broad.mit.edu	37	1	112304742	112304744	+	Intron	DEL	AGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112304742_112304744delAGA	uc001ebs.2	+						DDX20_uc010owf.1_Intron|DDX20_uc001ebt.2_5'UTR	NM_007204	NP_009135			DEAD (Asp-Glu-Ala-Asp) box polypeptide 20						assembly of spliceosomal tri-snRNP|ncRNA metabolic process	Cajal body|cytoskeleton|cytosol|spliceosomal complex	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding			lung(1)|kidney(1)	2		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112687244	112687245	+	IGR	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112687244_112687245delCT								KCND3 (155467 upstream) : CTTNBP2NL (251555 downstream)																																			---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113149785	113149785	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113149785delT	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron|ST7L_uc010owi.1_Intron|ST7L_uc001ech.2_Intron|ST7L_uc001eci.2_Intron|ST7L_uc009wgi.1_Intron|ST7L_uc010owj.1_Intron	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113433616	113433616	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113433616delT								FAM19A3 (163762 upstream) : SLC16A1 (20856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113439158	113439159	+	IGR	DEL	TT	-	-	rs113666676		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113439158_113439159delTT								FAM19A3 (169304 upstream) : SLC16A1 (15313 downstream)																																			---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114186352	114186352	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114186352delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron|MAGI3_uc001edj.2_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
TRIM33	51592	broad.mit.edu	37	1	115025401	115025402	+	Intron	DEL	CT	-	-	rs114522046	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115025401_115025402delCT	uc001eew.2	-						TRIM33_uc001eex.2_Intron	NM_015906	NP_056990			tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)				T	RET	papillary thyroid								---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115279333	115279333	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115279333delA	uc001efk.2	-						CSDE1_uc001efi.2_Intron|CSDE1_uc001efj.2_Intron|CSDE1_uc001efl.2_Intron|CSDE1_uc001efm.2_Intron|CSDE1_uc009wgv.2_Intron|CSDE1_uc001efn.2_Intron	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
VANGL1	81839	broad.mit.edu	37	1	116201564	116201565	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116201564_116201565delAC	uc001efv.1	+						VANGL1_uc009wgy.1_Intron|VANGL1_uc001efw.1_Intron	NM_138959	NP_620409			vang-like 1						multicellular organismal development	integral to membrane	protein binding			central_nervous_system(1)	1	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120586488	120586488	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120586488delA	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	121122919	121122919	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121122919delA	uc001eis.2	+							NM_001042758	NP_001036223			SLIT-ROBO Rho GTPase activating protein 2																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143143304	143143304	+	Intron	DEL	T	-	-	rs145665359		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143143304delT	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143501968	143501969	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143501968_143501969delAC								None (None upstream) : LOC100286793 (145670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143532972	143532973	+	IGR	INS	-	G	G	rs111952315		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143532972_143532973insG								None (None upstream) : LOC100286793 (114666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143540668	143540669	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143540668_143540669insA								None (None upstream) : LOC100286793 (106970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	144007216	144007217	+	Intron	INS	-	A	A	rs144325392		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144007216_144007217insA	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	144023590	144023590	+	Intron	DEL	G	-	-	rs143399977	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144023590delG	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144843165	144843166	+	Intron	DEL	GG	-	-	rs150481179		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144843165_144843166delGG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144852792	144852793	+	Intron	DEL	TT	-	-	rs72112087		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144852792_144852793delTT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145109975	145109976	+	Intron	INS	-	C	C	rs11458983		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145109975_145109976insC	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145113131	145113140	+	Intron	DEL	CTTAGAACAG	-	-	rs60111159		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145113131_145113140delCTTAGAACAG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|SEC22B_uc001eml.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145180924	145180925	+	Intron	INS	-	G	G	rs147889822	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145180924_145180925insG	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145190622	145190623	+	Intron	INS	-	T	T	rs143031337	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145190622_145190623insT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145237179	145237179	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145237179delA	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145613109	145613109	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145613109delT	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_Intron|POLR3C_uc001eog.2_5'Flank|POLR3C_uc001eoh.2_5'Flank|POLR3C_uc001eoi.2_5'Flank|POLR3C_uc009wix.2_5'Flank	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146788985	146788985	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146788985delA	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146852552	146852553	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146852552_146852553delTT	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
BCL9	607	broad.mit.edu	37	1	147090441	147090442	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147090441_147090442delAA	uc001epq.2	+						BCL9_uc010ozr.1_Intron	NM_004326	NP_004317			B-cell CLL/lymphoma 9						Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)							T	IGH@|IGL@	B-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	1	147392377	147392381	+	IGR	DEL	AGAAC	-	-	rs5777663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147392377_147392381delAGAAC								GJA8 (10984 upstream) : GPR89B (8125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	148538283	148538283	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148538283delT								NBPF14 (191492 upstream) : NBPF15 (19986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	148924072	148924072	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148924072delA								NBPF16 (165761 upstream) : LOC645166 (4214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149094902	149094903	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149094902_149094903delAC								LOC645166 (141848 upstream) : LOC388692 (184573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149226394	149226394	+	IGR	DEL	G	-	-	rs113966689		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149226394delG								LOC645166 (273340 upstream) : LOC388692 (53082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149228529	149228531	+	5'Flank	DEL	AAA	-	-	rs77442270		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149228529_149228531delAAA	uc010pbe.1	+											Homo sapiens cDNA clone IMAGE:4734071, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	149689123	149689124	+	IGR	INS	-	G	G	rs138164517		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149689123_149689124insG								HIST2H2BF (289894 upstream) : FCGR1A (65126 downstream)																																			---	---	---	---
MTMR11	10903	broad.mit.edu	37	1	149902648	149902648	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149902648delA	uc001etl.3	-						SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etm.1_Intron|MTMR11_uc010pbm.1_3'UTR	NM_001145862	NP_001139334			myotubularin related protein 11 isoform a								phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149921365	149921365	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149921365delT	uc001etn.2	-							NM_020205	NP_064590			zinc finger protein Cezanne						negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
VPS45	11311	broad.mit.edu	37	1	150037090	150037091	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150037090_150037091delTT	uc001etp.2	+						VPS45_uc010pbp.1_5'Flank|VPS45_uc010pbq.1_5'Flank|VPS45_uc010pbs.1_5'Flank|VPS45_uc009wlm.1_5'Flank|VPS45_uc010pbr.1_5'Flank	NM_007259	NP_009190			vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
TARS2	80222	broad.mit.edu	37	1	150460671	150460672	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150460671_150460672insT	uc001euq.2	+						TARS2_uc010pcd.1_Intron|TARS2_uc001eur.2_Intron|TARS2_uc009wlt.2_Intron|TARS2_uc009wls.2_Intron	NM_025150	NP_079426			threonyl-tRNA synthetase 2, mitochondrial						threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)													---	---	---	---
HORMAD1	84072	broad.mit.edu	37	1	150686600	150686600	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150686600delA	uc001evk.1	-						HORMAD1_uc001evl.1_Intron|HORMAD1_uc001evm.1_Intron	NM_032132	NP_115508			HORMA domain containing 1						blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly	chromosome|nucleus				ovary(2)|central_nervous_system(1)	3	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150762584	150762584	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150762584delA								CTSS (24279 upstream) : CTSK (6103 downstream)																																			---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150920545	150920548	+	Intron	DEL	AAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150920545_150920548delAAAA	uc001evu.2	+						SETDB1_uc009wmf.2_Intron|SETDB1_uc001evv.2_Intron|SETDB1_uc009wmg.1_Intron	NM_001145415	NP_001138887			SET domain, bifurcated 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PRUNE	58497	broad.mit.edu	37	1	150983802	150983802	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150983802delA	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron|FAM63A_uc010pcn.1_5'Flank|FAM63A_uc001ewg.2_5'Flank	NM_021222	NP_067045			prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151017255	151017257	+	Intron	DEL	TTT	-	-	rs112736066		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151017255_151017257delTTT	uc001ewl.2	+						BNIPL_uc009wmi.2_Intron|BNIPL_uc009wmj.2_Intron	NM_138278	NP_612122			BCL2/adenovirus E1B 19kD interacting protein						apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
VPS72	6944	broad.mit.edu	37	1	151157057	151157057	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151157057delT	uc001exe.1	-						VPS72_uc001exf.1_Intron	NM_005997	NP_005988			transcription factor-like 1						chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|pancreas(1)	2	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151182829	151182831	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151182829_151182831delTTT	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151261355	151261355	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151261355delG	uc001exq.2	+						ZNF687_uc009wmo.2_Intron|ZNF687_uc009wmp.2_Intron	NM_020832	NP_065883			zinc finger protein 687						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151384306	151384306	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151384306delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915			pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151411359	151411359	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151411359delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron|POGZ_uc001eyg.1_Intron	NM_015100	NP_055915			pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151525574	151525575	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151525574_151525575delTT	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512			tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	151934831	151934833	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151934831_151934833delTTT								THEM4 (52718 upstream) : S100A10 (20554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152154926	152154926	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152154926delA								RPTN (23222 upstream) : HRNR (29632 downstream)																																			---	---	---	---
SMCP	4184	broad.mit.edu	37	1	152853651	152853652	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152853651_152853652insA	uc001fat.2	+							NM_030663	NP_109588			sperm mitochondria-associated cysteine-rich						penetration of zona pellucida|sperm motility	mitochondrial membrane					0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	153185101	153185101	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153185101delA								LELP1 (7507 upstream) : LOR (47078 downstream)																																			---	---	---	---
PGLYRP3	114771	broad.mit.edu	37	1	153275117	153275117	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153275117delT	uc001fbn.1	-							NM_052891	NP_443123			peptidoglycan recognition protein 3 precursor						defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
SNAPIN	23557	broad.mit.edu	37	1	153634037	153634037	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153634037delT	uc001fcq.2	+	4						NM_012437	NP_036569			SNAP-associated protein						intracellular protein transport|synaptic vesicle exocytosis	BLOC-1 complex|cell junction|perinuclear region of cytoplasm|synaptic vesicle membrane|synaptosome	SNARE binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154096356	154096356	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154096356delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
C1orf43	25912	broad.mit.edu	37	1	154186760	154186760	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154186760delA	uc001fei.2	-						C1orf43_uc001fef.1_5'Flank|C1orf43_uc001feg.2_Intron|C1orf43_uc001feh.2_Intron|C1orf43_uc001fej.2_Intron|C1orf43_uc009wos.1_Intron|C1orf43_uc001fek.2_Intron|C1orf43_uc001fel.2_Intron	NM_001098616	NP_001092086			hypothetical protein LOC25912 isoform 3							integral to membrane	coenzyme binding|oxidoreductase activity				0	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)																	---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154215938	154215939	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154215938_154215939delTT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ATP8B2	57198	broad.mit.edu	37	1	154305813	154305813	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154305813delA	uc001fey.1	+						ATP8B2_uc001few.2_Intron|ATP8B2_uc001fex.2_Intron	NM_001005855	NP_001005855			ATPase, class I, type 8B, member 2 isoform b						ATP biosynthetic process	plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(1)|skin(1)	2	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
SHE	126669	broad.mit.edu	37	1	154471885	154471885	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154471885delT	uc001ffb.2	-						SHE_uc001ffc.2_Intron|TDRD10_uc001ffd.2_5'Flank|TDRD10_uc009wow.2_5'Flank	NM_001010846	NP_001010846			Src homology 2 domain containing E											breast(3)|ovary(2)|central_nervous_system(1)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ADAR	103	broad.mit.edu	37	1	154557067	154557067	+	3'UTR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154557067delG	uc001ffh.2	-	15					ADAR_uc001ffj.2_3'UTR|ADAR_uc001ffi.2_3'UTR|ADAR_uc001ffk.2_3'UTR	NM_001111	NP_001102			adenosine deaminase, RNA-specific isoform a						adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)														---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154841236	154841236	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154841236delC	uc001ffp.2	-						KCNN3_uc009wox.1_Intron	NM_002249	NP_002240			small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
DCST1	149095	broad.mit.edu	37	1	155010528	155010528	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155010528delA	uc001fgn.1	+						DCST1_uc010per.1_Intron|DCST1_uc010pes.1_Intron	NM_152494	NP_689707			DC-STAMP domain containing 1 isoform 1							integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155350001	155350001	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155350001delA	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155394203	155394203	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155394203delT	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155500534	155500534	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155500534delA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqr.1_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155644954	155644954	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155644954delT	uc001fln.2	-						YY1AP1_uc010pgg.1_Intron|YY1AP1_uc010pgh.1_Intron|YY1AP1_uc010pgi.1_Intron|YY1AP1_uc001flh.2_Intron|YY1AP1_uc009wqt.2_Intron|YY1AP1_uc001flk.2_Intron|YY1AP1_uc001fll.2_Intron|YY1AP1_uc009wqv.2_Intron|YY1AP1_uc001flm.2_Intron|YY1AP1_uc001fli.2_Intron|YY1AP1_uc009wqu.2_Intron|YY1AP1_uc001flj.2_Intron|YY1AP1_uc009wqw.2_Intron|YY1AP1_uc001flo.2_Intron|YY1AP1_uc001flp.2_Intron|YY1AP1_uc010pgj.1_Intron|YY1AP1_uc009wqx.2_Intron|YY1AP1_uc010pgk.1_Intron	NM_139118	NP_620829			YY1-associated protein isoform 2						regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
DAP3	7818	broad.mit.edu	37	1	155698797	155698797	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155698797delT	uc001flq.2	+						DAP3_uc001flr.2_Intron|DAP3_uc001fls.2_Intron|DAP3_uc010pgl.1_Intron|DAP3_uc001flt.2_Intron|DAP3_uc001flu.2_Intron|DAP3_uc010pgm.1_Intron	NM_033657	NP_387506			death-associated protein 3						induction of apoptosis by extracellular signals	mitochondrial ribosome|nucleolus|small ribosomal subunit	protein binding			ovary(1)	1	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155800071	155800072	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155800071_155800072delTT	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155822905	155822905	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155822905delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156633805	156633807	+	IGR	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156633805_156633807delAAA								BCAN (4487 upstream) : NES (4750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157159255	157159256	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157159255_157159256delTT								ETV3 (50872 upstream) : FCRL5 (323912 downstream)																																			---	---	---	---
FCRL5	83416	broad.mit.edu	37	1	157522376	157522376	+	5'Flank	DEL	A	-	-	rs76456913		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157522376delA	uc001fqu.2	-						FCRL5_uc009wsm.2_5'Flank|FCRL5_uc010phv.1_5'Flank|FCRL5_uc010phw.1_5'Flank|FCRL5_uc001fqv.1_5'Flank|FCRL5_uc010phx.1_5'Flank	NM_031281	NP_112571			Fc receptor-like 5							integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	157840561	157840561	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157840561delA								CD5L (28927 upstream) : KIRREL (122502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158122219	158122219	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158122219delT								KIRREL (56377 upstream) : CD1D (27518 downstream)																																			---	---	---	---
CD1C	911	broad.mit.edu	37	1	158261595	158261595	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158261595delC	uc001fru.2	+						CD1C_uc001frv.2_5'Flank	NM_001765	NP_001756			CD1C antigen precursor						antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding			ovary(2)|skin(1)|pancreas(1)	4	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158416254	158416257	+	IGR	DEL	AAAC	-	-	rs72295046		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158416254_158416257delAAAC								OR10K2 (25598 upstream) : OR10K1 (19095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158577939	158577939	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158577939delT								OR10Z1 (770 upstream) : SPTA1 (2557 downstream)																																			---	---	---	---
MNDA	4332	broad.mit.edu	37	1	158817340	158817340	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158817340delA	uc001fsz.1	+							NM_002432	NP_002423			myeloid cell nuclear differentiation antigen						B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158894107	158894110	+	IGR	DEL	CACA	-	-	rs72434450		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158894107_158894110delCACA								MNDA (74837 upstream) : PYHIN1 (7232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159676443	159676444	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159676443_159676444delGT								APCS (117783 upstream) : CRP (5636 downstream)																																			---	---	---	---
IGSF8	93185	broad.mit.edu	37	1	160061939	160061939	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160061939delT	uc001fva.2	-						IGSF8_uc001fuz.2_Intron|IGSF8_uc009wtf.2_Intron	NM_052868	NP_443100			immunoglobulin superfamily, member 8						cell proliferation|cellular component movement|nervous system development|single fertilization|skeletal muscle tissue development	integral to membrane	protein binding				0	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160076051	160076052	+	IGR	DEL	AA	-	-	rs67254354		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160076051_160076052delAA								IGSF8 (7433 upstream) : ATP1A2 (9468 downstream)																																			---	---	---	---
SLAMF1	6504	broad.mit.edu	37	1	160582201	160582202	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160582201_160582202delAA	uc001fwl.3	-						SLAMF1_uc010pjk.1_Intron|SLAMF1_uc010pjl.1_Intron|SLAMF1_uc010pjm.1_Intron	NM_003037	NP_003028			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160640798	160640798	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160640798delT								SLAMF1 (23717 upstream) : CD48 (7740 downstream)																																			---	---	---	---
LY9	4063	broad.mit.edu	37	1	160788309	160788309	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160788309delA	uc001fwu.2	+						LY9_uc001fwv.2_Intron|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron|LY9_uc001fwz.2_Intron	NM_002348	NP_002339			lymphocyte antigen 9 isoform a						cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160932208	160932208	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160932208delA								ITLN2 (7619 upstream) : F11R (32794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161106775	161106775	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161106775delA								DEDD (4297 upstream) : UFC1 (16759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161260233	161260235	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161260233_161260235delTTT								PCP4L1 (4994 upstream) : MPZ (14292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161570233	161570233	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161570233delT								FCGR2C (202 upstream) : HSPA7 (5616 downstream)																																			---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162098556	162098558	+	Intron	DEL	ATC	-	-	rs145820907	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162098556_162098558delATC	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	162519567	162519567	+	IGR	DEL	T	-	-	rs35717674		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162519567delT								UHMK1 (25723 upstream) : UAP1 (11729 downstream)																																			---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162561580	162561581	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162561580_162561581delTT	uc001gce.3	+							NM_003115	NP_003106			UDP-N-acetylglucosamine pyrophosphorylase 1						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol|nucleus|plasma membrane	UDP-N-acetylglucosamine diphosphorylase activity			ovary(2)|skin(2)|kidney(1)	5	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	164135455	164135455	+	IGR	DEL	A	-	-	rs72276169		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164135455delA								NUF2 (809902 upstream) : PBX1 (393347 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164585341	164585342	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164585341_164585342delTC	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164742559	164742559	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164742559delC	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164839428	164839429	+	Intron	INS	-	CTTT	CTTT	rs77254277	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164839428_164839429insCTTT	uc010pkw.1	+							NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	164885348	164885349	+	IGR	INS	-	A	A	rs145433065	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164885348_164885349insA								PBX1 (31048 upstream) : LMX1A (285756 downstream)																																			---	---	---	---
TMCO1	54499	broad.mit.edu	37	1	165784656	165784656	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165784656delA	uc001gdn.3	-											Homo sapiens mRNA for putative membrane protein, complete cds.							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
UCK2	7371	broad.mit.edu	37	1	165877195	165877195	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165877195delT	uc001gdp.2	+	7					UCK2_uc010plb.1_3'UTR	NM_012474	NP_036606			uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	166338949	166338952	+	IGR	DEL	TTCC	-	-	rs71640498		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166338949_166338952delTTCC								FAM78B (202743 upstream) : FMO9P (234201 downstream)																																			---	---	---	---
MAEL	84944	broad.mit.edu	37	1	166964485	166964485	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166964485delT	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247			maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1																		---	---	---	---
CREG1	8804	broad.mit.edu	37	1	167515717	167515719	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167515717_167515719delAAA	uc001gel.2	-							NM_003851	NP_003842			cellular repressor of E1A-stimulated genes						cell proliferation|multicellular organismal development|regulation of growth|regulation of transcription from RNA polymerase II promoter	extracellular region	FMN binding|transcription corepressor activity				0																		---	---	---	---
CREG1	8804	broad.mit.edu	37	1	167515879	167515879	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167515879delA	uc001gel.2	-							NM_003851	NP_003842			cellular repressor of E1A-stimulated genes						cell proliferation|multicellular organismal development|regulation of growth|regulation of transcription from RNA polymerase II promoter	extracellular region	FMN binding|transcription corepressor activity				0																		---	---	---	---
DCAF6	55827	broad.mit.edu	37	1	168024985	168024985	+	Intron	DEL	G	-	-	rs35042830		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168024985delG	uc001gew.2	+						DCAF6_uc001gev.2_Intron|DCAF6_uc001gex.2_Intron|DCAF6_uc010plk.1_Intron|DCAF6_uc001gey.2_Intron|DCAF6_uc001gez.2_Intron	NM_001017977	NP_001017977			IQ motif and WD repeats 1 isoform b						positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	168122155	168122155	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168122155delA								GPR161 (15334 upstream) : TIPRL (26016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168133087	168133087	+	IGR	DEL	A	-	-	rs34923144		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168133087delA								GPR161 (26266 upstream) : TIPRL (15084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168140190	168140191	+	IGR	DEL	AG	-	-	rs145234100		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168140190_168140191delAG								GPR161 (33369 upstream) : TIPRL (7980 downstream)																																			---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169772269	169772269	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169772269delA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggo.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_5'Flank	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169817057	169817057	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169817057delA	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170193100	170193100	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170193100delA								METTL11B (56177 upstream) : LOC284688 (47447 downstream)																																			---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171452363	171452363	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171452363delA	uc010pmg.1	+						BAT2L2_uc001ghq.1_5'Flank|BAT2L2_uc001ghr.1_5'Flank	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171476753	171476753	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171476753delA	uc010pmg.1	+						BAT2L2_uc001ghq.1_Intron|BAT2L2_uc001ghr.1_Intron	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171841928	171841929	+	Intron	DEL	TG	-	-	rs68130879		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171841928_171841929delTG	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	172712685	172712685	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172712685delT								FASLG (76675 upstream) : TNFSF18 (297675 downstream)																																			---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173545908	173545908	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173545908delA	uc001giz.2	-						SLC9A11_uc009wwe.2_5'Flank|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622			solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173936458	173936458	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173936458delA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068			roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175296106	175296106	+	Intron	DEL	T	-	-	rs77303805		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175296106delT	uc001gkp.1	-						TNR_uc009wwu.1_Intron	NM_003285	NP_003276			tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
TNR	7143	broad.mit.edu	37	1	175401805	175401806	+	Intron	INS	-	T	T	rs34341419		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175401805_175401806insT	uc009wwu.1	-						TNR_uc010pmz.1_Intron	NM_003285	NP_003276			tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	176200270	176200271	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176200270_176200271delTT								RFWD2 (23900 upstream) : PAPPA2 (232036 downstream)																																			---	---	---	---
ASTN1	460	broad.mit.edu	37	1	177003830	177003830	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177003830delT	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_5'Flank	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177259345	177259345	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177259345delG								FAM5B (7788 upstream) : SEC16B (638144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177589992	177589992	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177589992delT								FAM5B (338435 upstream) : SEC16B (307497 downstream)																																			---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177952661	177952661	+	Intron	DEL	A	-	-	rs72197624		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177952661delA	uc001glj.1	-						SEC16B_uc001glk.1_Intron|SEC16B_uc009wwz.1_Intron	NM_033127	NP_149118			leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178026582	178026582	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178026582delT								SEC16B (19440 upstream) : LOC100302401 (34061 downstream)																																			---	---	---	---
LOC100302401	100302401	broad.mit.edu	37	1	178061150	178061150	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178061150delA	uc001gln.1	-	2					RASAL2_uc009wxb.2_5'Flank|RASAL2_uc001glq.2_5'Flank|LOC100302401_uc001glo.1_3'UTR|RASAL2_uc009wxa.2_5'Flank					Homo sapiens cDNA FLJ42473 fis, clone BRACE2030884.												0																		---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178785386	178785386	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178785386delT	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876			Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0																		---	---	---	---
ABL2	27	broad.mit.edu	37	1	179117349	179117349	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179117349delT	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron	NM_007314	NP_009298			arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)			T	ETV6	AML								---	---	---	---
ABL2	27	broad.mit.edu	37	1	179149263	179149263	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179149263delA	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron	NM_007314	NP_009298			arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)			T	ETV6	AML								---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179477849	179477850	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179477849_179477850delTT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179561674	179561674	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179561674delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|uc001gnd.2_5'Flank|uc001gne.2_5'Flank|uc010pno.1_5'Flank	NM_173533	NP_775804			tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	179679274	179679274	+	IGR	DEL	A	-	-	rs34563635		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179679274delA								TDRD5 (18876 upstream) : FAM163A (17641 downstream)																																			---	---	---	---
TOR1AIP2	163590	broad.mit.edu	37	1	179844102	179844103	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179844102_179844103delTC	uc001gnk.2	-						TOR1AIP2_uc001gnl.2_Intron|TOR1AIP2_uc001gnn.2_Intron	NM_145034	NP_659471			torsin A interacting protein 2							endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179975728	179975728	+	Intron	DEL	T	-	-	rs77614354		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179975728delT	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnu.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179989021	179989021	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179989021delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnu.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180119600	180119602	+	IGR	DEL	GTA	-	-	rs72501171		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180119600_180119602delGTA								CEP350 (35586 upstream) : QSOX1 (4366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	180194037	180194038	+	IGR	INS	-	G	G	rs142491197	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180194037_180194038insG								FLJ23867 (24180 upstream) : LHX4 (5404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	180247012	180247013	+	5'Flank	INS	-	G	G	rs145898864	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180247012_180247013insG	uc001gof.1	-											Homo sapiens cDNA FLJ38931 fis, clone NT2NE2013189.																														---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180362037	180362041	+	Intron	DEL	AAAAT	-	-	rs146917312		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180362037_180362041delAAAAT	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180404392	180404392	+	Intron	DEL	T	-	-	rs114573269	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180404392delT	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180544729	180544730	+	IGR	DEL	AA	-	-	rs142726090	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180544729_180544730delAA								ACBD6 (72707 upstream) : XPR1 (56416 downstream)																																			---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180683474	180683474	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180683474delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181316172	181316172	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181316172delT								IER5 (256195 upstream) : CACNA1E (136544 downstream)																																			---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181618811	181618811	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181618811delA	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181677140	181677141	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181677140_181677141insA	uc001gow.2	+						CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181937987	181937988	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181937987_181937988insG								CACNA1E (167274 upstream) : ZNF648 (85719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182592353	182592354	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182592353_182592354insA								RGS16 (18805 upstream) : RGS8 (23438 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182894110	182894110	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182894110delA	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195			chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)														---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183173591	183173594	+	Intron	DEL	AAAA	-	-	rs112473378		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183173591_183173594delAAAA	uc001gqa.2	+						LAMC2_uc001gpz.3_Intron|LAMC2_uc010poa.1_Intron	NM_005562	NP_005553			laminin, gamma 2 isoform a precursor						cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	183408478	183408478	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183408478delT								NMNAT2 (20741 upstream) : SMG7 (33156 downstream)																																			---	---	---	---
TSEN15	116461	broad.mit.edu	37	1	184035528	184035528	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184035528delT	uc001gqt.3	+						TSEN15_uc009wyg.2_Intron|TSEN15_uc001gqu.3_Intron	NM_052965	NP_443197			tRNA splicing endonuclease 15 isoform 1						mRNA processing|tRNA processing	nucleolus	protein binding				0																		---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184446788	184446788	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184446788delT	uc001gqv.1	+							NM_030806	NP_110433			chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	184751968	184751968	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184751968delT								EDEM3 (27927 upstream) : FAM129A (8199 downstream)																																			---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184940417	184940417	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184940417delA	uc001gra.2	-						FAM129A_uc009wyh.1_Intron|FAM129A_uc009wyi.1_Intron	NM_052966	NP_443198			niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	186480769	186480769	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186480769delC								PDC (50530 upstream) : PTGS2 (160176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	186545566	186545566	+	IGR	DEL	T	-	-	rs72326431		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186545566delT								PDC (115327 upstream) : PTGS2 (95379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187364751	187364752	+	IGR	INS	-	TG	TG	rs145817386	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187364751_187364752insTG								PLA2G4A (406646 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187865875	187865876	+	IGR	INS	-	T	T	rs5779371		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187865875_187865876insT								PLA2G4A (907770 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188733406	188733407	+	IGR	INS	-	GT	GT	rs144831172	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188733406_188733407insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191104413	191104414	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191104413_191104414delAA								FAM5C (657654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191977591	191977594	+	IGR	DEL	GAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191977591_191977594delGAAG								None (None upstream) : RGS18 (149998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192017637	192017639	+	IGR	DEL	AAG	-	-	rs66677562		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192017637_192017639delAAG								None (None upstream) : RGS18 (109953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193642833	193642834	+	IGR	DEL	TT	-	-	rs75557855		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193642833_193642834delTT								CDC73 (418893 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194590695	194590695	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194590695delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194726949	194726949	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194726949delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195144429	195144429	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195144429delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195437038	195437038	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195437038delT								None (None upstream) : KCNT2 (757875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195546258	195546258	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195546258delA								None (None upstream) : KCNT2 (648655 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196274286	196274286	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196274286delT	uc001gtd.1	-						KCNT2_uc009wyt.1_Intron|KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc001gth.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197154723	197154723	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197154723delA	uc001gtx.1	-						ZBTB41_uc009wyz.1_Intron	NM_194314	NP_919290			zinc finger and BTB domain containing 41						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	198086985	198086985	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198086985delT								LHX9 (185270 upstream) : NEK7 (39123 downstream)																																			---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198624751	198624752	+	Intron	INS	-	T	T	rs150259877	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198624751_198624752insT	uc001gur.1	+						PTPRC_uc001gus.1_Intron|PTPRC_uc001gut.1_Intron|PTPRC_uc001guq.2_Intron|PTPRC_uc009wze.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron|PTPRC_uc001guu.1_Intron|PTPRC_uc001guv.1_Intron|PTPRC_uc001guw.1_Intron	NM_002838	NP_002829			protein tyrosine phosphatase, receptor type, C						axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	199171653	199171653	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199171653delA								MIR181A1 (343371 upstream) : NR5A2 (825117 downstream)																																			---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200717887	200717888	+	Intron	DEL	TT	-	-	rs75982749		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200717887_200717888delTT	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200790297	200790299	+	Intron	DEL	CTT	-	-	rs78243257		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200790297_200790299delCTT	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CSRP1	1465	broad.mit.edu	37	1	201461672	201461672	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201461672delA	uc001gws.2	-						CSRP1_uc001gwr.1_RNA|CSRP1_uc010ppr.1_Intron|CSRP1_uc010pps.1_Intron	NM_004078	NP_004069			cysteine and glycine-rich protein 1 isoform 1							nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
CSRP1	1465	broad.mit.edu	37	1	201467138	201467138	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201467138delA	uc001gws.2	-						CSRP1_uc010ppr.1_Intron|CSRP1_uc010pps.1_Intron	NM_004078	NP_004069			cysteine and glycine-rich protein 1 isoform 1							nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201685144	201685144	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201685144delA	uc001gwu.2	+							NM_020443	NP_065176			neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201821197	201821197	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201821197delT	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202024063	202024063	+	IGR	DEL	A	-	-	rs111969245		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202024063delA								ELF3 (37757 upstream) : GPR37L1 (67966 downstream)																																			---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202525007	202525009	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202525007_202525009delTTT	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	202788203	202788204	+	5'Flank	DEL	TG	-	-	rs112050096		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202788203_202788204delTG	uc001gyh.2	+											Homo sapiens hypothetical protein LOC641515, mRNA (cDNA clone MGC:33633 IMAGE:4827085), complete cds.																														---	---	---	---
ADORA1	134	broad.mit.edu	37	1	203118012	203118013	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203118012_203118013delTT	uc001gze.1	+						ADORA1_uc001gzf.1_Intron|ADORA1_uc010pqg.1_Intron|ADORA1_uc009xak.1_Intron|ADORA1_uc010pqh.1_Intron	NM_000674	NP_000665			adenosine A1 receptor						induction of apoptosis by extracellular signals|inflammatory response|nervous system development|phagocytosis	integral to plasma membrane				large_intestine(1)	1					Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Gabapentin(DB00996)|Imipramine(DB00458)|Pegademase bovine(DB00061)|Theophylline(DB00277)													---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203244612	203244613	+	Intron	DEL	TT	-	-	rs71912855		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203244612_203244613delTT	uc010pqi.1	-						CHIT1_uc001gzm.1_5'Flank	NM_002023				fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
PRELP	5549	broad.mit.edu	37	1	203454876	203454877	+	Intron	INS	-	TCC	TCC	rs137970382	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203454876_203454877insTCC	uc001gzs.2	+						PRELP_uc001gzt.2_Intron	NM_002725	NP_002716			proline arginine-rich end leucine-rich repeat						skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(1)|central_nervous_system(1)|pancreas(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204507121	204507121	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204507121delT	uc001hba.2	+						MDM4_uc001hbd.1_Intron|MDM4_uc010pqw.1_Intron|MDM4_uc010pqx.1_Intron|MDM4_uc001hay.1_Intron|MDM4_uc001hbb.2_Intron|MDM4_uc010pqy.1_Intron|MDM4_uc001hbc.2_Intron|MDM4_uc009xbe.1_Intron	NM_002393	NP_002384			mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)					A		GBM|bladder|retinoblastoma								---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204844201	204844202	+	Intron	INS	-	TTG	TTG	rs10659578		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204844201_204844202insTTG	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204901647	204901648	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204901647_204901648delAA	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204928190	204928191	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204928190_204928191delTT	uc001hbj.2	+						NFASC_uc001hbh.2_Intron|NFASC_uc010pqz.1_Intron|NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc009xbg.1_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NUCKS1	64710	broad.mit.edu	37	1	205698104	205698104	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205698104delT	uc001hdb.2	-							NM_022731	NP_073568			nuclear casein kinase and cyclin-dependent							nucleus					0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	206500689	206500689	+	IGR	DEL	G	-	-	rs71245106		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206500689delG								CTSE (168586 upstream) : SRGAP2 (15511 downstream)																																			---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206718224	206718224	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206718224delA	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604			Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)													OREG0014173	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	207027479	207027479	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207027479delA								IL19 (11155 upstream) : IL20 (11220 downstream)																																			---	---	---	---
PFKFB2	5208	broad.mit.edu	37	1	207238862	207238862	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207238862delT	uc001hfg.2	+						PFKFB2_uc010psc.1_Intron|PFKFB2_uc001hfh.2_Intron|PFKFB2_uc009xcc.2_Intron|PFKFB2_uc010psd.1_Intron	NM_006212	NP_006203			6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	207273436	207273439	+	IGR	DEL	TGTA	-	-	rs55965140		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207273436_207273439delTGTA								C4BPB (101 upstream) : C4BPA (4072 downstream)																																			---	---	---	---
CD46	4179	broad.mit.edu	37	1	207943113	207943114	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207943113_207943114delTT	uc001hgc.2	+						CD46_uc001hgd.2_Intron|CD46_uc001hge.2_Intron|CD46_uc001hgf.2_Intron|CD46_uc001hgg.2_Intron|CD46_uc001hgh.2_Intron|CD46_uc001hgi.2_Intron|CD46_uc001hgj.2_Intron|CD46_uc001hgk.2_Intron|CD46_uc001hgl.2_Intron|CD46_uc001hgm.2_Intron|CD46_uc001hgn.2_Intron|CD46_uc001hgo.2_Intron|CD46_uc001hgp.2_Intron	NM_002389	NP_002380			CD46 antigen, complement regulatory protein						complement activation, classical pathway|innate immune response|interspecies interaction between organisms|single fertilization	inner acrosomal membrane|integral to plasma membrane	protein binding|receptor activity			large_intestine(2)|lung(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	209534011	209534011	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209534011delT								None (None upstream) : LOC642587 (68157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209701618	209701618	+	IGR	DEL	A	-	-	rs67620379		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209701618delA								LOC642587 (95728 upstream) : CAMK1G (55427 downstream)																																			---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211150788	211150788	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211150788delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	211416748	211416748	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211416748delA								KCNH1 (109291 upstream) : RCOR3 (15960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212050066	212050066	+	IGR	DEL	T	-	-	rs67906071		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212050066delT								LPGAT1 (45952 upstream) : INTS7 (64632 downstream)																																			---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212163628	212163631	+	Intron	DEL	AAAA	-	-	rs142333897		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212163628_212163631delAAAA	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249			integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212592295	212592295	+	IGR	DEL	T	-	-	rs75242529		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212592295delT								TMEM206 (4028 upstream) : NENF (13934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212726397	212726400	+	IGR	DEL	AAAG	-	-	rs72241615		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212726397_212726400delAAAG								NENF (106678 upstream) : ATF3 (12297 downstream)																																			---	---	---	---
NSL1	25936	broad.mit.edu	37	1	212957845	212957845	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212957845delA	uc001hjn.2	-						NSL1_uc001hjm.2_Intron|NSL1_uc010pti.1_Intron	NM_015471	NP_056286			NSL1, MIND kinetochore complex component isoform						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)														---	---	---	---
PTPN14	5784	broad.mit.edu	37	1	214582213	214582213	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214582213delA	uc001hkk.1	-						PTPN14_uc010pty.1_Intron	NM_005401	NP_005392			protein tyrosine phosphatase, non-receptor type						lymphangiogenesis	cytoplasm|cytoskeleton	protein tyrosine phosphatase activity|receptor tyrosine kinase binding			breast(2)|ovary(1)|kidney(1)|skin(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214730458	214730458	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214730458delT								PTPN14 (5816 upstream) : CENPF (46074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214999707	214999707	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214999707delT								CENPF (161795 upstream) : KCNK2 (179178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215159916	215159916	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215159916delA								CENPF (322004 upstream) : KCNK2 (18969 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215953166	215953166	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215953166delT	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216278908	216278908	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216278908delT	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216495187	216495187	+	Intron	DEL	T	-	-	rs79650190		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216495187delT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218834491	218834491	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218834491delT								TGFB2 (216532 upstream) : LYPLAL1 (512701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219847595	219847595	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219847595delT								LYPLAL1 (461389 upstream) : SLC30A10 (11174 downstream)																																			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324483	220324483	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220324483delA	uc010puk.1	-	35					RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_3'UTR|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	220614982	220614983	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220614982_220614983delTT								RAB3GAP2 (169139 upstream) : MARK1 (86585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221529707	221529708	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221529707_221529708insT								LOC400804 (20069 upstream) : DUSP10 (345058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222297275	222297276	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222297275_222297276insG								DUSP10 (381814 upstream) : HHIPL2 (398326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222472110	222472110	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222472110delA								DUSP10 (556649 upstream) : HHIPL2 (223492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222957718	222957719	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222957718_222957719insA								FAM177B (33717 upstream) : DISP1 (144064 downstream)																																			---	---	---	---
DISP1	84976	broad.mit.edu	37	1	223165177	223165177	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223165177delT	uc001hnu.1	+							NM_032890	NP_116279			dispatched A						diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)														---	---	---	---
SUSD4	55061	broad.mit.edu	37	1	223459357	223459357	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223459357delA	uc001hnx.2	-						SUSD4_uc001hny.3_Intron|SUSD4_uc010puw.1_Intron|SUSD4_uc001hnz.2_Intron|SUSD4_uc010pux.1_Intron	NM_017982	NP_060452			sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)														---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225377116	225377117	+	Intron	INS	-	T	T	rs72748640	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225377116_225377117insT	uc001how.2	+							NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225423150	225423150	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225423150delT	uc001how.2	+							NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225759075	225759075	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225759075delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493			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)														---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225833870	225833871	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225833870_225833871delAA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	225911968	225911968	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225911968delA	uc001hpe.1	+											Homo sapiens cDNA FLJ42062 fis, clone SYNOV2005673.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	226138377	226138377	+	IGR	DEL	C	-	-	rs149767773	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226138377delC								LEFTY2 (9457 upstream) : C1orf55 (32027 downstream)																																			---	---	---	---
ACBD3	64746	broad.mit.edu	37	1	226365621	226365622	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226365621_226365622insT	uc001hpy.2	-							NM_022735	NP_073572			acyl-Coenzyme A binding domain containing 3						steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)														---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226475508	226475508	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226475508delA	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226475683	226475685	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226475683_226475685delTTT	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
C1orf95	375057	broad.mit.edu	37	1	226759346	226759346	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226759346delT	uc010pvn.1	+							NM_001003665	NP_001003665			hypothetical protein LOC375057							integral to membrane				ovary(1)	1	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)														---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227484881	227484881	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227484881delA	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	227532296	227532297	+	IGR	DEL	TG	-	-	rs71837111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227532296_227532297delTG								CDC42BPA (26470 upstream) : ZNF678 (218947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	227714863	227714863	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227714863delT								CDC42BPA (209037 upstream) : ZNF678 (36381 downstream)																																			---	---	---	---
WNT3A	89780	broad.mit.edu	37	1	228234469	228234478	+	Intron	DEL	GTGTGCATGT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228234469_228234478delGTGTGCATGT	uc001hrq.1	+						WNT3A_uc001hrp.1_Intron	NM_033131	NP_149122			wingless-type MMTV integration site family,						axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of neuron projection development|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|positive regulation of transcription from RNA polymerase II promoter|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)																---	---	---	---
GUK1	2987	broad.mit.edu	37	1	228333923	228333924	+	Intron	DEL	AG	-	-	rs112695034		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228333923_228333924delAG	uc001hsh.2	+						GUK1_uc001hsi.2_Intron|GUK1_uc001hsj.2_Intron|GUK1_uc010pvv.1_Intron	NM_000858	NP_000849			guanylate kinase 1 isoform b						nucleobase, nucleoside and nucleotide interconversion|purine nucleotide metabolic process	cytosol	ATP binding|guanylate kinase activity				0		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228455270	228455270	+	Intron	DEL	T	-	-	rs142743891	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228455270delT	uc009xez.1	+						OBSCN_uc001hsn.2_Intron|OBSCN_uc001hso.2_5'Flank	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228707640	228707641	+	IGR	DEL	CA	-	-	rs111341592		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228707640_228707641delCA								RNF187 (23752 upstream) : DUSP5P (73016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229344954	229344954	+	IGR	DEL	A	-	-	rs35382290		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229344954delA								RHOU (462545 upstream) : RAB4A (61925 downstream)																																			---	---	---	---
URB2	9816	broad.mit.edu	37	1	229770586	229770586	+	Intron	DEL	T	-	-	rs113038970		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229770586delT	uc001hts.1	+						URB2_uc009xfd.1_Intron	NM_014777	NP_055592			URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GALNT2	2590	broad.mit.edu	37	1	230332192	230332193	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230332192_230332193insG	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472			polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	230452351	230452351	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230452351delT								GALNT2 (34476 upstream) : PGBD5 (5042 downstream)																																			---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230470351	230470352	+	Intron	INS	-	G	G	rs141945181	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230470351_230470352insG	uc010pwb.1	-						PGBD5_uc001htv.2_Intron	NM_024554	NP_078830			piggyBac transposable element derived 5							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)														---	---	---	---
FAM89A	375061	broad.mit.edu	37	1	231165247	231165247	+	Intron	DEL	A	-	-	rs12724398		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231165247delA	uc001hui.2	-						FAM89A_uc009xfm.2_Intron	NM_198552	NP_940954			family with sequence similarity 89, member A												0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	231189249	231189249	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231189249delA								FAM89A (13254 upstream) : TRIM67 (109425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231252536	231252536	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231252536delA								FAM89A (76541 upstream) : TRIM67 (46138 downstream)																																			---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231890959	231890959	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231890959delT	uc001huz.2	+						TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron	NM_018662	NP_061132			disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	232718052	232718052	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232718052delT								SIPA1L2 (66809 upstream) : KIAA1383 (222586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233062761	233062761	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233062761delT								KIAA1383 (116669 upstream) : C1orf57 (23609 downstream)																																			---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233224249	233224249	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233224249delT	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233285337	233285337	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233285337delA	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233329631	233329632	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233329631_233329632insA	uc001hvl.2	-						PCNXL2_uc001hvm.1_Intron|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_Intron|PCNXL2_uc009xfv.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
KCNK1	3775	broad.mit.edu	37	1	233789948	233789948	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233789948delG	uc010pxo.1	+						KCNK1_uc001hvw.2_Intron|KCNK1_uc001hvx.2_Intron	NM_002245	NP_002236			potassium channel, subfamily K, member 1							voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)													---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234128832	234128833	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234128832_234128833insA	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234149275	234149275	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234149275delA	uc001hvy.1	+							NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	235000731	235000736	+	IGR	DEL	ACACAC	-	-	rs71738849		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235000731_235000736delACACAC								IRF2BP2 (255460 upstream) : TOMM20 (271924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	235102852	235102853	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235102852_235102853insA								IRF2BP2 (357581 upstream) : TOMM20 (169807 downstream)																																			---	---	---	---
TBCE	6905	broad.mit.edu	37	1	235535943	235535944	+	Intron	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235535943_235535944delAG	uc001hwz.1	+						TBCE_uc010pxq.1_Intron|TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_003193	NP_003184			beta-tubulin cofactor E						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|nucleus|plasma membrane	chaperone binding				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)															---	---	---	---
TBCE	6905	broad.mit.edu	37	1	235606499	235606502	+	Intron	DEL	ACAT	-	-	rs56687414		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235606499_235606502delACAT	uc001hwz.1	+						TBCE_uc001hxa.1_Intron|TBCE_uc010pxr.1_Intron|TBCE_uc001hxb.1_Intron	NM_003193	NP_003184			beta-tubulin cofactor E						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|nucleus|plasma membrane	chaperone binding				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235634147	235634147	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235634147delA	uc001hxc.2	-						B3GALNT2_uc001hxd.1_Intron	NM_152490	NP_689703			beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)															---	---	---	---
GNG4	2786	broad.mit.edu	37	1	235763739	235763740	+	Intron	DEL	TA	-	-	rs4263986		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235763739_235763740delTA	uc001hxe.3	-						GNG4_uc009xfz.2_Intron|GNG4_uc001hxh.3_Intron	NM_001098722	NP_001092192			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|negative regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)															---	---	---	---
EDARADD	128178	broad.mit.edu	37	1	236590676	236590676	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236590676delT	uc001hxu.1	+						EDARADD_uc001hxv.1_Intron	NM_145861	NP_665860			EDAR-associated death domain isoform A						cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	236657498	236657498	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236657498delT								EDARADD (9490 upstream) : LGALS8 (24067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	237141233	237141236	+	IGR	DEL	AATT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237141233_237141236delAATT								MTR (73953 upstream) : RYR2 (64466 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237295029	237295029	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237295029delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237819091	237819091	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237819091delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237875200	237875200	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237875200delT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
LOC100130331	100130331	broad.mit.edu	37	1	238060750	238060750	+	Intron	DEL	T	-	-	rs79453379		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238060750delT	uc010pyc.1	+							NR_027247				Homo sapiens mRNA; cDNA DKFZp434B2115 (from clone DKFZp434B2115).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	238544242	238544243	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238544242_238544243delAA								LOC100130331 (452625 upstream) : LOC339535 (99443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239314447	239314447	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239314447delA								LOC339535 (665130 upstream) : CHRM3 (235418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239495794	239495794	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239495794delA								LOC339535 (846477 upstream) : CHRM3 (54071 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239932381	239932382	+	Intron	DEL	TC	-	-	rs525389	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239932381_239932382delTC	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241120153	241120153	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241120153delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241889125	241889125	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241889125delA	uc001hze.1	+						WDR64_uc001hzf.1_Intron					RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242173978	242173978	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242173978delA								MAP1LC3C (11593 upstream) : PLD5 (78294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242179141	242179141	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242179141delT								MAP1LC3C (16756 upstream) : PLD5 (73131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242187942	242187942	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242187942delT								MAP1LC3C (25557 upstream) : PLD5 (64330 downstream)																																			---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242355864	242355864	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242355864delA	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242490173	242490174	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242490173_242490174delTT	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242652678	242652679	+	Intron	DEL	AA	-	-	rs34360384		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242652678_242652679delAA	uc001hzn.1	-						PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242662844	242662844	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242662844delT	uc001hzn.1	-						PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242767252	242767252	+	IGR	DEL	T	-	-	rs111526196		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242767252delT								PLD5 (79254 upstream) : CEP170 (520479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242949007	242949007	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242949007delA								PLD5 (261009 upstream) : CEP170 (338724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	243107289	243107290	+	IGR	INS	-	TG	TG	rs4658518	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243107289_243107290insTG								PLD5 (419291 upstream) : CEP170 (180441 downstream)																																			---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243465650	243465650	+	Intron	DEL	A	-	-	rs35702682		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243465650delA	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron|SDCCAG8_uc001hzy.1_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
AKT3	10000	broad.mit.edu	37	1	243987947	243987947	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243987947delA	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456			AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244371186	244371186	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244371186delA								ZNF238 (150410 upstream) : C1orf100 (144751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244438590	244438591	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244438590_244438591delAG								ZNF238 (217814 upstream) : C1orf100 (77346 downstream)																																			---	---	---	---
EFCAB2	84288	broad.mit.edu	37	1	245222846	245222846	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245222846delA	uc001ibd.2	+						EFCAB2_uc001ibc.2_Intron|EFCAB2_uc010pyo.1_Intron|EFCAB2_uc010pyp.1_Intron|EFCAB2_uc001ibe.2_Intron	NR_026586				RecName: Full=EF-hand calcium-binding domain-containing protein 2;								calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245423080	245423080	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245423080delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245433080	245433080	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245433080delT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	245920102	245920104	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245920102_245920104delTTT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246504298	246504298	+	Intron	DEL	A	-	-	rs76927168		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246504298delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	247001713	247001713	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247001713delT								LOC149134 (46028 upstream) : AHCTF1 (689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247459138	247459138	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247459138delT								VN1R5 (38692 upstream) : ZNF496 (4485 downstream)																																			---	---	---	---
TRIM58	25893	broad.mit.edu	37	1	248030992	248030993	+	Intron	INS	-	A	A	rs113791151		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248030992_248030993insA	uc001ido.2	+						OR2W3_uc001idp.1_5'Flank	NM_015431	NP_056246			tripartite motif-containing 58							intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248111517	248111517	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248111517delA	uc001ids.2	+						OR2L8_uc001idt.1_5'Flank	NM_175911	NP_787107			olfactory receptor, family 2, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)															---	---	---	---
SH3BP5L	80851	broad.mit.edu	37	1	249117845	249117846	+	Intron	INS	-	CACA	CACA	rs148997281	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249117845_249117846insCACA	uc001iew.1	-						SH3BP5L_uc001iev.1_Intron|hsa-mir-3124|MI0014140_5'Flank	NM_030645	NP_085148			SH3-binding domain protein 5-like												0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)															---	---	---	---
SH3YL1	26751	broad.mit.edu	37	2	252831	252831	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:252831delT	uc002qvx.2	-						SH3YL1_uc002qvy.2_Intron|SH3YL1_uc002qvz.2_Intron|SH3YL1_uc002qwa.2_Intron|SH3YL1_uc010ewe.2_Intron|SH3YL1_uc002qwc.1_Intron|SH3YL1_uc002qvu.2_5'Flank|SH3YL1_uc002qvv.2_Intron|SH3YL1_uc002qvw.2_Intron	NM_015677	NP_056492			SH3 domain containing, Ysc84-like 1 isoform 1											ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)														---	---	---	---
FAM150B	285016	broad.mit.edu	37	2	279919	279919	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:279919delT	uc002qwi.3	-	6						NM_001002919	NP_001002919			hypothetical protein LOC285016 precursor							extracellular region					0	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.00091)|Epithelial(75;0.00656)|OV - Ovarian serous cystadenocarcinoma(76;0.00954)|GBM - Glioblastoma multiforme(21;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	1548796	1548797	+	IGR	INS	-	TCTA	TCTA	rs139339118	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1548796_1548797insTCTA								TPO (2298 upstream) : PXDN (86863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2824135	2824136	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2824135_2824136insA								MYT1L (489090 upstream) : TSSC1 (368605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5656807	5656807	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5656807delA								None (None upstream) : SOX11 (175992 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7001234_7001235delCG	uc002qyo.2	-						CMPK2_uc010yis.1_Intron|CMPK2_uc010ewv.2_Intron	NM_207315	NP_997198			UMP-CMP kinase 2 precursor						dTDP biosynthetic process	mitochondrion	ATP binding|cytidylate kinase activity|thymidylate kinase activity|UMP kinase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	7768798	7768798	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7768798delA								RNF144A (584491 upstream) : LOC339788 (293760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8303101	8303101	+	Intron	DEL	T	-	-	rs74582248		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8303101delT	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9350691	9350691	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9350691delT	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0																		---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	10065718	10065719	+	Intron	INS	-	T	T	rs142118247	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10065718_10065719insT	uc002qzz.2	+						TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671			TBP-associated factor 1B						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10095021	10095021	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10095021delT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron|uc002rac.2_RNA	NM_198182	NP_937825			grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10140707	10140707	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10140707delC	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron	NM_198182	NP_937825			grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10747299	10747299	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10747299delT	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron	NM_024894	NP_079170			nucleolar protein 10							nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13096673	13096673	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13096673delT								TRIB2 (213817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14217893	14217897	+	IGR	DEL	TTTTT	-	-	rs71910807		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14217893_14217897delTTTTT								None (None upstream) : FAM84A (554959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17450470	17450470	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17450470delA								FAM49A (603374 upstream) : RAD51AP2 (241516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17553965	17553965	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17553965delT								FAM49A (706869 upstream) : RAD51AP2 (138021 downstream)																																			---	---	---	---
RAD51AP2	729475	broad.mit.edu	37	2	17696275	17696276	+	Intron	DEL	AA	-	-	rs34060092		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17696275_17696276delAA	uc002rcl.1	-						RAD51AP2_uc010exn.1_Intron	NM_001099218	NP_001092688			RAD51 associated protein 2											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17949982	17949982	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17949982delT	uc010exo.2	-						GEN1_uc002rct.2_Intron|GEN1_uc010yjs.1_Intron|GEN1_uc002rcu.2_Intron	NM_024624	NP_078900			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20130442	20130444	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20130442_20130444delTTT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	23695557	23695557	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23695557delG								None (None upstream) : KLHL29 (59898 downstream)																																			---	---	---	---
KLHL29	114818	broad.mit.edu	37	2	23771203	23771204	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23771203_23771204delAC	uc002ref.2	+											SubName: Full=KLHL29 protein; Flags: Fragment;											ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	24733428	24733428	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24733428delT								ITSN2 (150031 upstream) : NCOA1 (53751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	25012181	25012182	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25012181_25012182insA								NCOA1 (18613 upstream) : C2orf79 (956 downstream)																																			---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26054360	26054360	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26054360delA	uc002rgs.2	-							NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PPP1CB	5500	broad.mit.edu	37	2	29006196	29006196	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29006196delT	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron|SPDYA_uc002rmi.2_Intron	NM_206876	NP_996759			protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ALK	238	broad.mit.edu	37	2	29482130	29482131	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29482130_29482131insT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ALK	238	broad.mit.edu	37	2	29757880	29757880	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29757880delA	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ALK	238	broad.mit.edu	37	2	29955767	29955769	+	Intron	DEL	TTT	-	-	rs67735315		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29955767_29955769delTTT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ALK	238	broad.mit.edu	37	2	30024491	30024491	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30024491delT	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
YPEL5	51646	broad.mit.edu	37	2	30381863	30381864	+	3'UTR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30381863_30381864insT	uc002rna.3	+	5					YPEL5_uc002rnb.3_3'UTR|YPEL5_uc002rnc.3_3'UTR|YPEL5_uc002rmz.3_3'UTR|YPEL5_uc010ezn.2_RNA|YPEL5_uc002rnd.2_3'UTR	NM_001127401	NP_001120873			yippee-like 5								peptide-methionine-(S)-S-oxide reductase activity				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	30893021	30893021	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30893021delT								LCLAT1 (25931 upstream) : CAPN13 (52619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	31502690	31502693	+	IGR	DEL	ATGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31502690_31502693delATGA								EHD3 (11431 upstream) : XDH (54495 downstream)																																			---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32430506	32430506	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32430506delT	uc002roe.1	+						SLC30A6_uc002rof.1_Intron|SLC30A6_uc010ymw.1_Intron|SLC30A6_uc010ezr.1_Intron|SLC30A6_uc002rog.1_Intron|SLC30A6_uc010ezs.1_Intron|SLC30A6_uc002roh.1_Intron	NM_017964	NP_060434			solute carrier family 30 (zinc transporter),							Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
YIPF4	84272	broad.mit.edu	37	2	32507132	32507132	+	Intron	DEL	A	-	-	rs111892477		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32507132delA	uc002rok.2	+							NM_032312	NP_115688			Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32602282	32602285	+	Intron	DEL	TGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32602282_32602285delTGTG	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33174056	33174056	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33174056delG	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	33946147	33946148	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33946147_33946148delGT								FAM98A (121785 upstream) : MYADML (4984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34041837	34041838	+	IGR	INS	-	CCTCC	CCTCC	rs141683394	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34041837_34041838insCCTCC								MYADML (88553 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34892200	34892203	+	IGR	DEL	AACC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34892200_34892203delAACC								MYADML (938916 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35801543	35801543	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35801543delT								None (None upstream) : CRIM1 (781854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36779350	36779350	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36779350delA								CRIM1 (1073 upstream) : FEZ2 (54 downstream)																																			---	---	---	---
STRN	6801	broad.mit.edu	37	2	37152390	37152390	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37152390delA	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153			striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)																---	---	---	---
STRN	6801	broad.mit.edu	37	2	37189675	37189675	+	Intron	DEL	T	-	-	rs67397746		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37189675delT	uc002rpn.2	-						STRN_uc010ezx.2_Intron	NM_003162	NP_003153			striatin, calmodulin binding protein						dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37393745	37393745	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37393745delT								EIF2AK2 (9555 upstream) : SULT6B1 (1219 downstream)																																			---	---	---	---
SULT6B1	391365	broad.mit.edu	37	2	37414553	37414553	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37414553delT	uc002rpu.2	-	2	164	c.143delA	c.(142-144)AAGfs	p.K48fs	SULT6B1_uc010yni.1_RNA	NM_001032377	NP_001027549	Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member	86						cytoplasm	sulfotransferase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(82;0.248)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37674236	37674236	+	IGR	DEL	T	-	-	rs111655210		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37674236delT								QPCT (73772 upstream) : CDC42EP3 (196507 downstream)																																			---	---	---	---
CDC42EP3	10602	broad.mit.edu	37	2	37872829	37872829	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37872829delA	uc002rqi.1	-	2						NM_006449	NP_006440			Cdc42 effector protein 3						regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding				0		all_hematologic(82;0.172)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	38090550	38090550	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38090550delT								CDC42EP3 (191224 upstream) : FAM82A1 (61912 downstream)																																			---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	41794145	41794146	+	IGR	INS	-	T	T	rs139812719	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41794145_41794146insT								None (None upstream) : PKDCC (481015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41902804	41902804	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41902804delA								None (None upstream) : PKDCC (372357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42243180	42243180	+	IGR	DEL	T	-	-	rs113391782		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42243180delT								None (None upstream) : PKDCC (31981 downstream)																																			---	---	---	---
COX7A2L	9167	broad.mit.edu	37	2	42578275	42578275	+	3'UTR	DEL	A	-	-	rs71682791		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42578275delA	uc002rsk.2	-	3					COX7A2L_uc002rsl.2_RNA	NM_004718	NP_004709			cytochrome c oxidase subunit VIIa polypeptide 2						respiratory electron transport chain	mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	42612885	42612885	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42612885delG								COX7A2L (16735 upstream) : KCNG3 (56274 downstream)																																			---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42950013	42950013	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42950013delT	uc002rso.1	+						MTA3_uc002rsp.1_Intron	NM_020744	NP_065795			metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
THADA	63892	broad.mit.edu	37	2	43494095	43494095	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43494095delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron	NM_001083953	NP_001077422			thyroid adenoma associated								binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44570817	44570817	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44570817delA	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027			prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44769269	44769271	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44769269_44769271delAAA	uc002rum.2	+							NM_024766	NP_079042			hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46339632	46339632	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46339632delT	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
MSH6	2956	broad.mit.edu	37	2	48013859	48013859	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48013859delT	uc002rwd.3	+						MSH6_uc002rwc.2_Intron|MSH6_uc010fbj.2_Intron|MSH6_uc010yoi.1_Intron|MSH6_uc010yoj.1_Intron	NM_000179	NP_000170			mutS homolog 6						determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
FOXN2	3344	broad.mit.edu	37	2	48564616	48564616	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48564616delT	uc002rwh.1	+							NM_002158	NP_002149			T-cell leukemia virus enhancer factor						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51017273	51017274	+	Intron	INS	-	CACA	CACA	rs144521920	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51017273_51017274insCACA	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	53548557	53548557	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53548557delT								None (None upstream) : ASB3 (348561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53820187	53820187	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53820187delA								None (None upstream) : ASB3 (76931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53886119	53886119	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53886119delA								None (None upstream) : ASB3 (10999 downstream)																																			---	---	---	---
RTN4	57142	broad.mit.edu	37	2	55236597	55236597	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55236597delA	uc002rye.2	-						RTN4_uc002ryc.2_Intron|RTN4_uc002ryd.2_Intron|RTN4_uc002ryf.2_Intron|RTN4_uc002ryg.2_Intron	NM_020532	NP_065393			reticulon 4 isoform A						apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	56037305	56037305	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56037305delA								PNPT1 (116294 upstream) : EFEMP1 (55798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57051962	57051963	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57051962_57051963delAA								CCDC85A (438654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57958865	57958865	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57958865delA								None (None upstream) : VRK2 (175921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59099064	59099065	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59099064_59099065delTC	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	60279096	60279097	+	IGR	DEL	GA	-	-	rs71400229		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60279096_60279097delGA								None (None upstream) : BCL11A (399206 downstream)																																			---	---	---	---
REL	5966	broad.mit.edu	37	2	61119084	61119084	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61119084delT	uc002sam.1	+						REL_uc002san.1_Intron	NM_002908	NP_002899			v-rel reticuloendotheliosis viral oncogene						positive regulation of I-kappaB kinase/NF-kappaB cascade	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)					A		Hodgkin Lymphoma								---	---	---	---
USP34	9736	broad.mit.edu	37	2	61577668	61577668	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61577668delA	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62228216	62228216	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62228216delA	uc002sbp.2	+							NM_152516	NP_689729			MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62465975	62465977	+	IGR	DEL	TTT	-	-	rs72294671		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62465975_62465977delTTT								B3GNT2 (14111 upstream) : TMEM17 (261379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62573969	62573970	+	IGR	INS	-	ATTT	ATTT	rs149636688	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62573969_62573970insATTT								B3GNT2 (122105 upstream) : TMEM17 (153386 downstream)																																			---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63058395	63058395	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63058395delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63675572	63675575	+	Intron	DEL	ACAC	-	-	rs142474794		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63675572_63675575delACAC	uc002sch.2	-						C2orf86_uc002sci.1_Intron|C2orf86_uc010fcr.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64584680	64584681	+	IGR	DEL	TC	-	-	rs113023900		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64584680_64584681delTC								PELI1 (213075 upstream) : HSPC159 (96646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66242063	66242063	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66242063delA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
WDR92	116143	broad.mit.edu	37	2	68361749	68361749	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68361749delA	uc002see.1	-						WDR92_uc002sed.1_Intron|WDR92_uc002sef.1_3'UTR|WDR92_uc002seg.1_3'UTR	NM_138458	NP_612467			monad						apoptosis|histone lysine methylation		methylated histone residue binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	69195175	69195182	+	IGR	DEL	AGGAAGGA	-	-	rs71397315		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69195175_69195182delAGGAAGGA								GKN2 (15073 upstream) : GKN1 (6523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	69682488	69682488	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69682488delA								NFU1 (17735 upstream) : AAK1 (2639 downstream)																																			---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69855417	69855417	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69855417delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
ASPRV1	151516	broad.mit.edu	37	2	70293376	70293377	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70293376_70293377delTT	uc002sga.2	-						uc002sgb.1_Intron|uc002sgd.2_Intron|uc002sge.1_Intron					Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70545022	70545022	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70545022delT								FAM136A (15802 upstream) : TGFA (129397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	70613095	70613095	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70613095delT								FAM136A (83875 upstream) : TGFA (61324 downstream)																																			---	---	---	---
ADD2	119	broad.mit.edu	37	2	70930227	70930227	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70930227delG	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002sgx.2_Intron|ADD2_uc010fdt.1_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608			adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
MCEE	84693	broad.mit.edu	37	2	71341232	71341232	+	Intron	DEL	C	-	-	rs13000428	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71341232delC	uc002shs.2	-							NM_032601	NP_115990			methylmalonyl CoA epimerase precursor						fatty acid beta-oxidation|L-methylmalonyl-CoA metabolic process	mitochondrial matrix	methylmalonyl-CoA epimerase activity			ovary(1)	1																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71629145	71629147	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71629145_71629147delAGA	uc002shx.2	+	16	3076_3078	c.2757_2759delAGA	c.(2755-2760)GTAGAA>GTA	p.E921del	ZNF638_uc010yqw.1_In_Frame_Del_p.E500del|ZNF638_uc002shy.2_In_Frame_Del_p.E921del|ZNF638_uc002shz.2_In_Frame_Del_p.E921del|ZNF638_uc002sia.2_In_Frame_Del_p.E921del|ZNF638_uc002sib.1_In_Frame_Del_p.E921del|ZNF638_uc010fed.2_RNA|ZNF638_uc002sic.2_In_Frame_Del_p.E18del	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	921	RRM 2.				RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72439155	72439155	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72439155delA	uc010fep.2	-							NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72516285	72516285	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72516285delA	uc010fep.2	-							NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72958237	72958237	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72958237delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	73054724	73054725	+	5'Flank	DEL	AA	-	-	rs79749605		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73054724_73054725delAA	uc010fep.2	-						EXOC6B_uc002sij.2_5'Flank	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73548956	73548957	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73548956_73548957delTT								EGR4 (28127 upstream) : ALMS1 (63929 downstream)																																			---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73731864	73731864	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73731864delT	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjg.2_Intron|ALMS1_uc002sjh.1_Intron	NM_015120	NP_055935			Alstrom syndrome 1						G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
DGUOK	1716	broad.mit.edu	37	2	74176518	74176518	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74176518delG	uc002sjx.2	+						DGUOK_uc002sjy.2_Intron|DGUOK_uc002sjz.2_Intron	NM_080916	NP_550438			deoxyguanosine kinase isoform a precursor						guanosine metabolic process|purine base metabolic process|purine deoxyribonucleoside metabolic process|purine-containing compound salvage	mitochondrial matrix	ATP binding|deoxyguanosine kinase activity|phosphotransferase activity, alcohol group as acceptor				0																		---	---	---	---
DGUOK	1716	broad.mit.edu	37	2	74180384	74180385	+	Intron	INS	-	TGG	TGG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74180384_74180385insTGG	uc002sjx.2	+						DGUOK_uc002sjy.2_Intron|DGUOK_uc002sjz.2_Intron	NM_080916	NP_550438			deoxyguanosine kinase isoform a precursor						guanosine metabolic process|purine base metabolic process|purine deoxyribonucleoside metabolic process|purine-containing compound salvage	mitochondrial matrix	ATP binding|deoxyguanosine kinase activity|phosphotransferase activity, alcohol group as acceptor				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74258088	74258088	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74258088delT								DGUOK (72002 upstream) : TET3 (15362 downstream)																																			---	---	---	---
MOBKL1B	55233	broad.mit.edu	37	2	74400263	74400263	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74400263delA	uc002skh.3	-						MOBKL1B_uc002ski.2_Intron	NM_018221	NP_060691			Mob4B protein						hippo signaling cascade		metal ion binding|protein binding				0																		---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74778062	74778066	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74778062_74778066delTTTTT	uc002smp.1	-						LOXL3_uc002smo.1_5'Flank|LOXL3_uc010ffm.1_Intron|LOXL3_uc002smq.1_Intron|LOXL3_uc010ffn.1_Intron|DOK1_uc002smr.2_Intron	NM_032603	NP_115992			lysyl oxidase-like 3 precursor							extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	75142064	75142065	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75142064_75142065delTT								HK2 (21590 upstream) : POLE4 (43710 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77485248	77485248	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77485248delA	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217			leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78019880	78019881	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78019880_78019881delTT								LRRTM4 (270378 upstream) : SNAR-H (162152 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80224438	80224438	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80224438delA	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81202555	81202555	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81202555delT								CTNNA2 (326651 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81316341	81316341	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81316341delA								CTNNA2 (440437 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81517794	81517794	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81517794delT								CTNNA2 (641890 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83490568	83490568	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83490568delA								None (None upstream) : None (None downstream)																																			---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84650857	84650857	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84650857delT	uc002son.2	-	9						NM_003849	NP_003840			succinate-CoA ligase, GDP-forming alpha subunit						tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84777274	84777275	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84777274_84777275insA	uc010fgb.2	+						DNAH6_uc002soo.2_Intron|DNAH6_uc002sop.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85748569	85748570	+	IGR	INS	-	A	A	rs71390077		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85748569_85748570insA								SH2D6 (84419 upstream) : MAT2A (17718 downstream)																																			---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86273060	86273060	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86273060delA	uc002sqs.2	-						POLR1A_uc010ytb.1_Intron|POLR1A_uc002sqt.1_5'Flank	NM_015425	NP_056240			DNA-directed RNA polymerase I A						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
IMMT	10989	broad.mit.edu	37	2	86393771	86393771	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86393771delA	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron|IMMT_uc002src.1_Intron|IMMT_uc002srd.2_Intron|IMMT_uc002sre.3_Intron|IMMT_uc010ytf.1_Intron|IMMT_uc010fgs.1_Intron	NM_006839	NP_006830			inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	86612942	86612942	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86612942delC								REEP1 (48165 upstream) : KDM3A (55329 downstream)																																			---	---	---	---
RNF103	7844	broad.mit.edu	37	2	86831891	86831891	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86831891delA	uc002srn.2	-	4	2102	c.1133delT	c.(1132-1134)TTAfs	p.L378fs	VPS24_uc010ytl.1_Intron|RNF103_uc002srm.2_Frame_Shift_Del_p.L239fs|uc002sro.2_Intron	NM_005667	NP_005658	O00237	RN103_HUMAN	ring finger protein 103	378	Helical; (Potential).				central nervous system development|ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87095970	87095971	+	Intron	INS	-	A	A	rs72072547		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87095970_87095971insA	uc002srs.3	+						uc010fgu.1_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87114861	87114861	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87114861delT	uc002srs.3	+						uc010fgu.1_Intron					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87931616	87931616	+	Intron	DEL	C	-	-	rs115165991		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87931616delC	uc002srs.3	+											SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88496059	88496060	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88496059_88496060delAC								THNSL2 (9914 upstream) : FOXI3 (251666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88967897	88967897	+	IGR	DEL	C	-	-	rs34841948		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88967897delC								EIF2AK3 (40903 upstream) : RPIA (23279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	89879665	89879669	+	IGR	DEL	AGAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89879665_89879669delAGAAG								FLJ40330 (773540 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90472479	90472480	+	IGR	INS	-	GG	GG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90472479_90472480insGG								None (None upstream) : None (None downstream)																																			---	---	---	---
LOC654342	654342	broad.mit.edu	37	2	91833173	91833174	+	Intron	DEL	GT	-	-	rs141082857	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91833173_91833174delGT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0																		---	---	---	---
FKSG73	440888	broad.mit.edu	37	2	92126932	92126932	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92126932delA	uc010yuc.1	+							NR_027714				SubName: Full=FKSG73; SubName: Full=FKSG73 protein, isoform CRA_a;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	92317890	92317890	+	IGR	DEL	T	-	-	rs7597972		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92317890delT								FKSG73 (187396 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96234164	96234164	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96234164delA								FAHD2A (155286 upstream) : TRIM43 (23602 downstream)																																			---	---	---	---
LOC285033	285033	broad.mit.edu	37	2	96907431	96907431	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96907431delA	uc002svp.1	+						LOC285033_uc002svn.2_Intron|LOC285033_uc002svo.2_Intron	NM_001037228	NP_001032305			hypothetical protein LOC285033												0																		---	---	---	---
ITPRIPL1	150771	broad.mit.edu	37	2	96994051	96994051	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96994051delA	uc002svx.2	+	3					ITPRIPL1_uc010yuk.1_3'UTR|ITPRIPL1_uc002svy.2_3'UTR|ITPRIPL1_uc010yul.1_3'UTR	NM_001008949	NP_001008949			inositol 1,4,5-triphosphate receptor interacting							integral to membrane				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
FAM178B	51252	broad.mit.edu	37	2	97570791	97570792	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97570791_97570792delAA	uc002sxl.3	-						FAM178B_uc002sxk.3_Intron	NM_001122646	NP_001116118			hypothetical protein LOC51252 isoform A												0																		---	---	---	---
FAM178B	51252	broad.mit.edu	37	2	97613648	97613648	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97613648delA	uc002sxl.3	-						FAM178B_uc002sxk.3_Intron	NM_001122646	NP_001116118			hypothetical protein LOC51252 isoform A												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	98252866	98252866	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98252866delA								ANKRD36B (46438 upstream) : COX5B (9655 downstream)																																			---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98414183	98414183	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98414183delA	uc002syh.3	-							NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98783829	98783829	+	Intron	DEL	A	-	-	rs61708666		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98783829delA	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron	NM_144992	NP_659429			von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	99582538	99582539	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99582538_99582539insT								C2orf55 (29854 upstream) : TSGA10 (31186 downstream)																																			---	---	---	---
MRPL30	51263	broad.mit.edu	37	2	99779652	99779655	+	Intron	DEL	AAAC	-	-	rs756572		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99779652_99779655delAAAC	uc002szr.2	+						MRPL30_uc002szl.1_Intron	NM_145213	NP_660214			SubName: Full=HCG1989457, isoform CRA_a; SubName: Full=Putative uncharacterized protein MRPL30;						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99995646	99995647	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99995646_99995647insA	uc002tab.2	+							NM_015904	NP_056988			eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101564015	101564015	+	Intron	DEL	A	-	-	rs145694242		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101564015delA	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509			neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
C2orf29	55571	broad.mit.edu	37	2	101883073	101883073	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101883073delA	uc002taw.3	+							NM_017546	NP_060016			hypothetical protein LOC55571						cell proliferation|nuclear-transcribed mRNA poly(A) tail shortening	cytosol				ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103021502	103021502	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103021502delT								IL18R1 (6287 upstream) : IL18RAP (13752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	103767518	103767518	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103767518delT								TMEM182 (333382 upstream) : None (None downstream)																																			---	---	---	---
NCK2	8440	broad.mit.edu	37	2	106417876	106417876	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106417876delT	uc002tdg.2	+						NCK2_uc002tdh.2_Intron	NM_003581	NP_003572			NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107921178	107921179	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107921178_107921179insA								ST6GAL2 (417615 upstream) : LOC729121 (518341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108308593	108308593	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108308593delA								ST6GAL2 (805030 upstream) : LOC729121 (130927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108387641	108387641	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108387641delA								ST6GAL2 (884078 upstream) : LOC729121 (51879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108844552	108844553	+	IGR	INS	-	GGCA	GGCA	rs148068155	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108844552_108844553insGGCA								SLC5A7 (214113 upstream) : SULT1C3 (19098 downstream)																																			---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109086477	109086477	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109086477delA	uc002tec.2	+	6	846	c.692delA	c.(691-693)CAAfs	p.Q231fs	GCC2_uc002ted.2_Frame_Shift_Del_p.Q130fs	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	231	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109089309	109089309	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109089309delA	uc002tec.2	+	7	2968	c.2814delA	c.(2812-2814)GTAfs	p.V938fs	GCC2_uc002ted.2_Frame_Shift_Del_p.V837fs	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	938	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111529252	111529253	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111529252_111529253delCA	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986			acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112454827	112454827	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112454827delA								LOC541471 (202135 upstream) : ANAPC1 (71814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	112490326	112490326	+	IGR	DEL	T	-	-	rs10707606		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112490326delT								LOC541471 (237634 upstream) : ANAPC1 (36315 downstream)																																			---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113043538	113043538	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113043538delA	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
POLR1B	84172	broad.mit.edu	37	2	113307002	113307002	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113307002delT	uc002thw.2	+						POLR1B_uc010fkn.2_Intron|POLR1B_uc002thx.2_Intron|POLR1B_uc010fko.2_Intron|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Intron|POLR1B_uc002thy.2_Intron|POLR1B_uc010yxo.1_Intron	NM_019014	NP_061887			RNA polymerase I polypeptide B isoform 1						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1																		---	---	---	---
PAX8	7849	broad.mit.edu	37	2	114012743	114012745	+	Intron	DEL	AAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114012743_114012745delAAG	uc010yxt.1	-						PAX8_uc010yxu.1_Intron|PAX8_uc010yxv.1_Intron|PAX8_uc002tjm.2_Intron|PAX8_uc002tjn.2_Intron|PAX8_uc010fku.1_Intron|LOC654433_uc002tjq.3_Intron|LOC654433_uc010fks.2_Intron|LOC654433_uc010fkt.2_Intron|LOC654433_uc002tjr.3_Intron|LOC654433_uc002tjs.3_Intron	NM_003466	NP_003457			paired box 8 isoform PAX8A						branching involved in ureteric bud morphogenesis|cellular response to gonadotropin stimulus|central nervous system development|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|metanephric collecting duct development|metanephric comma-shaped body morphogenesis|metanephric distal convoluted tubule development|metanephric nephron tubule formation|metanephric S-shaped body morphogenesis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|otic vesicle development|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric field specification|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of thyroid-stimulating hormone secretion|thyroid gland development|transcription, DNA-dependent	nucleoplasm	protein binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|thyroid-stimulating hormone receptor activity			ovary(1)|lung(1)	2								T	PPARG	follicular thyroid		Thyroid dysgenesis 						---	---	---	---
Unknown	0	broad.mit.edu	37	2	114187466	114187466	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114187466delA								PAX8 (150968 upstream) : CBWD2 (7802 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115620008	115620009	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115620008_115620009insA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116283455	116283455	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116283455delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	118606669	118606669	+	IGR	DEL	A	-	-	rs77691303		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118606669delA								DDX18 (16716 upstream) : CCDC93 (66480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119671941	119671941	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119671941delG								EN1 (66182 upstream) : MARCO (27804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119691571	119691571	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119691571delT								EN1 (85812 upstream) : MARCO (8174 downstream)																																			---	---	---	---
PCDP1	200373	broad.mit.edu	37	2	120351819	120351819	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120351819delT	uc002tmb.2	+						PCDP1_uc010yyq.1_Intron	NM_001029996	NP_001025167			primary ciliary dyskinesia protein 1							cilium	calmodulin binding				0	Colorectal(110;0.196)																	---	---	---	---
EPB41L5	57669	broad.mit.edu	37	2	120779217	120779217	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120779217delA	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron	NM_020909	NP_065960			erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	122635747	122635747	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122635747delA								TSN (110321 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123043025	123043025	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123043025delT								TSN (517599 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123652632	123652632	+	IGR	DEL	T	-	-	rs56294635	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123652632delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127609718	127609718	+	IGR	DEL	T	-	-	rs11677887	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127609718delT								GYPC (155473 upstream) : BIN1 (195889 downstream)																																			---	---	---	---
CYP27C1	339761	broad.mit.edu	37	2	127961288	127961288	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127961288delT	uc002tod.2	-							NM_001001665	NP_001001665			cytochrome P450, family 27, subfamily C,							membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	128133485	128133485	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128133485delA								MAP3K2 (32680 upstream) : PROC (42532 downstream)																																			---	---	---	---
IWS1	55677	broad.mit.edu	37	2	128242573	128242578	+	Intron	DEL	AAAAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128242573_128242578delAAAAAG	uc002ton.2	-							NM_017969	NP_060439			IWS1 homolog						transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	128825103	128825104	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128825103_128825104delAA								SAP130 (39470 upstream) : UGGT1 (23650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129696516	129696516	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129696516delA								HS6ST1 (620345 upstream) : LOC389033 (983919 downstream)																																			---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130873034	130873034	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130873034delA	uc010fmh.2	-							NM_001099771	NP_001093241			prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5																		---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131804367	131804368	+	3'UTR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131804367_131804368delTG	uc002tsa.1	+	14					ARHGEF4_uc010fmw.1_3'UTR|ARHGEF4_uc002tsb.1_3'UTR|ARHGEF4_uc010fmx.1_3'UTR|ARHGEF4_uc002tsc.1_3'UTR	NM_015320	NP_056135			Rho guanine nucleotide exchange factor 4 isoform						apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)														---	---	---	---
FAM168B	130074	broad.mit.edu	37	2	131833073	131833073	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131833073delT	uc002tsd.2	-							NM_001009993	NP_001009993			hypothetical protein LOC130074												0																		---	---	---	---
C2orf27A	29798	broad.mit.edu	37	2	132509092	132509092	+	5'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132509092delT	uc002ttf.1	+	3						NM_013310	NP_037442			hypothetical protein LOC29798												0																		---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133016676	133016677	+	5'Flank	INS	-	TGTC	TGTC	rs67307110		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133016676_133016677insTGTC	uc002ttj.3	-						MIR663B_hsa-mir-663b|MI0006336_5'Flank	NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	133029926	133029932	+	IGR	DEL	CTGAAAT	-	-	rs71966065		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133029926_133029932delCTGAAAT								NCRNA00164 (14384 upstream) : GPR39 (144215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134836808	134836808	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134836808delT								NCKAP5 (510777 upstream) : MGAT5 (175022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134949030	134949030	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134949030delC								NCKAP5 (622999 upstream) : MGAT5 (62800 downstream)																																			---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135875021	135875026	+	Intron	DEL	CTTCTG	-	-	rs62170190	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135875021_135875026delCTTCTG	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_Intron|RAB3GAP1_uc010fnh.1_Intron	NM_012233	NP_036365			RAB3 GTPase-activating protein							centrosome|nucleus|soluble fraction	Rab GTPase activator activity|Rab GTPase binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
MCM6	4175	broad.mit.edu	37	2	136622864	136622865	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136622864_136622865insA	uc002tuw.2	-							NM_005915	NP_005906			minichromosome maintenance complex component 6						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)													---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137682045	137682045	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137682045delG	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139063376	139063377	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139063376_139063377delTT								HNMT (289443 upstream) : SPOPL (195973 downstream)																																			---	---	---	---
SPOPL	339745	broad.mit.edu	37	2	139329569	139329570	+	3'UTR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139329569_139329570delGT	uc002tvh.2	+	11						NM_001001664	NP_001001664			speckle-type POZ protein-like							nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139665766	139665766	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139665766delT								NXPH2 (127955 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140724936	140724936	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140724936delA								None (None upstream) : LRP1B (264060 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141307431	141307431	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141307431delT	uc002tvj.1	-							NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141625631	141625632	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141625631_141625632delAA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141684080	141684080	+	Intron	DEL	A	-	-	rs76837019		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141684080delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141751713	141751713	+	Intron	DEL	A	-	-	rs72029988		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141751713delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	142663562	142663563	+	Intron	DEL	TG	-	-	rs10588603		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142663562_142663563delTG	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144780530	144780530	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144780530delT	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	147198472	147198472	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147198472delA								None (None upstream) : PABPC1P2 (146153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148081646	148081646	+	IGR	DEL	A	-	-	rs76356018		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148081646delA								PABPC1P2 (733089 upstream) : ACVR2A (520440 downstream)																																			---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148928873	148928873	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148928873delC	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149204838	149204841	+	Intron	DEL	GAAA	-	-	rs3955149		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149204838_149204841delGAAA	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	149955279	149955280	+	Intron	INS	-	T	T	rs10658424		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149955279_149955280insT	uc002twv.1	+						LYPD6B_uc002tww.1_Intron|LYPD6B_uc002twx.1_Intron	NM_177964	NP_808879			LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0																		---	---	---	---
LYPD6	130574	broad.mit.edu	37	2	150305553	150305553	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150305553delT	uc002twy.2	+						LYPD6_uc010fnt.2_Intron|LYPD6_uc002twz.2_Intron|LYPD6_uc002txa.2_Intron	NM_194317	NP_919298			LY6/PLAUR domain containing 6 precursor							extracellular region					0				BRCA - Breast invasive adenocarcinoma(221;0.0667)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	150863625	150863625	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150863625delA								MMADHC (419295 upstream) : RND3 (461087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151415683	151415683	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151415683delA								RND3 (71503 upstream) : RBM43 (689046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152045793	152045798	+	IGR	DEL	CACAGG	-	-	rs55765870		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152045793_152045798delCACAGG								RND3 (701613 upstream) : RBM43 (58931 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152293643	152293643	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152293643delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc010zby.1_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152302071	152302071	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152302071delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152346394	152346394	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152346394delA	uc010fnx.2	-						NEB_uc002txr.2_Intron|RIF1_uc002txp.2_Intron|NEB_uc010zbz.1_Intron|NEB_uc002txq.2_Intron|NEB_uc010zca.1_Intron|NEB_uc010zcb.1_Intron	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152709898	152709898	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152709898delA	uc002tya.2	-						CACNB4_uc002txy.2_Intron|CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	156682334	156682334	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156682334delT								KCNJ3 (969320 upstream) : NR4A2 (498612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156945820	156945820	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156945820delT	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																														---	---	---	---
GALNT5	11227	broad.mit.edu	37	2	158135034	158135034	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158135034delT	uc002tzg.2	+						GALNT5_uc010zci.1_Intron	NM_014568	NP_055383			N-acetylgalactosaminyltransferase 5						glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(3)|skin(1)	4																		---	---	---	---
ERMN	57471	broad.mit.edu	37	2	158180606	158180607	+	Intron	DEL	AC	-	-	rs113083865		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158180606_158180607delAC	uc002tzh.2	-						ERMN_uc010zcj.1_Intron|ERMN_uc010zck.1_Intron|ERMN_uc002tzi.2_Intron	NM_020711	NP_065762			ermin, ERM-like protein isoform b							cytoplasm|cytoskeleton				ovary(1)|skin(1)	2																		---	---	---	---
CYTIP	9595	broad.mit.edu	37	2	158309256	158309256	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158309256delA	uc010zcl.1	-							NM_004288	NP_004279			cytohesin 1 interacting protein						regulation of cell adhesion	cell cortex|early endosome	protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
UPP2	151531	broad.mit.edu	37	2	158962598	158962598	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158962598delT	uc002tzp.2	+						UPP2_uc002tzo.2_Intron	NM_173355	NP_775491			uridine phosphorylase 2 isoform a						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0																		---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159514635	159514635	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159514635delT	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron|PKP4_uc002tzz.1_Intron|PKP4_uc002uaa.2_Intron	NM_003628	NP_003619			plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7															HNSCC(62;0.18)			---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159992561	159992562	+	Intron	DEL	GC	-	-	rs35231270		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159992561_159992562delGC	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc002uah.1_5'Flank	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160242853	160242853	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160242853delT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160872959	160872960	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160872959_160872960insA	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392			phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161282846	161282847	+	Intron	INS	-	AAGG	AAGG	rs138498508	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161282846_161282847insAAGG	uc002ubo.2	-						RBMS1_uc002ubn.2_Intron|RBMS1_uc002ubi.3_Intron|RBMS1_uc002ubm.2_Intron|RBMS1_uc002ubp.2_Intron|RBMS1_uc010fox.2_Intron	NM_016836	NP_058520			RNA binding motif, single stranded interacting						DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0																		---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162814920	162814920	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162814920delT	uc002ubx.3	+						SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341			solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162854728	162854728	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162854728delC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162889218	162889219	+	Intron	DEL	AC	-	-	rs147325520	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162889218_162889219delAC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162889219	162889219	+	Intron	DEL	C	-	-	rs57725323		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162889219delC	uc002ubz.2	-						DPP4_uc010fpb.2_Intron	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
GCG	2641	broad.mit.edu	37	2	163003049	163003050	+	Intron	DEL	TC	-	-	rs10557377		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163003049_163003050delTC	uc002ucc.2	-							NM_002054	NP_002045			glucagon preproprotein						cell proliferation|cellular response to glucagon stimulus|energy reserve metabolic process|feeding behavior|regulation of insulin secretion	plasma membrane|soluble fraction	hormone activity				0					Exenatide(DB01276)|Phentolamine(DB00692)													---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163542226	163542226	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163542226delA	uc002uch.1	-						KCNH7_uc002uci.2_Intron	NM_033272	NP_150375			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	165508936	165508936	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165508936delT								GRB14 (30576 upstream) : COBLL1 (32324 downstream)																																			---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165971884	165971884	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165971884delT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166460270	166460270	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166460270delT	uc002udf.2	+						CSRNP3_uc002udg.2_Intron	NM_024969	NP_079245			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																		---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166716009	166716009	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166716009delA	uc002udj.1	-											Homo sapiens mRNA for KIAA1992 protein.							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170050430	170050430	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170050430delA	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171283783	171283784	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171283783_171283784insA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482			myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171850598	171850599	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171850598_171850599delAA	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc010zdn.1_Intron	NM_012290	NP_036422			tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171853274	171853274	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171853274delA	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_Intron|TLK1_uc010zdn.1_Intron	NM_012290	NP_036422			tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172217029	172217029	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172217029delA	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046			methyltransferase like 8								methyltransferase activity			ovary(1)	1																		---	---	---	---
SLC25A12	8604	broad.mit.edu	37	2	172683813	172683813	+	Intron	DEL	T	-	-	rs34833030		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172683813delT	uc002uhh.2	-						SLC25A12_uc010fqh.2_Intron	NM_003705	NP_003696			solute carrier family 25, member 12						gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	173283726	173283726	+	IGR	DEL	C	-	-	rs13018053	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173283726delC								DLX2 (316248 upstream) : ITGA6 (8356 downstream)																																			---	---	---	---
PDK1	5163	broad.mit.edu	37	2	173471468	173471470	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173471468_173471470delAAA	uc010zea.1	+							NM_002610				pyruvate dehydrogenase kinase 1 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(3)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.12)											Autosomal_Dominant_Polycystic_Kidney_Disease				---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173662239	173662239	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173662239delT	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc010fqn.2_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174151071	174151071	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174151071delT								ZAK (18335 upstream) : CDCA7 (68490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174327279	174327279	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174327279delT								CDCA7 (93561 upstream) : SP3 (445980 downstream)																																			---	---	---	---
TTC30B	150737	broad.mit.edu	37	2	178415367	178415367	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415367delT	uc002uln.2	-	1					TTC30B_uc010zfc.1_3'UTR	NM_152517	NP_689730			tetratricopeptide repeat domain 30B						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)															---	---	---	---
TTC30A	92104	broad.mit.edu	37	2	178481375	178481375	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178481375delA	uc002ulo.2	-	1						NM_152275	NP_689488			tetratricopeptide repeat domain 30A						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)															---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178797816	178797816	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178797816delC	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649			phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)											Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	2	181576049	181576049	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181576049delT								CWC22 (704209 upstream) : UBE2E3 (269063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	182240268	182240269	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182240268_182240269insG	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																														---	---	---	---
CERKL	375298	broad.mit.edu	37	2	182463794	182463794	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182463794delA	uc002unx.2	-						CERKL_uc002uny.2_Intron|CERKL_uc010zfm.1_Intron|CERKL_uc002unz.2_Intron|CERKL_uc002uoa.2_Intron|CERKL_uc002uob.2_Intron|CERKL_uc002uoc.2_Intron|CERKL_uc010frk.2_Intron|CERKL_uc002uod.1_Intron|CERKL_uc002uoe.2_Intron	NM_001030311	NP_001025482			ceramide kinase-like isoform b						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183359415	183359415	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183359415delT	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uov.1_Intron	NM_001003683	NP_001003683			phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)															---	---	---	---
NCKAP1	10787	broad.mit.edu	37	2	183848206	183848206	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183848206delT	uc002upc.2	-						NCKAP1_uc002upb.2_Intron	NM_013436	NP_038464			NCK-associated protein 1 isoform 1						apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
DUSP19	142679	broad.mit.edu	37	2	183950316	183950316	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183950316delA	uc002upd.2	+						DUSP19_uc010frp.2_Intron|DUSP19_uc010zfr.1_Intron|DUSP19_uc002upe.2_Intron	NM_080876	NP_543152			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																		---	---	---	---
NUP35	129401	broad.mit.edu	37	2	184022345	184022345	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184022345delT	uc002upf.2	+						NUP35_uc010zfs.1_Intron|NUP35_uc010zft.1_Intron|NUP35_uc002upg.2_Intron	NM_138285	NP_612142			nucleoporin 35kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	185196997	185196997	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185196997delA								None (None upstream) : ZNF804A (266096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187688683	187688684	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187688683_187688684insA								FAM171B (57999 upstream) : ZSWIM2 (3523 downstream)																																			---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189861201	189861201	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189861201delC	uc002uqj.1	+	24	1857	c.1740delC	c.(1738-1740)TTCfs	p.F580fs		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	580	Triple-helical region.				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
ANKAR	150709	broad.mit.edu	37	2	190569693	190569693	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190569693delT	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron	NM_144708	NP_653309			ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)															---	---	---	---
PMS1	5378	broad.mit.edu	37	2	190685029	190685029	+	Intron	DEL	T	-	-	rs112459960		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190685029delT	uc002urh.3	+						PMS1_uc010zga.1_Intron|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Intron|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Intron|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_Intron|PMS1_uc010fry.1_Intron|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Intron	NM_000534	NP_000525			postmeiotic segregation 1 isoform a						mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)					Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191152423	191152424	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191152423_191152424insA	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
INPP1	3628	broad.mit.edu	37	2	191232221	191232221	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191232221delT	uc002ury.3	+						INPP1_uc010fsb.2_Intron|INPP1_uc002urx.3_Intron	NM_001128928	NP_001122400			inositol polyphosphate-1-phosphatase						signal transduction		inositol-1,4-bisphosphate 1-phosphatase activity|metal ion binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)		Lithium(DB01356)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	191268374	191268374	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191268374delT								INPP1 (31984 upstream) : MFSD6 (4707 downstream)																																			---	---	---	---
NAB1	4664	broad.mit.edu	37	2	191521769	191521769	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191521769delT	uc002usb.2	+						NAB1_uc010fsc.2_Intron|NAB1_uc010fsd.2_5'Flank|NAB1_uc002usc.2_5'Flank|NAB1_uc010zgh.1_5'Flank	NM_005966	NP_005957			NGFI-A binding protein 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)															---	---	---	---
OBFC2A	64859	broad.mit.edu	37	2	192548946	192548946	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192548946delT	uc002usx.2	+						OBFC2A_uc002usw.2_Intron|OBFC2A_uc002usy.2_Intron|OBFC2A_uc002usz.2_Intron|OBFC2A_uc002uta.2_Intron	NM_001031716	NP_001026886			oligonucleotide/oligosaccharide-binding fold						double-strand break repair via homologous recombination|G2/M transition checkpoint|response to ionizing radiation	SOSS complex	single-stranded DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.061)|Epithelial(96;0.244)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	193001417	193001420	+	Intron	DEL	CTCT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193001417_193001420delCTCT	uc002utc.2	-							NM_016192	NP_057276			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	193641931	193641931	+	IGR	DEL	C	-	-	rs111547505		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193641931delC								PCGEM1 (310 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195369896	195369896	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195369896delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196062479	196062479	+	IGR	DEL	G	-	-	rs139622435	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196062479delG								None (None upstream) : SLC39A10 (459053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196374846	196374846	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196374846delT								None (None upstream) : SLC39A10 (146686 downstream)																																			---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197762942	197762943	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197762942_197762943delAA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron|PGAP1_uc010zgv.1_Intron|PGAP1_uc010fsj.2_Intron	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
MOBKL3	25843	broad.mit.edu	37	2	198401624	198401624	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198401624delT	uc002uun.3	+						MOBKL3_uc002uum.3_Intron|MOBKL3_uc010fsn.2_Intron|MOBKL3_uc010fso.2_Intron|MOBKL3_uc010zgz.1_Intron	NM_015387	NP_056202			Mps One Binder kinase activator-like 3 isoform						transport	Golgi cisterna membrane|perinuclear region of cytoplasm	metal ion binding|protein binding				0			Epithelial(96;0.225)															---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198760668	198760668	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198760668delT	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133			RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	200623461	200623461	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200623461delG								FLJ32063 (281803 upstream) : C2orf69 (152518 downstream)																																			---	---	---	---
C2orf60	129450	broad.mit.edu	37	2	200805339	200805339	+	Intron	DEL	A	-	-	rs74915546		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200805339delA	uc002uvi.3	-						C2orf60_uc002uvj.3_Intron|C2orf60_uc002uvk.3_Intron|C2orf60_uc010fss.2_Intron	NM_001039693	NP_001034782			hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0																		---	---	---	---
AOX2P	344454	broad.mit.edu	37	2	201634907	201634908	+	5'Flank	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201634907_201634908delTC	uc002uwa.2	+							NR_001557				Homo sapiens aldehyde oxidase-like protein (AOX2) pseudogene mRNA, partial sequence.												0																		---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202672720	202672721	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202672720_202672721insC	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	202896239	202896239	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202896239delT								CDK15 (137976 upstream) : FZD7 (3071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203021708	203021708	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203021708delT	uc002uyy.1	+											RecName: Full=Uncharacterized protein KIAA2012;																														---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203358601	203358601	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203358601delT	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195			bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203420130	203420130	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203420130delA	uc002uzf.3	+	12	2890	c.1742delA	c.(1741-1743)GAAfs	p.E581fs	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	581	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205869892	205869893	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205869892_205869893delAC	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206613706	206613706	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206613706delA	uc002vaw.2	+						NRP2_uc002vau.2_Intron|NRP2_uc002vav.2_Intron|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron	NM_201266	NP_957718			neuropilin 2 isoform 1 precursor						angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	206965658	206965658	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206965658delA								INO80D (14752 upstream) : NDUFS1 (22146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208177555	208177558	+	IGR	DEL	AATG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208177555_208177558delAATG								MIR1302-4 (43407 upstream) : CREB1 (217058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208254064	208254064	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208254064delT								MIR1302-4 (119916 upstream) : CREB1 (140552 downstream)																																			---	---	---	---
C2orf80	389073	broad.mit.edu	37	2	209047928	209047929	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209047928_209047929delTT	uc002vcr.2	-							NM_001099334	NP_001092804			hypothetical protein LOC389073											skin(1)	1																		---	---	---	---
PIKFYVE	200576	broad.mit.edu	37	2	209138183	209138183	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209138183delA	uc002vcz.2	+						PIKFYVE_uc010fun.1_Intron|PIKFYVE_uc002vcy.1_Intron|PIKFYVE_uc002vcv.2_Intron|PIKFYVE_uc002vcw.2_Intron|PIKFYVE_uc002vcx.2_Intron	NM_015040	NP_055855			phosphatidylinositol-3-phosphate 5-kinase type						cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding			ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	210219958	210219959	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210219958_210219959insA								PTH2R (515140 upstream) : MAP2 (68812 downstream)																																			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214739541	214739541	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214739541delA	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
VWC2L	402117	broad.mit.edu	37	2	215434061	215434062	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215434061_215434062delAC	uc002vet.2	+						VWC2L_uc010zjl.1_Intron	NM_001080500	NP_001073969			von Willebrand factor C domain-containing							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	216514605	216514606	+	Intron	INS	-	TA	TA	rs144130076	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216514605_216514606insTA	uc002vfm.1	-						uc002vfn.1_Intron					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	216779323	216779323	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216779323delA								FN1 (478532 upstream) : MREG (27992 downstream)																																			---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217232667	217232667	+	Intron	DEL	G	-	-	rs12464338	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217232667delG	uc002vgb.2	-							NM_020814	NP_065865			membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)														---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218407271	218407272	+	Intron	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218407271_218407272delAG	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
AAMP	14	broad.mit.edu	37	2	219134766	219134766	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219134766delG	uc002vhk.2	-	1	128	c.44delC	c.(43-45)CCAfs	p.P15fs	PNKD_uc002vhn.2_5'Flank|AAMP_uc002vhj.2_5'Flank|AAMP_uc010fvo.2_Frame_Shift_Del_p.P15fs|AAMP_uc002vhl.2_Frame_Shift_Del_p.P15fs|PNKD_uc002vhm.1_5'Flank	NM_001087	NP_001078	Q13685	AAMP_HUMAN	angio-associated, migratory cell protein	15					angiogenesis|cell differentiation|positive regulation of endothelial cell migration|smooth muscle cell migration	cell surface|cytoplasm|plasma membrane	heparin binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
CHPF	79586	broad.mit.edu	37	2	220407103	220407103	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220407103delT	uc002vmc.3	-						CHPF_uc010zlh.1_Intron|CHPF_uc002vmd.3_Intron|TMEM198_uc002vme.2_5'Flank|TMEM198_uc002vmf.2_5'Flank	NM_024536	NP_078812			chondroitin polymerizing factor							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity|protein binding				0		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)												OREG0015229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	2	220415418	220415419	+	5'Flank	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220415418_220415419insC	hsa-mir-3132|MI0014152	-																																									---	---	---	---
SLC4A3	6508	broad.mit.edu	37	2	220497729	220497729	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220497729delC	uc002vmp.3	+	9	1544	c.1275delC	c.(1273-1275)CACfs	p.H425fs	SLC4A3_uc002vmo.3_Frame_Shift_Del_p.H452fs|SLC4A3_uc010fwm.2_5'UTR|SLC4A3_uc010fwn.1_5'UTR	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	425	Cytoplasmic.				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	220550860	220550861	+	IGR	INS	-	TC	TC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220550860_220550861insTC								SLC4A3 (44159 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221205971	221205971	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221205971delA								SLC4A3 (699270 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221733946	221733946	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221733946delT								None (None upstream) : EPHA4 (548803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222710171	222710171	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222710171delT								EPHA4 (271249 upstream) : PAX3 (354436 downstream)																																			---	---	---	---
FARSB	10056	broad.mit.edu	37	2	223498057	223498057	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223498057delT	uc002vne.1	-						FARSB_uc010zlq.1_Intron|FARSB_uc002vnf.1_Intron	NM_005687	NP_005678			phenylalanyl-tRNA synthetase, beta subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)													---	---	---	---
MOGAT1	116255	broad.mit.edu	37	2	223562830	223562831	+	Intron	INS	-	T	T	rs148576038	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223562830_223562831insT	uc010fws.1	+						MOGAT1_uc010fwt.1_Intron	NM_058165	NP_477513			monoacylglycerol O-acyltransferase 1						glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224793618	224793618	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224793618delG	uc002vnq.2	-							NM_020830	NP_065881			WD repeat and FYVE domain containing 1							cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225019324	225019325	+	IGR	DEL	TT	-	-	rs111751176		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225019324_225019325delTT								SERPINE2 (115288 upstream) : FAM124B (224091 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225729790	225729790	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225729790delA	uc010fwz.1	-	12	1511	c.1272delT	c.(1270-1272)TTTfs	p.F424fs	DOCK10_uc002vob.2_Frame_Shift_Del_p.F418fs|DOCK10_uc002vod.1_Frame_Shift_Del_p.F424fs	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	424							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228267980	228267980	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228267980delG								TM4SF20 (23958 upstream) : AGFG1 (68908 downstream)																																			---	---	---	---
AGFG1	3267	broad.mit.edu	37	2	228388444	228388444	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228388444delT	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495			HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	229458565	229458566	+	IGR	DEL	AG	-	-	rs10677866		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229458565_229458566delAG								SPHKAP (412204 upstream) : PID1 (430124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229551539	229551539	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229551539delA								SPHKAP (505178 upstream) : PID1 (337151 downstream)																																			---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230652431	230652431	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230652431delA	uc002vpw.1	-						TRIP12_uc002vpx.1_Intron|TRIP12_uc002vpy.1_Intron	NM_004238	NP_004229			thyroid hormone receptor interactor 12						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
SP110	3431	broad.mit.edu	37	2	231070314	231070315	+	Intron	DEL	AA	-	-	rs35825596		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231070314_231070315delAA	uc002vqh.3	-						SP110_uc002vqg.3_Intron|SP110_uc002vqi.3_Intron|SP110_uc010fxk.2_Intron|SP110_uc010fxj.2_Intron	NM_004509	NP_004500			SP110 nuclear body protein isoform a						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
SP100	6672	broad.mit.edu	37	2	231293162	231293162	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231293162delT	uc002vqt.2	+						SP100_uc002vqs.2_Intron|SP100_uc002vqu.1_Intron|SP100_uc010zmb.1_Intron|SP100_uc002vqq.1_Intron|SP100_uc002vqr.1_Intron|SP100_uc010zmc.1_Intron|SP100_uc002vqv.1_Intron	NM_003113	NP_003104			nuclear antigen Sp100 isoform 2						DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231524598	231524598	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231524598delT								SP100 (114281 upstream) : CAB39 (52959 downstream)																																			---	---	---	---
PSMD1	5707	broad.mit.edu	37	2	232018844	232018844	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232018844delA	uc002vrn.1	+						PSMD1_uc002vrm.1_Intron|PSMD1_uc010fxu.1_Intron	NM_002807	NP_002798			proteasome 26S non-ATPase subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)|skin(1)	2		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)													---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	232858790	232858792	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232858790_232858792delTTT	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron	NM_152383	NP_689596			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)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233747792	233747793	+	Intron	DEL	CG	-	-	rs139306005	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233747792_233747793delCG	uc002vts.2	-						NGEF_uc010zmm.1_Intron|NGEF_uc010fyg.1_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233765413	233765414	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233765413_233765414delCA	uc002vts.2	-						NGEF_uc010zmm.1_Intron|NGEF_uc010fyg.1_Intron|NGEF_uc002vtt.2_Intron	NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	233962602	233962602	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233962602delT	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
UGT1A8	54576	broad.mit.edu	37	2	234526224	234526226	+	5'Flank	DEL	TTT	-	-	rs72113678		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234526224_234526226delTTT	uc002vup.2	+						UGT1A8_uc010zmv.1_5'Flank	NM_019076	NP_061949			UDP glycosyltransferase 1 family, polypeptide A8						drug metabolic process|fatty acid metabolic process|flavone metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme inhibitor activity|fatty acid binding|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|steroid binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;2.56e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000482)|Lung(119;0.00404)|LUSC - Lung squamous cell carcinoma(224;0.008)												OREG0003838	type=REGULATORY REGION|Gene=UGT1A8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
UGT1A5	54579	broad.mit.edu	37	2	234675952	234675952	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234675952delT	uc002vuw.2	+						UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Intron|UGT1A4_uc010zna.1_Intron|UGT1A4_uc002vux.2_Intron|UGT1A3_uc010znb.1_Intron|UGT1A3_uc002vuy.2_Intron|UGT1A9_uc002vva.2_Intron|UGT1A1_uc010znc.1_Intron|UGT1A1_uc002vvb.2_Intron	NM_019078	NP_061951			UDP glycosyltransferase 1 family, polypeptide A5						xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)														---	---	---	---
HJURP	55355	broad.mit.edu	37	2	234761358	234761358	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234761358delA	uc002vvg.2	-						HJURP_uc010znd.1_Intron|HJURP_uc010zne.1_Intron	NM_018410	NP_060880			Holliday junction recognition protein						cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	234809169	234809170	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234809169_234809170delGT								MSL3L2 (32114 upstream) : TRPM8 (16873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235264580	235264581	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235264580_235264581delTT								SPP2 (278804 upstream) : ARL4C (137107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237853389	237853390	+	IGR	DEL	GA	-	-	rs71402713		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237853389_237853390delGA								CXCR7 (362397 upstream) : COPS8 (140694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	238038614	238038615	+	IGR	INS	-	GA	GA	rs142024753	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238038614_238038615insGA								COPS8 (31127 upstream) : COL6A3 (194040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	238850103	238850104	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238850103_238850104delCA								RAMP1 (29350 upstream) : UBE2F (25596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	239484690	239484691	+	IGR	INS	-	A	A	rs140369669	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239484690_239484691insA								ASB1 (123800 upstream) : TWIST2 (271982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240835379	240835380	+	IGR	INS	-	A	A	rs144749671	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240835379_240835380insA								HDAC4 (512033 upstream) : NDUFA10 (64778 downstream)																																			---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241753100	241753100	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241753100delC	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312			axonal transport of synaptic vesicles						anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	242853390	242853391	+	IGR	DEL	CC	-	-	rs72357251		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242853390_242853391delCC								C2orf85 (37908 upstream) : LOC728323 (177453 downstream)																																			---	---	---	---
CHL1	10752	broad.mit.edu	37	3	417110	417110	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:417110delT	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.1_Intron|CHL1_uc011asi.1_Intron|uc003box.1_Intron	NM_006614	NP_006605			cell adhesion molecule with homology to L1CAM						axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	1003193	1003194	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs62230836		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1003193_1003194insTTCCTTCC								CHL1 (552098 upstream) : CNTN6 (131426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	1032577	1032580	+	IGR	DEL	CATA	-	-	rs10582752		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1032577_1032580delCATA								CHL1 (581482 upstream) : CNTN6 (102040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	1086463	1086463	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1086463delA								CHL1 (635368 upstream) : CNTN6 (48157 downstream)																																			---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1339718	1339718	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1339718delT	uc003boz.2	+						CNTN6_uc010hbo.2_3'UTR|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	1721984	1721985	+	IGR	DEL	AA	-	-	rs111577796		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1721984_1721985delAA								CNTN6 (276707 upstream) : CNTN4 (418565 downstream)																																			---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4419019	4419019	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4419019delA	uc003bpz.1	-						SUMF1_uc003bps.1_Intron|SUMF1_uc011ass.1_Intron|SUMF1_uc010hby.1_Intron|SUMF1_uc011ast.1_Intron	NM_182760	NP_877437			sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5215858	5215858	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5215858delT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5951433	5951433	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5951433delT								EDEM1 (689784 upstream) : GRM7 (951369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6104682	6104682	+	IGR	DEL	C	-	-	rs34639837		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6104682delC								EDEM1 (843033 upstream) : GRM7 (798120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6474595	6474595	+	IGR	DEL	A	-	-	rs78939584		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6474595delA								None (None upstream) : GRM7 (428207 downstream)																																			---	---	---	---
GRM7	2917	broad.mit.edu	37	3	6927783	6927784	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6927783_6927784delTG	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7456574	7456574	+	Intron	DEL	T	-	-	rs79755836		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7456574delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	8478191	8478192	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8478191_8478192delCA	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
LMCD1	29995	broad.mit.edu	37	3	8561428	8561428	+	Intron	DEL	A	-	-	rs111689264		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8561428delA	uc003bqq.2	+						LMCD1_uc011atd.1_Intron|LMCD1_uc011ate.1_Intron	NM_014583	NP_055398			LIM and cysteine-rich domains 1						positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.124)														---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8718840	8718840	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8718840delC	uc003bqz.2	-						C3orf32_uc003bqx.2_Intron|C3orf32_uc003bqy.2_Intron	NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
LHFPL4	375323	broad.mit.edu	37	3	9586548	9586548	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9586548delT	uc003bry.2	-							NM_198560	NP_940962			lipoma HMGIC fusion partner-like 4							integral to membrane				ovary(2)|skin(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9739253	9739253	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9739253delT	uc003brz.2	+						MTMR14_uc003bsa.2_Intron|MTMR14_uc003bsb.2_Intron|MTMR14_uc011ath.1_Intron|MTMR14_uc010hcl.2_Intron|MTMR14_uc003bsc.2_Intron	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
CPNE9	151835	broad.mit.edu	37	3	9757583	9757597	+	Intron	DEL	CCTATGGGCCTCACT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9757583_9757597delCCTATGGGCCTCACT	uc003bsd.2	+							NM_153635	NP_705899			copine-like protein											ovary(2)	2	Medulloblastoma(99;0.227)															OREG0015381	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PRRT3	285368	broad.mit.edu	37	3	9991859	9991859	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9991859delA	uc003bul.2	-						CIDEC_uc003bto.2_Intron|PRRT3_uc003buk.2_Intron|PRRT3_uc003bum.2_Intron	NM_207351	NP_997234			proline-rich transmembrane protein 3 precursor							integral to membrane					0																		---	---	---	---
CIDEC	63924	broad.mit.edu	37	3	10046360	10046361	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10046360_10046361delTG	uc003bto.2	-						uc003bup.1_3'UTR|uc003buq.1_3'UTR					Homo sapiens unknown mRNA.						apoptosis|induction of apoptosis	cytosol|focal adhesion|nucleus				central_nervous_system(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10081677	10081677	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10081677delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_3'UTR	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10222993	10222993	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10222993delA	uc003bve.1	+							NM_001570	NP_001561			interleukin-1 receptor-associated kinase 2						activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated 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	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10600428	10600428	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10600428delT	uc003bvw.2	-							NM_001683	NP_001674			plasma membrane calcium ATPase 2 isoform 2						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10718210	10718211	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10718210_10718211delCA	uc003bvw.2	-							NM_001683	NP_001674			plasma membrane calcium ATPase 2 isoform 2						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10928780	10928783	+	Intron	DEL	GGAT	-	-	rs112236505		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10928780_10928783delGGAT	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11258566	11258566	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11258566delA	uc010hdr.2	+						HRH1_uc010hds.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
LSM3	27258	broad.mit.edu	37	3	14226558	14226558	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14226558delA	uc003byn.2	+							NM_014463	NP_055278			Lsm3 protein						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	catalytic step 2 spliceosome|cytosol	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	14354428	14354429	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14354428_14354429delAC								LSM3 (114592 upstream) : SLC6A6 (89677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	14620226	14620228	+	IGR	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14620226_14620228delAAA								GRIP2 (36638 upstream) : C3orf19 (73025 downstream)																																			---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16019897	16019897	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16019897delT	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17300086	17300086	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17300086delA	uc003cbf.2	-						TBC1D5_uc010heu.2_Intron|TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron|TBC1D5_uc010hew.1_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	18124012	18124012	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18124012delT	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																														---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22082666	22082666	+	Intron	DEL	C	-	-	rs5847156		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22082666delC	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	24564308	24564308	+	IGR	DEL	G	-	-	rs76783435		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24564308delG								THRB (27855 upstream) : RARB (651515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	25113370	25113370	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25113370delA								THRB (576917 upstream) : RARB (102453 downstream)																																			---	---	---	---
RARB	5915	broad.mit.edu	37	3	25470412	25470412	+	Intron	DEL	A	-	-	rs77824017		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25470412delA	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	NM_016152	NP_057236			retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)													---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25792763	25792763	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25792763delA	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_Intron	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	26232513	26232513	+	IGR	DEL	T	-	-	rs112917111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26232513delT								OXSM (396489 upstream) : LRRC3B (431787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26990550	26990557	+	IGR	DEL	AGGAAGGG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26990550_26990557delAGGAAGGG								LRRC3B (238287 upstream) : NEK10 (161838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27091315	27091315	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27091315delT								LRRC3B (339052 upstream) : NEK10 (61080 downstream)																																			---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27418138	27418138	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27418138delA	uc003cdv.2	-	25					SLC4A7_uc011awu.1_RNA|SLC4A7_uc011awv.1_RNA|SLC4A7_uc003cdu.3_3'UTR|SLC4A7_uc011aww.1_3'UTR|SLC4A7_uc011awx.1_3'UTR|SLC4A7_uc011awy.1_3'UTR|SLC4A7_uc011awz.1_RNA|SLC4A7_uc011axa.1_3'UTR|SLC4A7_uc011axb.1_3'UTR|SLC4A7_uc010hfl.2_3'UTR|SLC4A7_uc003cdw.2_3'UTR	NM_003615	NP_003606			solute carrier family 4, sodium bicarbonate							apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	29235027	29235027	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29235027delT								ZCWPW2 (668397 upstream) : RBMS3 (87916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30076140	30076141	+	IGR	INS	-	AAGA	AAGA	rs71612090	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30076140_30076141insAAGA								RBMS3 (29521 upstream) : TGFBR2 (571853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30317956	30317956	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30317956delA								RBMS3 (271337 upstream) : TGFBR2 (330038 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30936740	30936741	+	5'Flank	DEL	TG	-	-	rs71852979		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30936740_30936741delTG	uc003cep.2	-						GADL1_uc003ceq.1_5'Flank	NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31843888	31843888	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31843888delA	uc003cev.2	-						OSBPL10_uc003ceu.1_Intron|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254			oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	32677111	32677112	+	IGR	INS	-	GA	GA	rs57104538		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32677111_32677112insGA								DYNC1LI1 (64761 upstream) : CNOT10 (49586 downstream)																																			---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33636262	33636262	+	Intron	DEL	A	-	-	rs75838008		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33636262delA	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33706595	33706595	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33706595delA	uc003cfu.2	-						CLASP2_uc010hgb.2_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	34984015	34984026	+	IGR	DEL	TTCCTTCCCTTT	-	-	rs112606310		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34984015_34984026delTTCCTTCCCTTT								None (None upstream) : ARPP21 (697055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35850633	35850634	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35850633_35850634insT								ARPP21 (14646 upstream) : STAC (571463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36411331	36411332	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36411331_36411332insT								ARPP21 (575344 upstream) : STAC (10765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36810381	36810381	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36810381delT								DCLK3 (29029 upstream) : TRANK1 (57930 downstream)																																			---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37547431	37547431	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37547431delT	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38668179	38668180	+	Intron	DEL	AA	-	-	rs34589254		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38668179_38668180delAA	uc003cio.2	-						SCN5A_uc003cin.2_Intron|SCN5A_uc003cil.3_Intron|SCN5A_uc010hhi.2_Intron|SCN5A_uc010hhk.2_Intron|SCN5A_uc011ayr.1_Intron	NM_198056	NP_932173			voltage-gated sodium channel type V alpha						blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39028104	39028105	+	IGR	DEL	TC	-	-	rs72008746		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39028104_39028105delTC								SCN11A (36052 upstream) : WDR48 (65402 downstream)																																			---	---	---	---
CX3CR1	1524	broad.mit.edu	37	3	39308291	39308293	+	Intron	DEL	TTA	-	-	rs4271863	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39308291_39308293delTTA	uc003cjl.2	-							NM_001337	NP_001328			chemokine (C-X3-C motif) receptor 1						cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40129426	40129427	+	Intron	INS	-	T	T	rs148428266	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40129426_40129427insT	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40609897	40609898	+	IGR	DEL	AA	-	-	rs71870489		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40609897_40609898delAA								ZNF621 (28854 upstream) : CTNNB1 (626503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40756389	40756390	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40756389_40756390insA								ZNF621 (175346 upstream) : CTNNB1 (480011 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41795749	41795749	+	Intron	DEL	A	-	-	rs58341418	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41795749delA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41939991	41939991	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41939991delT	uc003ckv.3	-						ULK4_uc003ckw.2_Intron|ULK4_uc003ckx.1_Intron	NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42202060	42202061	+	Intron	DEL	TG	-	-	rs59260540		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42202060_42202061delTG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42229380	42229380	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42229380delT	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42678146	42678146	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42678146delA	uc003clo.2	+						NKTR_uc003clm.1_Intron|NKTR_uc003clp.2_Intron|NKTR_uc011azp.1_Intron|NKTR_uc003clq.1_Intron|NKTR_uc003clr.1_Intron|NKTR_uc003cls.2_Intron	NM_005385	NP_005376			natural killer-tumor recognition sequence						protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)														---	---	---	---
CCDC13	152206	broad.mit.edu	37	3	42789569	42789570	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42789569_42789570delTT	uc003cly.3	-						CCDC13_uc003clz.2_Intron|CCDC13_uc011azq.1_Intron	NM_144719	NP_653320			coiled-coil domain containing 13											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43000075	43000076	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43000075_43000076insT								ZNF662 (39250 upstream) : FAM198A (20683 downstream)																																			---	---	---	---
C3orf77	375337	broad.mit.edu	37	3	44285883	44285883	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44285883delA	uc003cna.3	+	2	2053	c.1885delA	c.(1885-1887)AAAfs	p.K629fs		NM_001145030	NP_001138502	Q8N9V7	CC077_HUMAN	hypothetical protein LOC375337	629										pancreas(1)	1																		---	---	---	---
ZNF445	353274	broad.mit.edu	37	3	44484354	44484354	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44484354delA	uc003cnf.2	-	8					ZNF445_uc011azv.1_3'UTR|ZNF445_uc011azw.1_3'UTR	NM_181489	NP_852466			zinc finger protein 445						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44816593	44816593	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44816593delA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44868019	44868019	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44868019delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
LIMD1	8994	broad.mit.edu	37	3	45694693	45694693	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45694693delA	uc003coq.2	+							NM_014240	NP_055055			LIM domains containing 1						cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46055622	46055622	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46055622delT								FYCO1 (18315 upstream) : XCR1 (6670 downstream)																																			---	---	---	---
CCR3	1232	broad.mit.edu	37	3	46240590	46240590	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46240590delA	uc003cpg.1	+							NM_178329	NP_847899			CC chemokine receptor 3 isoform 1						cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis	integral to plasma membrane				ovary(3)|lung(3)|breast(1)|kidney(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46320204	46320205	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46320204_46320205delAA								CCR3 (12042 upstream) : CCR2 (75030 downstream)																																			---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47320966	47320966	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47320966delA	uc010hjp.2	-						KIF9_uc003cqx.2_Intron|KIF9_uc003cqy.2_Intron|KIF9_uc011bat.1_Intron|KIF9_uc011bau.1_Intron|KIF9_uc003cra.3_Intron	NM_001134878	NP_001128350			kinesin family member 9 isoform 2						blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48392909	48392909	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48392909delT								SPINK8 (23078 upstream) : FBXW12 (20800 downstream)																																			---	---	---	---
USP19	10869	broad.mit.edu	37	3	49156180	49156181	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49156180_49156181delAA	uc003cwd.1	-						USP19_uc003cwa.2_5'Flank|USP19_uc003cvz.3_Intron|USP19_uc011bcg.1_Intron|USP19_uc003cwb.2_Intron|USP19_uc003cwc.1_5'Flank|USP19_uc011bch.1_Intron|USP19_uc011bci.1_Intron	NM_006677	NP_006668			ubiquitin thioesterase 19						ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
LOC646498	646498	broad.mit.edu	37	3	49222698	49222698	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49222698delA	uc011bcj.1	-							NM_001080528	NP_001073997			hypothetical LOC646498												0				BRCA - Breast invasive adenocarcinoma(193;8.04e-05)|Kidney(197;0.00221)|KIRC - Kidney renal clear cell carcinoma(197;0.00247)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	50551247	50551247	+	IGR	DEL	A	-	-	rs58559172	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50551247delA								CACNA2D2 (10355 upstream) : C3orf18 (44216 downstream)																																			---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51296826	51296826	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51296826delT	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51482934	51482934	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51482934delT	uc003dbe.1	-						VPRBP_uc003dbg.1_Intron	NM_014703	NP_055518			HIV-1 Vpr binding protein						interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51664703	51664703	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51664703delT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron|RAD54L2_uc011bdu.1_Intron|RAD54L2_uc003dbj.2_Intron	NM_015106	NP_055921			RAD54-like 2							nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
GPR62	118442	broad.mit.edu	37	3	51987402	51987403	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51987402_51987403delTT	uc003dca.3	+							NM_080865	NP_543141			G protein-coupled receptor 62							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	52211696	52211696	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52211696delA								POC1A (22990 upstream) : ALAS1 (20420 downstream)																																			---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52240857	52240857	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52240857delT	uc003dcy.1	+						ALAS1_uc003dcz.1_Intron|ALAS1_uc011bec.1_Intron	NM_000688	NP_000679			5-aminolevulinate synthase 1 precursor						heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	53310326	53310326	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53310326delT								TKT (20258 upstream) : DCP1A (7124 downstream)																																			---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53595252	53595252	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53595252delT	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
CHDH	55349	broad.mit.edu	37	3	53877212	53877213	+	Intron	DEL	CA	-	-	rs149540803	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53877212_53877213delCA	uc003dgz.2	-							NM_018397	NP_060867			choline dehydrogenase precursor						alcohol metabolic process		choline dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)|central_nervous_system(1)	2		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	54097849	54097849	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54097849delT								SELK (171860 upstream) : CACNA2D3 (58844 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54300944	54300944	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54300944delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			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)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54872838	54872838	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54872838delT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			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)														---	---	---	---
WNT5A	7474	broad.mit.edu	37	3	55507683	55507683	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55507683delA	uc003dhn.2	-						WNT5A_uc003dhm.2_Intron|WNT5A_uc010hmw.2_Intron|WNT5A_uc010hmx.2_Intron	NM_003392	NP_003383			wingless-type MMTV integration site family,						activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55543262	55543262	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55543262delT	uc003dhr.1	-	18					ERC2_uc003dho.1_RNA|ERC2_uc003dhp.1_RNA|ERC2_uc003dhq.1_RNA	NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55711368	55711369	+	Intron	INS	-	A	A	rs146952167	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55711368_55711369insA	uc003dhr.1	-						ERC2_uc003dhq.1_Intron	NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
CCDC66	285331	broad.mit.edu	37	3	56653283	56653283	+	Intron	DEL	T	-	-	rs113282062		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56653283delT	uc003dhz.2	+						CCDC66_uc003dhy.2_Intron|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_Intron|CCDC66_uc003dia.2_Intron	NM_001141947	NP_001135419			coiled-coil domain containing 66 isoform 1											breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	56862066	56862066	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56862066delA	uc003dih.2	-						ARHGEF3_uc011bew.1_Intron	NM_001128615	NP_001122087			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
IL17RD	54756	broad.mit.edu	37	3	57137199	57137199	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57137199delT	uc003dil.2	-						IL17RD_uc003dik.2_Intron|IL17RD_uc010hna.2_Intron|IL17RD_uc011bex.1_Intron	NM_017563	NP_060033			interleukin 17 receptor D precursor							Golgi membrane|integral to membrane|plasma membrane	receptor activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57509313	57509313	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57509313delT	uc003dit.2	-	4	457	c.276delA	c.(274-276)AAAfs	p.K92fs	DNAH12_uc003diu.2_Frame_Shift_Del_p.K92fs	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1	92	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58100435	58100435	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58100435delT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
ABHD6	57406	broad.mit.edu	37	3	58241837	58241838	+	Intron	INS	-	AC	AC	rs141170161	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58241837_58241838insAC	uc003djs.3	+						ABHD6_uc003djr.2_Intron|ABHD6_uc003djt.3_Intron	NM_020676	NP_065727			abhydrolase domain containing 6							integral to membrane	acylglycerol lipase activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(55;0.000225)|KIRC - Kidney renal clear cell carcinoma(284;0.0471)|Kidney(284;0.0589)|OV - Ovarian serous cystadenocarcinoma(275;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59077537	59077537	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59077537delT								C3orf67 (41779 upstream) : FHIT (657501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59288234	59288234	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59288234delC								C3orf67 (252476 upstream) : FHIT (446804 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	59738056	59738056	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59738056delA	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60235417	60235418	+	Intron	INS	-	ACAC	ACAC	rs144926779	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60235417_60235418insACAC	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61833422	61833422	+	Intron	DEL	A	-	-	rs67213932		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61833422delA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832			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)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62106422	62106424	+	Intron	DEL	AAA	-	-	rs72103244		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62106422_62106424delAAA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832			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)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63341401	63341401	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63341401delC	uc003dlp.2	+						SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron	NM_001130003	NP_001123475			synaptoporin isoform 1							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64808391	64808391	+	Intron	DEL	A	-	-	rs141579250		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64808391delA	uc003dml.2	+											Homo sapiens cDNA FLJ25194 fis, clone REC04095.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	65272984	65272984	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65272984delT								ADAMTS9 (599619 upstream) : MAGI1 (66923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66590176	66590177	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66590176_66590177delAG								LRIG1 (39331 upstream) : KBTBD8 (458550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66682462	66682462	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66682462delT								LRIG1 (131617 upstream) : KBTBD8 (366265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66687519	66687519	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66687519delA								LRIG1 (136674 upstream) : KBTBD8 (361208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66845762	66845762	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66845762delT								LRIG1 (294917 upstream) : KBTBD8 (202965 downstream)																																			---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67477350	67477350	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67477350delA	uc003dna.3	-						SUCLG2_uc010hob.2_Intron	NM_003848	NP_003839			succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67548824	67548824	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67548824delT	uc003dna.3	-						SUCLG2_uc010hob.2_Intron	NM_003848	NP_003839			succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68291967	68291968	+	Intron	INS	-	GT	GT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68291967_68291968insGT	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774			family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	70430834	70430834	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70430834delA								MITF (413348 upstream) : FOXP1 (573903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	70554553	70554553	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70554553delT								MITF (537067 upstream) : FOXP1 (450184 downstream)																																			---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71203247	71203248	+	Intron	INS	-	T	T	rs142389444	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71203247_71203248insT	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	3	72176384	72176384	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72176384delA								PROK2 (342027 upstream) : RYBP (247367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72651215	72651215	+	IGR	DEL	T	-	-	rs113851038		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72651215delT								RYBP (155441 upstream) : SHQ1 (147215 downstream)																																			---	---	---	---
PPP4R2	151987	broad.mit.edu	37	3	73110024	73110024	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73110024delC	uc003dph.1	+						PPP4R2_uc003dpi.1_Intron|FLJ10213_uc003dpj.2_5'Flank	NM_174907	NP_777567			protein phosphatase 4, regulatory subunit 2						mRNA processing|protein modification process|regulation of double-strand break repair via homologous recombination|RNA splicing	centrosome|nucleus|protein phosphatase 4 complex	protein binding, bridging|protein phosphatase type 4 regulator activity			lung(1)	1		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;1.76e-07)|BRCA - Breast invasive adenocarcinoma(55;9.42e-05)|LUSC - Lung squamous cell carcinoma(21;0.00211)|Lung(16;0.00643)|KIRC - Kidney renal clear cell carcinoma(39;0.0164)|Kidney(39;0.0193)|OV - Ovarian serous cystadenocarcinoma(275;0.031)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	73331686	73331686	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73331686delT								PPP4R2 (216675 upstream) : PDZRN3 (99966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75737322	75737322	+	IGR	DEL	T	-	-	rs112035386		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75737322delT								MIR1324 (57313 upstream) : ZNF717 (21472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76087919	76087922	+	IGR	DEL	GTGT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76087919_76087922delGTGT								ZNF717 (253249 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76612257	76612257	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76612257delT								ZNF717 (777587 upstream) : ROBO2 (477037 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77295467	77295468	+	Intron	INS	-	GTCTAT	GTCTAT	rs67301474		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77295467_77295468insGTCTAT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			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)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79199401	79199401	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79199401delT	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	79873785	79873785	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79873785delC								ROBO1 (56726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81374479	81374479	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81374479delA								None (None upstream) : GBE1 (164371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81524300	81524301	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81524300_81524301insT								None (None upstream) : GBE1 (14549 downstream)																																			---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81695676	81695676	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81695676delA	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81718776	81718776	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81718776delA	uc003dqg.2	-						GBE1_uc011bgm.1_Intron	NM_000158	NP_000149			glucan (1,4-alpha-), branching enzyme 1						glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
Unknown	0	broad.mit.edu	37	3	82124086	82124086	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82124086delA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	83099282	83099283	+	IGR	INS	-	TC	TC	rs112408572		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83099282_83099283insTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84053520	84053521	+	IGR	DEL	TT	-	-	rs139856524		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84053520_84053521delTT								None (None upstream) : CADM2 (954612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84425626	84425626	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84425626delT								None (None upstream) : CADM2 (582507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84741480	84741483	+	Intron	DEL	AAAA	-	-	rs140144338		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84741480_84741483delAAAA	uc003dqi.2	-											Homo sapiens cDNA clone IMAGE:4824471.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86203624	86203625	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86203624_86203625delGT								CADM2 (85676 upstream) : VGLL3 (783500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87679200	87679203	+	IGR	DEL	TGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87679200_87679203delTGTG								POU1F1 (353463 upstream) : HTR1F (352523 downstream)																																			---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89207014	89207014	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89207014delA	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224			ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)											TSP Lung(6;0.00050)			---	---	---	---
PROS1	5627	broad.mit.edu	37	3	93648325	93648325	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93648325delA	uc003drb.3	-						PROS1_uc010hoo.2_5'Flank|PROS1_uc003dqz.3_Intron	NM_000313	NP_000304			protein S, alpha preproprotein						leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	94628284	94628285	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94628284_94628285delTC								NSUN3 (782654 upstream) : LOC255025 (28822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95434888	95434888	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95434888delA								LOC255025 (539809 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95550452	95550452	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95550452delA								LOC255025 (655373 upstream) : EPHA6 (982973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95680452	95680452	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95680452delA								LOC255025 (785373 upstream) : EPHA6 (852973 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96533752	96533752	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96533752delG	uc010how.1	+	1	328	c.285delG	c.(283-285)ATGfs	p.M95fs	EPHA6_uc003drp.1_Frame_Shift_Del_p.M95fs	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	1						integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96642327	96642327	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96642327delT	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
ARL6	84100	broad.mit.edu	37	3	97499620	97499620	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97499620delT	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931			ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)										Bardet-Biedl_syndrome				---	---	---	---
ARL6	84100	broad.mit.edu	37	3	97511820	97511820	+	Intron	DEL	A	-	-	rs73138803	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97511820delA	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931			ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)										Bardet-Biedl_syndrome				---	---	---	---
GABRR3	200959	broad.mit.edu	37	3	97744540	97744540	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97744540delA	uc011bgr.1	-							NM_001105580	NP_001099050			gamma-aminobutyric acid (GABA) receptor, rho 3						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98627707	98627707	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98627707delA								DCBLD2 (7174 upstream) : COL8A1 (729747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98694911	98694911	+	IGR	DEL	A	-	-	rs143190954		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98694911delA								DCBLD2 (74378 upstream) : COL8A1 (662543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99159320	99159323	+	IGR	DEL	ACAC	-	-	rs10559491		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99159320_99159323delACAC								DCBLD2 (538787 upstream) : COL8A1 (198131 downstream)																																			---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99778310	99778310	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99778310delT	uc003dtm.2	-						C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
TMEM45A	55076	broad.mit.edu	37	3	100272149	100272149	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100272149delT	uc003dtz.1	+						TMEM45A_uc003dua.1_Intron	NM_018004	NP_060474			transmembrane protein 45A							integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100353844	100353845	+	Intron	INS	-	AC	AC	rs142620077	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100353844_100353845insAC	uc003duc.2	+						GPR128_uc011bhc.1_5'Flank	NM_032787	NP_116176			G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100476954	100476954	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100476954delA	uc003dun.2	-						ABI3BP_uc003duj.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100555388	100555388	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100555388delG	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc003duk.2_Intron|ABI3BP_uc003dul.2_Intron|ABI3BP_uc011bhd.1_Intron|ABI3BP_uc003dum.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100569453	100569453	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100569453delT	uc003dun.2	-						ABI3BP_uc003duo.2_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100583652	100583652	+	Intron	DEL	A	-	-	rs10711419		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100583652delA	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc003dup.3_Frame_Shift_Del_p.F363fs	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101070484	101070484	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101070484delT	uc003dut.2	-	12	1746	c.1635delA	c.(1633-1635)AAAfs	p.K545fs	SENP7_uc003duu.2_Frame_Shift_Del_p.K480fs|SENP7_uc003duv.2_Frame_Shift_Del_p.K512fs|SENP7_uc003duw.2_Frame_Shift_Del_p.K479fs|SENP7_uc003dux.2_Frame_Shift_Del_p.K381fs	NM_020654	NP_065705	Q9BQF6	SENP7_HUMAN	sentrin/SUMO-specific protease 7 isoform 1	545					proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5																		---	---	---	---
RPL24	6152	broad.mit.edu	37	3	101403012	101403013	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101403012_101403013delTT	uc003dvh.1	-						RPL24_uc003dvi.1_Intron	NM_000986	NP_000977			ribosomal protein L24						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	103045007	103045007	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103045007delA								ZPLD1 (846322 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104863216	104863216	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104863216delA								None (None upstream) : ALCAM (222497 downstream)																																			---	---	---	---
ALCAM	214	broad.mit.edu	37	3	105214285	105214286	+	Intron	DEL	AA	-	-	rs72017030		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105214285_105214286delAA	uc003dvx.2	+						ALCAM_uc003dvv.2_Intron|ALCAM_uc003dvw.1_Intron|ALCAM_uc003dvy.2_Intron|ALCAM_uc011bhh.1_Intron	NM_001627	NP_001618			activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	106094807	106094809	+	IGR	DEL	AAA	-	-	rs112857814	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106094807_106094809delAAA								CBLB (506541 upstream) : LOC100302640 (460851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107865896	107865896	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107865896delG								CD47 (55961 upstream) : IFT57 (13764 downstream)																																			---	---	---	---
KIAA1524	57650	broad.mit.edu	37	3	108288977	108288977	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108288977delG	uc003dxb.3	-						KIAA1524_uc003dxc.1_Intron|KIAA1524_uc010hpw.1_Intron	NM_020890	NP_065941			p90 autoantigen							cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109111278	109111279	+	IGR	DEL	TG	-	-	rs148396871	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109111278_109111279delTG								DPPA4 (54859 upstream) : FLJ25363 (17558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109648950	109648953	+	IGR	DEL	TCCC	-	-	rs113948167		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109648950_109648953delTCCC								FLJ25363 (434936 upstream) : None (None downstream)																																			---	---	---	---
CD96	10225	broad.mit.edu	37	3	111282228	111282228	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111282228delA	uc003dxw.2	+						CD96_uc003dxv.2_Intron|CD96_uc003dxx.2_Intron|CD96_uc010hpy.1_Intron	NM_198196	NP_937839			CD96 antigen isoform 1 precursor						cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3														Opitz_Trigonocephaly_syndrome				---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111460149	111460149	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111460149delA	uc003dyc.2	+						PLCXD2_uc003dya.2_Intron|PLCXD2_uc003dxz.2_Intron	NM_001134437	NP_001127909			pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6																		---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113207969	113207969	+	Intron	DEL	T	-	-	rs75840421		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113207969delT	uc003eag.3	-						CCDC52_uc003eaf.3_Intron|CCDC52_uc003eah.1_Intron	NM_144718	NP_653319			coiled-coil domain containing 52						cell division|mitosis	centriole|spindle	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	113363045	113363046	+	IGR	INS	-	TCTCTC	TCTCTC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113363045_113363046insTCTCTC								SIDT1 (14624 upstream) : KIAA2018 (4189 downstream)																																			---	---	---	---
ATP6V1A	523	broad.mit.edu	37	3	113514687	113514687	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113514687delT	uc003eao.2	+						ATP6V1A_uc011bik.1_Intron	NM_001690	NP_001681			ATPase, H+ transporting, lysosomal V1 subunit A						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114129067	114129067	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114129067delT	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	114937501	114937501	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114937501delA								ZBTB20 (71374 upstream) : GAP43 (404650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	114951095	114951096	+	IGR	DEL	TG	-	-	rs113291888		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114951095_114951096delTG								ZBTB20 (84968 upstream) : GAP43 (391055 downstream)																																			---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118693764	118693764	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118693764delA	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887			immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120909020	120909021	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120909020_120909021delTC	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
ILDR1	286676	broad.mit.edu	37	3	121724290	121724290	+	Intron	DEL	A	-	-	rs34370755		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121724290delA	uc003ees.2	-						ILDR1_uc003eeq.2_Intron|ILDR1_uc003eer.2_Intron|ILDR1_uc010hrg.2_Intron	NM_175924	NP_787120			immunoglobulin-like domain containing receptor							cytosol|integral to membrane|plasma membrane	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.156)														---	---	---	---
CCDC58	131076	broad.mit.edu	37	3	122081335	122081335	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122081335delT	uc003eey.2	-							NM_001017928	NP_001017928			coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
CCDC58	131076	broad.mit.edu	37	3	122081882	122081882	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122081882delA	uc003eey.2	-							NM_001017928	NP_001017928			coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
KPNA1	3836	broad.mit.edu	37	3	122214675	122214676	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122214675_122214676delAA	uc003efd.1	-						KPNA1_uc011bjr.1_Intron|KPNA1_uc010hrh.2_Intron|KPNA1_uc003efe.2_Intron	NM_002264	NP_002255			karyopherin alpha 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|regulation of DNA recombination|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein binding|protein transporter activity				0				GBM - Glioblastoma multiforme(114;0.0898)														---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122411614	122411615	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122411614_122411615delGT	uc003efq.3	+						PARP14_uc010hrk.2_5'Flank	NM_017554	NP_060024			poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
SEC22A	26984	broad.mit.edu	37	3	122959660	122959660	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122959660delA	uc003ege.2	+						SEC22A_uc003egf.2_Intron	NM_012430	NP_036562			SEC22 vesicle trafficking protein homolog A						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123406530	123406530	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123406530delT	uc003ego.2	-						MYLK_uc011bjv.1_Intron|MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc003egt.2_Intron	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124098777	124098777	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124098777delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124141564	124141565	+	Intron	INS	-	G	G	rs143322569	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124141564_124141565insG	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125030059	125030060	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125030059_125030060insA	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
C3orf22	152065	broad.mit.edu	37	3	126269957	126269958	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126269957_126269958delTG	uc003ejb.2	-							NM_152533	NP_689746			hypothetical protein LOC152065												0				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
MGLL	11343	broad.mit.edu	37	3	127538267	127538270	+	Intron	DEL	GAGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127538267_127538270delGAGA	uc003ejx.2	-						MGLL_uc003ejw.2_Intron|MGLL_uc011bko.1_Intron|MGLL_uc010hsp.1_Intron	NM_001003794	NP_001003794			monoglyceride lipase isoform 2						arachidonic acid metabolic process|fatty acid biosynthetic process|inflammatory response|platelet activation|regulation of endocannabinoid signaling pathway|regulation of inflammatory response|regulation of sensory perception of pain|triglyceride catabolic process	plasma membrane	acylglycerol lipase activity|carboxylesterase activity|lysophospholipase activity|protein homodimerization activity				0																		---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128363639	128363639	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128363639delA	uc003ekr.1	-						RPN1_uc011bkq.1_Intron	NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128614030	128614030	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128614030delT	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron|ACAD9_uc003elc.1_5'Flank	NM_014049	NP_054768			acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129432868	129432868	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129432868delA	uc003emz.3	-						TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129473920	129473920	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129473920delA	uc003emz.3	-						TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130061575	130061575	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130061575delA	uc010htj.1	+						COL29A1_uc010hti.1_5'Flank	NM_153264	NP_694996			collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130324217	130324218	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130324217_130324218delTG	uc010htl.2	+						COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078			collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130494587	130494588	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130494587_130494588delAG								PIK3R4 (28891 upstream) : ATP2C1 (74857 downstream)																																			---	---	---	---
NCRNA00119	348808	broad.mit.edu	37	3	132495282	132495284	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132495282_132495284delAAA	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132613529	132613531	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132613529_132613531delTTT								NCRNA00119 (20479 upstream) : TMEM108 (143640 downstream)																																			---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133168731	133168731	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133168731delA	uc003epn.1	+						uc003epo.2_Intron	NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
TOPBP1	11073	broad.mit.edu	37	3	133342872	133342872	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133342872delG	uc003eps.2	-						TOPBP1_uc003ept.1_Intron	NM_007027	NP_008958			topoisomerase (DNA) II binding protein 1						DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7													Other_conserved_DNA_damage_response_genes					---	---	---	---
Unknown	0	broad.mit.edu	37	3	133995260	133995260	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133995260delT								RYK (25674 upstream) : AMOTL2 (75434 downstream)																																			---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134631376	134631377	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134631376_134631377delCT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135601087	135601087	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135601087delA								EPHB1 (621782 upstream) : PPP2R3A (83480 downstream)																																			---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136087910	136087910	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136087910delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	136479550	136479551	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136479550_136479551delTT								STAG1 (8305 upstream) : TMEM22 (58310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136988736	136988736	+	IGR	DEL	T	-	-	rs67404408		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136988736delT								IL20RB (258816 upstream) : SOX14 (494843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137598754	137598754	+	IGR	DEL	T	-	-	rs111336197		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137598754delT								SOX14 (114358 upstream) : CLDN18 (118904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137686351	137686351	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137686351delT								SOX14 (201955 upstream) : CLDN18 (31307 downstream)																																			---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137993076	137993077	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137993076_137993077delTG	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138461382	138461382	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138461382delA	uc011bmq.1	-							NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139770328	139770328	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139770328delT	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			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															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140148041	140148041	+	Intron	DEL	T	-	-	rs77649675		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140148041delT	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			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															HNSCC(16;0.037)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140435813	140435813	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140435813delT								TRIM42 (15822 upstream) : SLC25A36 (224849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140451874	140451874	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140451874delT								TRIM42 (31883 upstream) : SLC25A36 (208788 downstream)																																			---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141244158	141244158	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141244158delT	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.1_Intron	NM_006506	NP_006497			RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141784352	141784353	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141784352_141784353delGT	uc003eun.3	-						TFDP2_uc003eum.3_Intron|TFDP2_uc003euo.2_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141851642	141851643	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141851642_141851643delAA	uc003eun.3	-						TFDP2_uc003eum.3_Intron|TFDP2_uc003euo.2_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142935420	142935420	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142935420delT								CHST2 (93610 upstream) : SLC9A9 (48645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143967799	143967800	+	IGR	INS	-	CCCC	CCCC	rs147286016	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143967799_143967800insCCCC								C3orf58 (256590 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144086544	144086544	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144086544delG								C3orf58 (375335 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144563260	144563261	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144563260_144563261insT								C3orf58 (852051 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145389636	145389636	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145389636delA								None (None upstream) : PLOD2 (397592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145694312	145694313	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145694312_145694313insA								None (None upstream) : PLOD2 (92915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146634050	146634051	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146634050_146634051delTT								PLSCR5 (310047 upstream) : ZIC4 (469786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146755170	146755170	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146755170delA								PLSCR5 (431167 upstream) : ZIC4 (348667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147601629	147601629	+	IGR	DEL	T	-	-	rs112789637	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147601629delT								ZIC1 (467125 upstream) : AGTR1 (814029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147702684	147702685	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147702684_147702685delAC								ZIC1 (568180 upstream) : AGTR1 (712973 downstream)																																			---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148582960	148582960	+	5'Flank	DEL	A	-	-	rs143382113		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148582960delA	uc003ewm.2	+							NM_001870	NP_001861			carboxypeptidase A3 precursor						proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
GYG1	2992	broad.mit.edu	37	3	148711907	148711907	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148711907delT	uc003ewn.2	+						GYG1_uc011bnp.1_Intron|GYG1_uc003ewo.2_Intron|GYG1_uc003ewp.2_Intron	NM_004130	NP_004121			glycogenin 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	glycogenin glucosyltransferase activity|metal ion binding|protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148757291	148757291	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148757291delT	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636			helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
HPS3	84343	broad.mit.edu	37	3	148859307	148859307	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148859307delT	uc003ewu.1	+						HPS3_uc003ewt.1_Intron|HPS3_uc011bnq.1_Intron	NM_032383	NP_115759			Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											Hermansky-Pudlak_syndrome				---	---	---	---
CP	1356	broad.mit.edu	37	3	148899609	148899609	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148899609delT	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003eww.3_5'Flank|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron	NM_000096	NP_000087			ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
TM4SF18	116441	broad.mit.edu	37	3	149042947	149042948	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149042947_149042948delAA	uc003exa.2	-							NM_138786	NP_620141			transmembrane 4 L six family member 18							integral to membrane				ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149390304	149390306	+	Intron	DEL	CTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149390304_149390306delCTT	uc003exh.2	-							NM_015472	NP_056287			WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149639764	149639764	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149639764delT	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213			ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
CLRN1OS	116933	broad.mit.edu	37	3	150589339	150589340	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150589339_150589340delAA	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150908388	150908389	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150908388_150908389insT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	153381153	153381153	+	IGR	DEL	G	-	-	rs9289922	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153381153delG								C3orf79 (160670 upstream) : SGEF (457996 downstream)																																			---	---	---	---
DHX36	170506	broad.mit.edu	37	3	153995289	153995289	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153995289delA	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916			DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154007619	154007619	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154007619delA	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916			DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154010602	154010602	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154010602delT	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916			DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
MME	4311	broad.mit.edu	37	3	154834153	154834153	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154834153delT	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
MME	4311	broad.mit.edu	37	3	154870634	154870635	+	Intron	DEL	AA	-	-	rs112860597		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154870634_154870635delAA	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
MME	4311	broad.mit.edu	37	3	154886666	154886666	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154886666delA	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	155753118	155753119	+	IGR	INS	-	CCTCCTCCTCCC	CCTCCTCCTCCC	rs150484872	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155753118_155753119insCCTCCTCCTCCC								GMPS (97600 upstream) : KCNAB1 (85218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155761051	155761051	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155761051delT								GMPS (105533 upstream) : KCNAB1 (77286 downstream)																																			---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156177892	156177893	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156177892_156177893insG	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron|KCNAB1_uc011boo.1_Intron	NM_172160	NP_751892			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)															---	---	---	---
VEPH1	79674	broad.mit.edu	37	3	157199255	157199256	+	Intron	INS	-	C	C	rs60332684		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157199255_157199256insC	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron|VEPH1_uc003fbm.2_Intron|VEPH1_uc003fbn.2_Intron	NM_024621	NP_078897			ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	157652650	157652650	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157652650delG								C3orf55 (333631 upstream) : SHOX2 (161151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157717958	157717958	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157717958delA								C3orf55 (398939 upstream) : SHOX2 (95843 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157864868	157864868	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157864868delT	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	158097604	158097605	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158097604_158097605delCA	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	158808005	158808005	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158808005delC	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159218502	159218502	+	Intron	DEL	A	-	-	rs79405720		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159218502delA	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
KPNA4	3840	broad.mit.edu	37	3	160219096	160219096	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160219096delA	uc003fdn.2	-	17						NM_002268	NP_002259			karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160734764	160734764	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160734764delT	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160960578	160960578	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160960578delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160965263	160965263	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160965263delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161683859	161683859	+	IGR	DEL	A	-	-	rs9874929	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161683859delA								OTOL1 (462131 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162571491	162571492	+	Intron	INS	-	C	C	rs145281929	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162571491_162571492insC	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	165608377	165608377	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165608377delA								BCHE (53124 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165738107	165738108	+	IGR	DEL	TG	-	-	rs146726780		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165738107_165738108delTG								BCHE (182854 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166579565	166579565	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166579565delT								None (None upstream) : ZBBX (378516 downstream)																																			---	---	---	---
SERPINI2	5276	broad.mit.edu	37	3	167167197	167167197	+	Intron	DEL	A	-	-	rs78539252	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167167197delA	uc003fer.1	-						SERPINI2_uc003fes.1_Intron|SERPINI2_uc003fet.1_Intron	NM_006217	NP_006208			serpin peptidase inhibitor, clade I (pancpin),						cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3																		---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169847493	169847494	+	Intron	DEL	AT	-	-	rs79158343		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169847493_169847494delAT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron	NM_024947	NP_079223			polyhomeotic like 3						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	171147828	171147828	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171147828delC	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhq.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	171990448	171990448	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171990448delA	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron	NM_022763	NP_073600			fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	172314182	172314184	+	5'Flank	DEL	TCT	-	-	rs138385156		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172314182_172314184delTCT	uc003fif.1	-											Homo sapiens cDNA FLJ45650 fis, clone CTONG2009923.																														---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173613481	173613481	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173613481delT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174652957	174652957	+	Intron	DEL	A	-	-	rs72435365		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174652957delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175472857	175472857	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175472857delA	uc003fit.2	+							NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	175626740	175626741	+	IGR	INS	-	G	G	rs145154255	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175626740_175626741insG								NAALADL2 (103314 upstream) : None (None downstream)																																			---	---	---	---
TBL1XR1	79718	broad.mit.edu	37	3	176771862	176771863	+	Intron	DEL	GC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176771862_176771863delGC	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	NM_024665	NP_078941			transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	178569316	178569317	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178569316_178569317insA	uc003fjb.1	-						uc003fjc.1_Intron					Homo sapiens clone N11 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	178634090	178634090	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178634090delA								KCNMB2 (71874 upstream) : ZMAT3 (107437 downstream)																																			---	---	---	---
ACTL6A	86	broad.mit.edu	37	3	179305643	179305643	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179305643delA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292			actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180182658	180182658	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180182658delT								PEX5L (428141 upstream) : TTC14 (137260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180247654	180247654	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180247654delT								PEX5L (493137 upstream) : TTC14 (72264 downstream)																																			---	---	---	---
TTC14	151613	broad.mit.edu	37	3	180320662	180320663	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180320662_180320663insT	uc003fkk.2	+						TTC14_uc003fkl.2_Intron|TTC14_uc003fkm.2_Intron	NM_133462	NP_597719			tetratricopeptide repeat domain 14 isoform a								RNA binding			ovary(1)	1	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)															---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180379570	180379570	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180379570delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091			coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)															---	---	---	---
DNAJC19	131118	broad.mit.edu	37	3	180706140	180706141	+	Intron	DEL	TC	-	-	rs116790641		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180706140_180706141delTC	uc003fkt.2	-						DNAJC19_uc003fku.2_Intron	NM_145261	NP_660304			DnaJ homolog, subfamily C, member 19						genitalia development|protein folding|protein targeting to mitochondrion|transmembrane transport|visual perception	integral to membrane|mitochondrial inner membrane	heat shock protein binding				0	all_cancers(143;3.12e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-36)|OV - Ovarian serous cystadenocarcinoma(80;1.55e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180716686	180716686	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180716686delT								DNAJC19 (9156 upstream) : SOX2OT (564823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180918885	180918885	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180918885delA								DNAJC19 (211355 upstream) : SOX2OT (362624 downstream)																																			---	---	---	---
ATP11B	23200	broad.mit.edu	37	3	182537879	182537880	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182537879_182537880insA	uc003flb.2	+						ATP11B_uc003fla.2_Intron	NM_014616	NP_055431			ATPase, class VI, type 11B						aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)															---	---	---	---
DCUN1D1	54165	broad.mit.edu	37	3	182665289	182665290	+	Intron	DEL	AT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182665289_182665290delAT	uc003fld.1	-						DCUN1D1_uc011bqn.1_Intron	NM_020640	NP_065691			RP42 homolog							ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183796101	183796101	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183796101delT								HTR3C (17642 upstream) : HTR3E (18751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183921175	183921175	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183921175delA								ABCF3 (9380 upstream) : VWA5B2 (27142 downstream)																																			---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185028498	185028498	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185028498delA	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron	NM_004721	NP_004712			mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
ETV5	2119	broad.mit.edu	37	3	185823802	185823802	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185823802delT	uc003fpz.2	-						ETV5_uc003fpy.2_Intron	NM_004454	NP_004445			ets variant gene 5 (ets-related molecule)						cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)					T	TMPRSS2|SCL45A3	Prostate 								---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185916743	185916743	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185916743delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185935059	185935059	+	Intron	DEL	T	-	-	rs139113323		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185935059delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186045180	186045180	+	Intron	DEL	T	-	-	rs36076414		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186045180delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	186160933	186160933	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186160933delA								DGKG (80910 upstream) : CRYGS (95300 downstream)																																			---	---	---	---
KNG1	3827	broad.mit.edu	37	3	186435632	186435635	+	Intron	DEL	CCAC	-	-	rs10575985		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186435632_186435635delCCAC	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886			kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)													---	---	---	---
RFC4	5984	broad.mit.edu	37	3	186527046	186527046	+	5'Flank	DEL	T	-	-	rs63135364		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186527046delT	uc003fqz.2	-						RFC4_uc011bsc.1_5'Flank|RFC4_uc011bsd.1_5'Flank	NM_002916	NP_002907			replication factor C 4						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	186609497	186609497	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186609497delA								ADIPOQ (33247 upstream) : ST6GAL1 (39019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187837938	187837939	+	IGR	DEL	TT	-	-	rs5855175		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187837938_187837939delTT								BCL6 (374463 upstream) : LPP (33780 downstream)																																			---	---	---	---
LPP	4026	broad.mit.edu	37	3	188227400	188227400	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188227400delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188295546	188295549	+	Intron	DEL	TTCG	-	-	rs72048204		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188295546_188295549delTTCG	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188310941	188310942	+	Intron	INS	-	GT	GT	rs138109445	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188310941_188310942insGT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188955077	188955078	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188955077_188955078delCA	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189772299	189772299	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189772299delT	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	190925176	190925177	+	IGR	INS	-	T	T	rs138266549	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190925176_190925177insT								SNAR-I (329337 upstream) : OSTN (5145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194278499	194278500	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194278499_194278500delTT								ATP13A3 (89531 upstream) : TMEM44 (29903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194360653	194360653	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194360653delA								TMEM44 (6235 upstream) : LSG1 (865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194712076	194712081	+	IGR	DEL	CTCCTA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194712076_194712081delCTCCTA								FAM43A (302312 upstream) : C3orf21 (76934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195320162	195320162	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195320162delC								APOD (9086 upstream) : SDHAP2 (64748 downstream)																																			---	---	---	---
SDHAP2	727956	broad.mit.edu	37	3	195401079	195401079	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195401079delT	uc003fuw.2	+						SDHAP2_uc011btc.1_Intron|SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0																		---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195448754	195448755	+	Intron	INS	-	G	G	rs144078556	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195448754_195448755insG	uc010hzo.2	+						MUC20_uc010hzp.2_5'Flank	NM_152673	NP_689886			mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195462031	195462032	+	3'UTR	INS	-	T	T	rs139052122	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195462031_195462032insT	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886			mucin 20 isoform L						protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
PCYT1A	5130	broad.mit.edu	37	3	195975231	195975231	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195975231delT	uc003fwg.2	-						PCYT1A_uc003fwh.2_Intron	NM_005017	NP_005008			choline phosphate cytidylyltransferase 1 alpha							cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity				0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)													---	---	---	---
TCTEX1D2	255758	broad.mit.edu	37	3	196025950	196025950	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196025950delT	uc003fwi.2	-							NM_152773	NP_689986			Tctex1 domain containing 2								protein binding			ovary(1)|breast(1)	2	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
FBXO45	200933	broad.mit.edu	37	3	196302553	196302553	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196302553delT	uc010iai.2	+							NM_001105573	NP_001099043			F-box protein 45						nervous system development|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	cell junction|postsynaptic membrane|presynaptic membrane	protein binding			skin(1)	1	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
PAK2	5062	broad.mit.edu	37	3	196538116	196538117	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196538116_196538117insA	uc003fwy.3	+							NM_002577	NP_002568			p21-activated kinase 2						axon guidance|cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of apoptosis|regulation of defense response to virus by virus|regulation of growth|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|nucleus|perinuclear region of cytoplasm|plasma membrane	ATP binding|identical protein binding|protein kinase binding|protein serine/threonine kinase activity|protein tyrosine kinase activator activity			ovary(1)|lung(1)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196589036	196589036	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196589036delT								PAK2 (29520 upstream) : SENP5 (5691 downstream)																																			---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196793772	196793772	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196793772delA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	197023514	197023514	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197023514delA	uc003fxo.3	-						DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_Intron|uc003fxq.2_5'Flank	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	197225052	197225053	+	IGR	INS	-	AAAC	AAAC	rs149298759	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197225052_197225053insAAAC								DLG1 (198909 upstream) : BDH1 (11602 downstream)																																			---	---	---	---
LRCH3	84859	broad.mit.edu	37	3	197605327	197605327	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197605327delA	uc011bul.1	+						LRCH3_uc011bum.1_Intron|LRCH3_uc011bun.1_Intron|LRCH3_uc003fyk.2_Intron	NM_032773	NP_116162			leucine-rich repeats and calponin homology (CH)							extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	567681	567681	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:567681delC								PIGG (34362 upstream) : PDE6B (51682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	581316	581316	+	IGR	DEL	T	-	-	rs137923295		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:581316delT								PIGG (47997 upstream) : PDE6B (38047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	1139962	1139964	+	IGR	DEL	ATC	-	-	rs35004357		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1139962_1139964delATC								RNF212 (32380 upstream) : SPON2 (20758 downstream)																																			---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1962561	1962561	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1962561delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gei.3_Intron|WHSC1_uc011bvh.1_Intron|WHSC1_uc010icf.2_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2374199	2374200	+	Intron	INS	-	CT	CT	rs72598775		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2374199_2374200insCT	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023			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																		---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2659497	2659498	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2659497_2659498insT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron|FAM193A_uc003gfe.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3314657	3314657	+	5'Flank	DEL	T	-	-	rs60434800	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3314657delT	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_5'Flank	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3319285	3319285	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3319285delG	uc003ggw.2	+	2	2292	c.1388delG	c.(1387-1389)AGGfs	p.R463fs	RGS12_uc003ggu.2_Frame_Shift_Del_p.R463fs|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_Frame_Shift_Del_p.R463fs|RGS12_uc003ggx.1_Frame_Shift_Del_p.R463fs	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	463						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3432431	3432431	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3432431delC	uc003ggw.2	+	17	4767	c.3863delC	c.(3862-3864)ACCfs	p.T1288fs	RGS12_uc003ggv.2_Frame_Shift_Del_p.T1288fs|RGS12_uc003ggy.1_3'UTR|RGS12_uc003ggz.2_Frame_Shift_Del_p.T640fs|RGS12_uc011bvs.1_3'UTR|RGS12_uc003gha.2_Frame_Shift_Del_p.T630fs|RGS12_uc010icv.2_Frame_Shift_Del_p.T487fs	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	1288						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3693812	3693812	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3693812delT								LRPAP1 (159588 upstream) : ADRA2C (74263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3938947	3938948	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3938947_3938948insG								ADRA2C (168696 upstream) : LOC348926 (4722 downstream)																																			---	---	---	---
TMEM128	85013	broad.mit.edu	37	4	4241997	4241997	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4241997delA	uc003ghr.1	-						TMEM128_uc003ghq.1_Intron|TMEM128_uc003ghs.2_3'UTR|TMEM128_uc011bvv.1_Intron|TMEM128_uc011bvw.1_Intron	NM_032927	NP_116316			transmembrane protein 128							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)														---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6064870	6064871	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6064870_6064871delAA	uc003giu.3	-						JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_Intron|JAKMIP1_uc003giv.3_Intron|JAKMIP1_uc010ide.2_Intron	NM_144720	NP_653321			janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
MAN2B2	23324	broad.mit.edu	37	4	6580720	6580722	+	Intron	DEL	ACC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6580720_6580722delACC	uc003gjf.1	+						MAN2B2_uc003gje.1_Intron|MAN2B2_uc011bwf.1_Intron	NM_015274	NP_056089			mannosidase, alpha, class 2B, member 2						mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7776640	7776640	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7776640delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron|LOC84740_uc003gkd.3_RNA	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7815567	7815567	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7815567delC	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7858934	7858934	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7858934delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	9237738	9237739	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9237738_9237739delCA								LOC650293 (285612 upstream) : USP17 (122370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	13948876	13948876	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13948876delA								BOD1L (319548 upstream) : None (None downstream)																																			---	---	---	---
CPEB2	132864	broad.mit.edu	37	4	15059946	15059946	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15059946delT	uc003gni.1	+						CPEB2_uc003gnj.1_Intron|CPEB2_uc003gnk.1_Intron|CPEB2_uc003gnl.1_Intron|CPEB2_uc003gnm.1_Intron|CPEB2_uc003gnn.1_Intron	NM_182485	NP_872291			cytoplasmic polyadenylation element binding						regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	19430937	19430938	+	IGR	INS	-	G	G	rs140344064	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19430937_19430938insG								None (None upstream) : SLIT2 (824297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	20213429	20213430	+	IGR	DEL	CA	-	-	rs56061254		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20213429_20213430delCA								None (None upstream) : SLIT2 (41805 downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21513788	21513811	+	Intron	DEL	GGAGGGAGGAAGGAAGGAACGAAC	-	-	rs68124536		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21513788_21513811delGGAGGGAGGAAGGAAGGAACGAAC	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175			Kv channel interacting protein 4 isoform 5							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21864639	21864639	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21864639delT	uc003gqi.1	-							NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	23422342	23422347	+	IGR	DEL	GTGTGA	-	-	rs10000884		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23422342_23422347delGTGTGA								GBA3 (601151 upstream) : PPARGC1A (371298 downstream)																																			---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24532477	24532477	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24532477delA	uc003gqx.2	-						DHX15_uc003gqv.2_Intron|DHX15_uc003gqw.2_Intron	NM_001358	NP_001349			DEAH (Asp-Glu-Ala-His) box polypeptide 15						mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	26075241	26075242	+	IGR	DEL	AA	-	-	rs71989731		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26075241_26075242delAA								C4orf52 (143741 upstream) : RBPJ (246090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29280737	29280740	+	IGR	DEL	CTTC	-	-	rs71649265		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29280737_29280740delCTTC								None (None upstream) : None (None downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30732334	30732334	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30732334delT	uc003gsk.1	+						PCDH7_uc011bxw.1_Intron|PCDH7_uc011bxx.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	33172316	33172317	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33172316_33172317delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
TLR10	81793	broad.mit.edu	37	4	38777276	38777276	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38777276delA	uc003gti.2	-						TLR10_uc003gtj.2_Intron|TLR10_uc003gtk.2_Intron	NM_030956	NP_112218			toll-like receptor 10 precursor						inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane	transmembrane receptor activity			lung(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39129241	39129241	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39129241delT								KLHL5 (5413 upstream) : WDR19 (54783 downstream)																																			---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39478849	39478849	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39478849delA	uc003guf.2	+	11					LIAS_uc003gug.2_3'UTR|LIAS_uc003guh.2_3'UTR	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39847506	39847506	+	Intron	DEL	A	-	-	rs79426492		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39847506delA	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869			PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39989777	39989777	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39989777delA								PDS5A (10201 upstream) : LOC344967 (54760 downstream)																																			---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41699388	41699388	+	3'UTR	DEL	T	-	-	rs113753743		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41699388delT	uc003gvu.3	+	27					LIMCH1_uc003gvv.3_3'UTR|LIMCH1_uc003gvw.3_3'UTR|LIMCH1_uc003gvx.3_3'UTR|LIMCH1_uc003gwe.3_3'UTR|LIMCH1_uc003gvy.3_3'UTR|LIMCH1_uc003gwa.3_3'UTR|LIMCH1_uc003gvz.3_3'UTR|LIMCH1_uc011byu.1_3'UTR|LIMCH1_uc003gwc.3_3'UTR|LIMCH1_uc003gwd.3_3'UTR|LIMCH1_uc011byv.1_3'UTR|LIMCH1_uc011byw.1_3'UTR|LIMCH1_uc010ifv.2_RNA	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	41763168	41763168	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41763168delA								PHOX2B (12181 upstream) : TMEM33 (173969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42791027	42791027	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42791027delT								ATP8A1 (131905 upstream) : GRXCR1 (104257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43901421	43901421	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43901421delA								GRXCR1 (868748 upstream) : KCTD8 (274501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49099749	49099753	+	IGR	DEL	TCCGG	-	-	rs60947727		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49099749_49099753delTCCGG								CWH43 (35656 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49160129	49160129	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49160129delC								CWH43 (96036 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49213584	49213585	+	IGR	INS	-	A	A	rs141768505		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49213584_49213585insA								CWH43 (149491 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49535585	49535586	+	IGR	DEL	TC	-	-	rs60544689		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49535585_49535586delTC								CWH43 (471492 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52960531	52960531	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52960531delA	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54256109	54256109	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54256109delT	uc003haa.2	+						FIP1L1_uc003gzx.3_Intron|FIP1L1_uc011bzt.1_Intron|FIP1L1_uc003gzy.2_Intron|FIP1L1_uc011bzu.1_Intron|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron	NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54777740	54777740	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54777740delA	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
KIT	3815	broad.mit.edu	37	4	55569860	55569860	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55569860delT	uc010igr.2	+						KIT_uc010igs.2_Intron	NM_000222	NP_000213			v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				---	---	---	---
Unknown	0	broad.mit.edu	37	4	55801809	55801810	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55801809_55801810insT								KIT (194930 upstream) : KDR (142617 downstream)																																			---	---	---	---
KDR	3791	broad.mit.edu	37	4	55981760	55981761	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55981760_55981761delTG	uc003has.2	-						KDR_uc003hat.1_Intron|KDR_uc011bzx.1_Intron	NM_002253	NP_002244			kinase insert domain receptor precursor						angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56988564	56988564	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56988564delA								CEP135 (89038 upstream) : KIAA1211 (47797 downstream)																																			---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57871705	57871705	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57871705delA	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron	NM_000938	NP_000929			DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	58734275	58734275	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58734275delA								IGFBP7 (757736 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60817497	60817497	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60817497delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60982720	60982720	+	IGR	DEL	A	-	-	rs33963855		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60982720delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66725929	66725932	+	IGR	DEL	TGTA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66725929_66725932delTGTA								EPHA5 (190276 upstream) : MIR1269 (416610 downstream)																																			---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68499206	68499206	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68499206delA	uc003hdg.3	-							NM_018227	NP_060697			ubiquitin-activating enzyme E1-like 2						protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																		---	---	---	---
TMPRSS11B	132724	broad.mit.edu	37	4	69101558	69101558	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69101558delT	uc003hdw.3	-							NM_182502	NP_872308			transmembrane protease, serine 11B						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69197627	69197628	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69197627_69197628delAA	uc003hdx.2	-						YTHDC1_uc003hdy.2_Intron	NM_001031732	NP_001026902			splicing factor YT521-B isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
UGT2B10	7365	broad.mit.edu	37	4	69876024	69876024	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69876024delA	uc011cao.1	-						UGT2B10_uc011can.1_Intron					RecName: Full=UDP-glucuronosyltransferase 2B28;          Short=UDPGT 2B28;          EC=2.4.1.17; Flags: Precursor;						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
UGT2B4	7363	broad.mit.edu	37	4	70361792	70361792	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70361792delT	uc003hek.3	-						UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_5'Flank	NM_021139	NP_066962			UDP glucuronosyltransferase 2B4 precursor						estrogen catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(2)	2																		---	---	---	---
C4orf40	401137	broad.mit.edu	37	4	71015422	71015423	+	5'Flank	INS	-	A	A	rs138401309	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71015422_71015423insA	uc003hfa.3	+							NM_214711	NP_999876			hypothetical protein LOC401137 precursor							extracellular region					0																		---	---	---	---
ENAM	10117	broad.mit.edu	37	4	71501620	71501620	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71501620delT	uc011caw.1	+							NM_031889	NP_114095			enamelin precursor						bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)															---	---	---	---
RASSF6	166824	broad.mit.edu	37	4	74442037	74442039	+	Intron	DEL	AGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74442037_74442039delAGA	uc003hhd.1	-						RASSF6_uc003hhc.1_Intron|RASSF6_uc010iik.1_Intron|RASSF6_uc010iil.1_Intron	NM_201431	NP_958834			Ras association (RalGDS/AF-6) domain family 6						apoptosis|signal transduction		protein binding			pancreas(2)	2	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	76010133	76010136	+	IGR	DEL	AGGG	-	-	rs9991977		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76010133_76010136delAGGG								PARM1 (34810 upstream) : RCHY1 (394219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	76212400	76212400	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76212400delG								PARM1 (237077 upstream) : RCHY1 (191955 downstream)																																			---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77700964	77700964	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77700964delT	uc011cbx.1	+	11					SHROOM3_uc003hkg.2_3'UTR	NM_020859	NP_065910			shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79101922	79101922	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79101922delT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	79685470	79685470	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79685470delA								ANXA3 (153868 upstream) : BMP2K (12062 downstream)																																			---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81307673	81307674	+	Intron	INS	-	C	C	rs138985849		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81307673_81307674insC	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83740164	83740165	+	3'UTR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83740164_83740165delTT	uc003hnf.2	-	27					SEC31A_uc003hnd.2_3'UTR|SEC31A_uc003hne.2_3'UTR|SEC31A_uc011ccl.1_3'UTR|SEC31A_uc003hnl.2_3'UTR|SEC31A_uc003hng.2_3'UTR|SEC31A_uc003hnh.2_3'UTR|SEC31A_uc003hni.2_3'UTR|SEC31A_uc003hnj.2_3'UTR|SEC31A_uc011ccm.1_3'UTR|SEC31A_uc011ccn.1_3'UTR|SEC31A_uc003hnk.2_3'UTR|SEC31A_uc003hnm.2_3'UTR	NM_001077207	NP_001070675			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)																---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83792991	83792992	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83792991_83792992delAA	uc003hnf.2	-						SEC31A_uc003hne.2_5'UTR|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			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)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84837214	84837214	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84837214delC	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85724742	85724742	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85724742delA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86689930	86689930	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86689930delA	uc003hpk.2	+						ARHGAP24_uc003hpj.2_Intron	NM_001025616	NP_001020787			Rho GTPase activating protein 24 isoform 1						angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87339400	87339400	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87339400delT	uc003hpu.2	-						MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|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|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88152755	88152755	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88152755delT								KLHL8 (11081 upstream) : HSD17B13 (72186 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93946280	93946280	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93946280delA	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98753415	98753415	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98753415delA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98909178	98909181	+	Intron	DEL	CACA	-	-	rs3047311		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98909178_98909181delCACA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99970155	99970155	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99970155delA	uc003huf.3	+						METAP1_uc003hug.2_Intron|METAP1_uc010ild.2_Intron	NM_015143	NP_055958			methionyl aminopeptidase 1						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102839362	102839362	+	Intron	DEL	A	-	-	rs3733198	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102839362delA	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103594061	103594061	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103594061delA	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	106254753	106254753	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106254753delA								TET2 (53795 upstream) : PPA2 (35482 downstream)																																			---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106551895	106551895	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106551895delA	uc003hxu.2	+							NM_017700	NP_060170			hypothetical protein LOC54848						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	112553945	112553945	+	IGR	DEL	T	-	-	rs67005470		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112553945delT								MIR297 (772142 upstream) : C4orf32 (512608 downstream)																																			---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113178967	113178967	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113178967delA	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039			adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113530964	113530964	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113530964delA	uc003iau.2	-						C4orf21_uc003iaw.2_Intron	NM_018392	NP_060862			prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	113946914	113946914	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113946914delG	uc003ibd.3	+						ANK2_uc003ibc.2_Intron	NM_001127493	NP_001120965			ankyrin 2 isoform 3						axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114473292	114473292	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114473292delA	uc003ibi.2	-						CAMK2D_uc003ibj.2_Intron|CAMK2D_uc003ibk.2_Intron|CAMK2D_uc003ibo.3_Intron|CAMK2D_uc003ibm.2_Intron|CAMK2D_uc003ibn.2_Intron|CAMK2D_uc003ibl.2_Intron	NM_001221	NP_001212			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	115220729	115220729	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115220729delT								ARSJ (319851 upstream) : UGT8 (298882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115512380	115512380	+	IGR	DEL	T	-	-	rs36090063		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115512380delT								ARSJ (611502 upstream) : UGT8 (7231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117379141	117379141	+	IGR	DEL	A	-	-	rs35304951		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117379141delA								MIR1973 (158217 upstream) : TRAM1L1 (625575 downstream)																																			---	---	---	---
SYNPO2	171024	broad.mit.edu	37	4	119846556	119846556	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119846556delT	uc003icm.3	+						SYNPO2_uc010ina.2_Intron|SYNPO2_uc010inb.2_Intron|SYNPO2_uc011cgh.1_Intron	NM_001128933	NP_001122405			synaptopodin 2 isoform b							nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2																		---	---	---	---
PRDM5	11107	broad.mit.edu	37	4	121631446	121631446	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121631446delA	uc003idn.2	-						PRDM5_uc003ido.2_Intron|PRDM5_uc010ine.2_Intron	NM_018699	NP_061169			PR domain containing 5						histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	repressing transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	122048722	122048722	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122048722delG								C4orf31 (55049 upstream) : TNIP3 (3844 downstream)																																			---	---	---	---
BBS7	55212	broad.mit.edu	37	4	122768876	122768876	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122768876delT	uc003ied.2	-						BBS7_uc003iee.1_Intron	NM_176824	NP_789794			Bardet-Biedl syndrome 7 protein isoform a						cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	124010740	124010740	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124010740delT	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	124284403	124284403	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124284403delC								SPATA5 (43801 upstream) : SPRY1 (33553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125665895	125665896	+	IGR	INS	-	AGAAAGAAAG	AGAAAGAAAG	rs67043313		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125665895_125665896insAGAAAGAAAG								ANKRD50 (32008 upstream) : FAT4 (571671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125827325	125827327	+	IGR	DEL	AAA	-	-	rs72181496		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125827325_125827327delAAA								ANKRD50 (193438 upstream) : FAT4 (410240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126577457	126577458	+	IGR	DEL	TG	-	-	rs61336759		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126577457_126577458delTG								MIR2054 (148995 upstream) : None (None downstream)																																			---	---	---	---
MFSD8	256471	broad.mit.edu	37	4	128861148	128861148	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128861148delA	uc003ifp.2	-	7	721	c.558delT	c.(556-558)TTTfs	p.F186fs	MFSD8_uc011cgu.1_Frame_Shift_Del_p.F141fs|MFSD8_uc011cgv.1_Frame_Shift_Del_p.F148fs|MFSD8_uc011cgw.1_RNA|MFSD8_uc011cgx.1_Intron	NM_152778	NP_689991	Q8NHS3	MFSD8_HUMAN	major facilitator superfamily domain containing	186	Helical; (Potential).				cell death|transmembrane transport	integral to membrane|lysosomal membrane				ovary(1)|liver(1)	2																		---	---	---	---
C4orf29	80167	broad.mit.edu	37	4	128938073	128938073	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128938073delT	uc003ifr.2	+						C4orf29_uc003ifs.2_Intron|C4orf29_uc003ift.2_Intron|C4orf29_uc003ifu.2_Intron|C4orf29_uc010inz.2_Intron|C4orf29_uc003ifv.2_Intron	NM_001039717	NP_001034806			hypothetical protein LOC80167 precursor							extracellular region				ovary(1)	1																		---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129864050	129864050	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129864050delA	uc003igp.2	-						SCLT1_uc003ign.2_Intron|SCLT1_uc003igo.2_Intron|SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron	NM_144643	NP_653244			sodium channel associated protein 1							centrosome				ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	132727047	132727047	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132727047delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134867858	134867859	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134867858_134867859insA								PCDH10 (755127 upstream) : PABPC4L (249632 downstream)																																			---	---	---	---
NAA15	80155	broad.mit.edu	37	4	140270590	140270590	+	Intron	DEL	T	-	-	rs112955393		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140270590delT	uc003ihu.1	+							NM_057175	NP_476516			NMDA receptor regulated 1						angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	141086687	141086687	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141086687delT								MAML3 (11454 upstream) : SCOC (91753 downstream)																																			---	---	---	---
TBC1D9	23158	broad.mit.edu	37	4	141652848	141652849	+	Intron	INS	-	AT	AT	rs56768107		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141652848_141652849insAT	uc010ioj.2	-							NM_015130	NP_055945			TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	141722864	141722864	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141722864delT								TBC1D9 (45393 upstream) : RNF150 (63861 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	142950187	142950187	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142950187delT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143159169	143159169	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143159169delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144108896	144108896	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144108896delT	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946			ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144130643	144130643	+	Intron	DEL	A	-	-	rs111830994		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144130643delA	uc003ijb.2	+						USP38_uc003ija.3_Intron|USP38_uc003ijc.2_Intron	NM_032557	NP_115946			ubiquitin specific peptidase 38						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144442477	144442477	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144442477delT	uc003ijg.2	+							NM_003601	NP_003592			SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)																	---	---	---	---
GYPA	2993	broad.mit.edu	37	4	145037886	145037886	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145037886delA	uc003ijo.3	-						GYPA_uc003ijn.2_Intron|GYPA_uc011cia.1_Intron|GYPA_uc011cib.1_Intron|GYPA_uc003ijp.3_Intron|GYPA_uc010ioq.2_Intron|GYPA_uc010ior.2_Intron|GYPA_uc010ios.1_Intron	NM_002099	NP_002090			glycophorin A precursor						interspecies interaction between organisms	membrane fraction	receptor activity			central_nervous_system(2)	2	all_hematologic(180;0.15)																	---	---	---	---
OTUD4	54726	broad.mit.edu	37	4	146073871	146073872	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146073871_146073872delTT	uc003ika.3	-						OTUD4_uc003ijz.3_Intron	NM_001102653	NP_001096123			OTU domain containing 4 protein isoform 3								protein binding			ovary(2)|breast(1)	3	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	148064865	148064865	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148064865delC								TTC29 (197831 upstream) : MIR548G (200916 downstream)																																			---	---	---	---
TMEM184C	55751	broad.mit.edu	37	4	148549705	148549705	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148549705delA	uc003ila.3	+							NM_018241	NP_060711			transmembrane protein 184C							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	149854640	149854641	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149854640_149854641insG								NR3C2 (490997 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	151986222	151986222	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151986222delA								LRBA (49343 upstream) : RPS3A (34532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152029269	152029273	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152029269_152029273delTTTTT								RPS3A (3467 upstream) : SH3D19 (12160 downstream)																																			---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152099944	152099944	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152099944delA	uc010ipl.1	-						SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	153121146	153121146	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153121146delC								PET112L (439000 upstream) : FBXW7 (121265 downstream)																																			---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154679927	154679928	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154679927_154679928delAA	uc003int.2	-						RNF175_uc003inu.1_Intron	NM_173662	NP_775933			ring finger protein 175							integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	155146779	155146780	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155146779_155146780delAC								SFRP2 (436551 upstream) : DCHS2 (8747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	156217411	156217411	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156217411delA								NPY2R (79185 upstream) : MAP9 (46403 downstream)																																			---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156270141	156270142	+	Intron	INS	-	AAC	AAC	rs139999827		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156270141_156270142insAAC	uc003ios.2	-						MAP9_uc011cin.1_Intron	NM_001039580	NP_001034669			aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	157096258	157096259	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157096258_157096259delTT								CTSO (221210 upstream) : PDGFC (586505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157546073	157546073	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157546073delA								CTSO (671025 upstream) : PDGFC (136691 downstream)																																			---	---	---	---
C4orf45	152940	broad.mit.edu	37	4	159953372	159953372	+	Intron	DEL	A	-	-	rs79804808		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159953372delA	uc003iqf.1	-						C4orf45_uc010iqt.1_Intron	NM_152543	NP_689756			hypothetical protein LOC152940												0																		---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	168006599	168006599	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168006599delT	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	168011989	168011989	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168011989delT	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron|SPOCK3_uc011cjw.1_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	168970030	168970030	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168970030delC								SPOCK3 (814289 upstream) : ANXA10 (43677 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169232227	169232227	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169232227delA	uc003irp.2	-							NM_017631	NP_060101			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)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169439180	169439181	+	Intron	INS	-	CTT	CTT	rs34196612		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169439180_169439181insCTT	uc011cjx.1	+						PALLD_uc003iru.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169612351	169612351	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169612351delT	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	4	169940261	169940261	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169940261delA								CBR4 (8839 upstream) : SH3RF1 (75146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	170722044	170722044	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170722044delT								C4orf27 (42951 upstream) : MFAP3L (185706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	176295498	176295499	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176295498_176295499insG								ADAM29 (396168 upstream) : GPM6A (258590 downstream)																																			---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176736170	176736170	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176736170delT	uc003iuf.2	-						GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885			glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	180406973	180406974	+	IGR	DEL	CA	-	-	rs111718493		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180406973_180406974delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184223673	184223674	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184223673_184223674delTC	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron|WWC2_uc003ivo.3_Intron	NM_024949	NP_079225			WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	184446957	184446957	+	IGR	DEL	C	-	-	rs75796545		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184446957delC								ING2 (14708 upstream) : RWDD4A (113832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185167114	185167114	+	IGR	DEL	A	-	-	rs111893708	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185167114delA								ENPP6 (28000 upstream) : IRF2 (141764 downstream)																																			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187516451	187516452	+	Intron	DEL	GT	-	-	rs72489341		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187516451_187516452delGT	uc003izf.2	-						FAT1_uc010isn.2_Intron|FAT1_uc003ize.2_Intron	NM_005245	NP_005236			FAT tumor suppressor 1 precursor						actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190191490	190191490	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190191490delG								None (None upstream) : FRG1 (670484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190198108	190198109	+	IGR	DEL	TA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190198108_190198109delTA								None (None upstream) : FRG1 (663865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190511955	190511956	+	IGR	INS	-	T	T	rs142515391		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190511955_190511956insT								None (None upstream) : FRG1 (350018 downstream)																																			---	---	---	---
IRX1	79192	broad.mit.edu	37	5	3599265	3599266	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3599265_3599266delTC	uc003jde.2	+							NM_024337	NP_077313			iroquois homeobox protein 1							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	4213464	4213464	+	IGR	DEL	T	-	-	rs11284959		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4213464delT								IRX1 (611948 upstream) : LOC340094 (821008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4438464	4438466	+	IGR	DEL	AGG	-	-	rs70963784		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4438464_4438466delAGG								IRX1 (836948 upstream) : LOC340094 (596006 downstream)																																			---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5457380	5457381	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5457380_5457381delTT	uc003jdm.3	+							NM_015325	NP_056140			hypothetical protein LOC23379											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	6310334	6310335	+	IGR	INS	-	A	A	rs150638341	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6310334_6310335insA								KIAA0947 (819997 upstream) : FLJ33360 (219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6889242	6889243	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6889242_6889243insA								PAPD7 (132081 upstream) : ADCY2 (507100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8218049	8218049	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8218049delG								MTRR (316816 upstream) : SEMA5A (817089 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9293303	9293304	+	Intron	DEL	TC	-	-	rs72477914		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9293303_9293304delTC	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10390429	10390429	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10390429delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10676718	10676718	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10676718delG								ROPN1L (211581 upstream) : DAP (2625 downstream)																																			---	---	---	---
DAP	1611	broad.mit.edu	37	5	10752751	10752752	+	Intron	DEL	TG	-	-	rs35087570		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10752751_10752752delTG	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385			death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	10847050	10847050	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10847050delA								DAP (85663 upstream) : CTNND2 (124902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14073170	14073170	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14073170delA								DNAH5 (128581 upstream) : TRIO (70659 downstream)																																			---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14287249	14287249	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14287249delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						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|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14711209	14711209	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14711209delA	uc003jfm.3	-	12					ANKH_uc003jfl.3_3'UTR	NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	15193215	15193216	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15193215_15193216delGT								ANKH (321328 upstream) : FBXL7 (307089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	16042361	16042361	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16042361delT								FBXL7 (102461 upstream) : MARCH11 (25113 downstream)																																			---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16783624	16783624	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16783624delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	18076948	18076948	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18076948delA								BASP1 (800013 upstream) : None (None downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21535337	21535340	+	Intron	DEL	AAAG	-	-	rs146609299		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21535337_21535340delAAAG	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22626248	22626248	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22626248delC	uc003jgk.2	-							NM_004061	NP_004052			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															HNSCC(59;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24797175	24797175	+	IGR	DEL	T	-	-	rs11318322		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24797175delT								CDH10 (152264 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26867601	26867602	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26867601_26867602delTT								None (None upstream) : CDH9 (13107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28311589	28311590	+	IGR	DEL	TG	-	-	rs76796177		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28311589_28311590delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29610389	29610389	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29610389delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29931137	29931137	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29931137delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31138765	31138765	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31138765delC								None (None upstream) : CDH6 (55031 downstream)																																			---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31541313	31541313	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31541313delT	uc003jhj.3	+						C5orf22_uc011cnw.1_Intron|C5orf22_uc003jhk.3_Intron	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31980401	31980401	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31980401delC	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32203545	32203545	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32203545delT								GOLPH3 (29120 upstream) : MTMR12 (23567 downstream)																																			---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32277803	32277803	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32277803delA	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32636696	32636696	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32636696delT								SUB1 (32511 upstream) : NPR3 (74064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32910827	32910827	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32910827delT								C5orf23 (119008 upstream) : TARS (529975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34650723	34650724	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34650723_34650724delAA								C1QTNF3 (607406 upstream) : RAI14 (5709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34976693	34976693	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34976693delC								DNAJC21 (17625 upstream) : AGXT2 (21513 downstream)																																			---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35683197	35683197	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35683197delA	uc003jjo.2	+						SPEF2_uc003jjq.3_Intron	NM_024867	NP_079143			KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
CAPSL	133690	broad.mit.edu	37	5	35910710	35910710	+	Intron	DEL	A	-	-	rs112546964		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35910710delA	uc003jjt.1	-						CAPSL_uc003jju.1_Intron	NM_001042625	NP_001036090			calcyphosine-like							cytoplasm	calcium ion binding			skin(1)	1	all_lung(31;0.000268)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.167)|Colorectal(62;0.202)															---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37063796	37063797	+	Intron	INS	-	CA	CA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37063796_37063797insCA	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron|NIPBL_uc003jkn.2_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37516587	37516587	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37516587delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37686425	37686426	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37686425_37686426delAA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37728460	37728466	+	Intron	DEL	AAAAAAC	-	-	rs2366668		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37728460_37728466delAAAAAAC	uc003jkv.2	+							NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	39002501	39002504	+	Intron	DEL	TGTA	-	-	rs1239251	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39002501_39002504delTGTA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	39557090	39557093	+	IGR	DEL	TCTT	-	-	rs145528782		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39557090_39557093delTCTT								DAB2 (131755 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42112405	42112405	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42112405delC								FBXO4 (170742 upstream) : GHR (311621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43348269	43348270	+	IGR	INS	-	A	A	rs139927632	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43348269_43348270insA								HMGCS1 (34674 upstream) : CCL28 (28480 downstream)																																			---	---	---	---
PAIP1	10605	broad.mit.edu	37	5	43535227	43535227	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43535227delA	uc003job.2	-						PAIP1_uc003joa.2_Intron|PAIP1_uc010ivp.2_Intron|PAIP1_uc010ivo.2_Intron|PAIP1_uc003joc.2_Intron	NM_006451	NP_006442			poly(A) binding protein interacting protein 1						mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation	cytosol	protein binding|RNA binding|translation activator activity			ovary(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	46327960	46327960	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46327960delC								HCN1 (631740 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	53708503	53708503	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53708503delA								ARL15 (102100 upstream) : HSPB3 (42942 downstream)																																			---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54641101	54641102	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54641101_54641102insT	uc003jpy.3	+						SKIV2L2_uc011cqi.1_Intron	NM_015360	NP_056175			superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)																---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56177104	56177104	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56177104delT	uc003jqw.3	+							NM_005921	NP_005912			mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	56338958	56338959	+	IGR	DEL	AA	-	-	rs111821113		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56338958_56338959delAA								MIER3 (71457 upstream) : GPBP1 (130816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56976671	56976672	+	IGR	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56976671_56976672delGA								ACTBL2 (198035 upstream) : PLK2 (773140 downstream)																																			---	---	---	---
PLK2	10769	broad.mit.edu	37	5	57754160	57754160	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57754160delA	uc003jrn.2	-						PLK2_uc011cql.1_Frame_Shift_Del_p.Y133fs	NM_006622	NP_006613			polo-like kinase 2						positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)														---	---	---	---
RAB3C	115827	broad.mit.edu	37	5	57967057	57967058	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57967057_57967058insA	uc003jrp.2	+							NM_138453	NP_612462			RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)														---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59284581	59284581	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59284581delA	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
ELOVL7	79993	broad.mit.edu	37	5	60131248	60131248	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60131248delT	uc003jsi.3	-						ELOVL7_uc010iwk.2_Intron|ELOVL7_uc003jsj.3_Intron	NM_024930	NP_079206			elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	60593074	60593075	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60593074_60593075delTT								C5orf43 (134772 upstream) : ZSWIM6 (35025 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61617757	61617757	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61617757delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61749804	61749804	+	Intron	DEL	A	-	-	rs76986604		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61749804delA	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	62313913	62313913	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62313913delT								ISCA1P1 (240743 upstream) : HTR1A (942366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	62596888	62596888	+	IGR	DEL	T	-	-	rs140328439		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62596888delT								ISCA1P1 (523718 upstream) : HTR1A (659391 downstream)																																			---	---	---	---
CENPK	64105	broad.mit.edu	37	5	64838465	64838466	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64838465_64838466delAA	uc003jts.2	-						CENPK_uc003jtt.2_Intron|CENPK_uc003jtu.2_Intron	NM_022145	NP_071428			SoxLZ/Sox6 leucine zipper binding protein						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00466)														---	---	---	---
TRIM23	373	broad.mit.edu	37	5	64906672	64906673	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64906672_64906673insA	uc003jty.2	-						TRIM23_uc003jtw.2_Intron|TRIM23_uc003jtx.2_Intron	NM_001656	NP_001647			ADP-ribosylation factor domain protein 1 isoform						interspecies interaction between organisms|small GTPase mediated signal transduction	Golgi membrane|lysosomal membrane	enzyme activator activity|GDP binding|GTP binding|GTPase activity|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|lung(1)	4		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	67350788	67350788	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67350788delG								CD180 (858171 upstream) : PIK3R1 (160816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67876073	67876073	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67876073delA								PIK3R1 (278426 upstream) : SLC30A5 (513745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68303143	68303144	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68303143_68303144delAA	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	68483890	68483890	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68483890delT	uc003jvn.1	-						uc003jvo.3_RNA|CENPH_uc003jvp.2_5'Flank|CENPH_uc010ixc.2_5'Flank					Homo sapiens cDNA clone IMAGE:8327734.																														---	---	---	---
CCDC125	202243	broad.mit.edu	37	5	68606833	68606833	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68606833delA	uc003jvv.1	-						CCDC125_uc003jvx.1_Intron|CCDC125_uc003jvy.1_Intron|CCDC125_uc003jvw.2_Intron|CCDC125_uc003jvz.1_3'UTR	NM_176816	NP_789786			coiled-coil domain containing 125							cytoplasm					0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70777001	70777002	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70777001_70777002delAA	uc003kbp.1	+						BDP1_uc003kbn.1_Intron|BDP1_uc003kbo.2_Intron	NM_018429	NP_060899			transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70820157	70820157	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70820157delT	uc003kbp.1	+						BDP1_uc003kbo.2_Intron|BDP1_uc003kbq.1_Intron	NM_018429	NP_060899			transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)														---	---	---	---
FCHO2	115548	broad.mit.edu	37	5	72378882	72378882	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72378882delT	uc003kcl.2	+						FCHO2_uc011csl.1_Intron|FCHO2_uc010izb.2_Intron|FCHO2_uc011csn.1_Intron	NM_138782	NP_620137			FCH domain only 2 isoform a											ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73165730	73165731	+	Intron	INS	-	A	A	rs143184703	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73165730_73165731insA	uc011csq.1	+						RGNEF_uc003kcx.2_Intron|RGNEF_uc010izf.2_Intron|RGNEF_uc011csr.1_Intron	NM_001080479	NP_001073948			Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)														---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74675414	74675414	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74675414delT	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704			alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75732882	75732882	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75732882delT	uc003kek.2	+							NM_006633	NP_006624			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)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76563265	76563266	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76563265_76563266delAA	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710			phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	76896705	76896705	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76896705delA								WDR41 (108373 upstream) : OTP (27833 downstream)																																			---	---	---	---
LHFPL2	10184	broad.mit.edu	37	5	77924142	77924143	+	Intron	INS	-	TC	TC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77924142_77924143insTC	uc003kfo.2	-						LHFPL2_uc003kfp.1_Intron	NM_005779	NP_005770			lipoma HMGIC fusion partner-like 2							integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)														---	---	---	---
ARSB	411	broad.mit.edu	37	5	78272993	78272993	+	Intron	DEL	G	-	-	rs67756663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78272993delG	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
JMY	133746	broad.mit.edu	37	5	78573910	78573910	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78573910delT	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618			junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)														---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78905517	78905517	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78905517delT	uc010jae.1	+						PAPD4_uc003kgb.2_5'Flank|PAPD4_uc010jaf.1_5'Flank|PAPD4_uc003kga.2_5'Flank|PAPD4_uc003kfz.2_5'Flank	NM_001114393	NP_001107865			PAP associated domain containing 4						histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79086098	79086098	+	Intron	DEL	T	-	-	rs67610704		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79086098delT	uc003kgc.2	+							NM_153610	NP_705838			cardiomyopathy associated 5							perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79372814	79372814	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79372814delC	uc003kgh.2	+	17	2352	c.2029delC	c.(2029-2031)CCCfs	p.P677fs	uc003kgi.3_Intron	NM_003248	NP_003239	P35443	TSP4_HUMAN	thrombospondin 4 precursor	677	TSP type-3 7.				endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity				0		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)														---	---	---	---
SERINC5	256987	broad.mit.edu	37	5	79516606	79516606	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79516606delA	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060			developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79804019	79804019	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79804019delT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111			hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	80216726	80216726	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80216726delA								MSH3 (44093 upstream) : RASGRF2 (39832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81957991	81957991	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81957991delC								ATP6AP1L (343845 upstream) : TMEM167A (390676 downstream)																																			---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83550040	83550040	+	Intron	DEL	A	-	-	rs55795105	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83550040delA	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702			EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87105803	87105804	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87105803_87105804delTT								CCNH (396967 upstream) : TMEM161B (385220 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87733857	87733858	+	IGR	DEL	AA	-	-	rs35183321		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87733857_87733858delAA								TMEM161B (169192 upstream) : LOC645323 (102739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89071953	89071953	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89071953delA								MEF2C (872084 upstream) : CETN3 (617578 downstream)																																			---	---	---	---
LYSMD3	116068	broad.mit.edu	37	5	89821125	89821125	+	Intron	DEL	A	-	-	rs13361350	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89821125delA	uc003kjr.2	-						LYSMD3_uc010jaz.1_Intron|LYSMD3_uc003kjs.1_Intron	NM_198273	NP_938014			LysM, putative peptidoglycan-binding, domain						cell wall macromolecule catabolic process	integral to membrane					0		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	92412562	92412562	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92412562delT								None (None upstream) : FLJ42709 (332503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96964042	96964042	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96964042delA								RIOK2 (445037 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96970702	96970704	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96970702_96970704delTTT								RIOK2 (451697 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98309092	98309094	+	IGR	DEL	AAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98309092_98309094delAAG								CHD1 (46854 upstream) : None (None downstream)																																			---	---	---	---
PAM	5066	broad.mit.edu	37	5	102230698	102230698	+	Intron	DEL	A	-	-	rs112288632		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102230698delA	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron	NM_000919	NP_000910			peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	103148824	103148824	+	IGR	DEL	A	-	-	rs74597549		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103148824delA								NUDT12 (250334 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103184416	103184417	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103184416_103184417delTG								NUDT12 (285926 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104225539	104225540	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104225539_104225540delAC								None (None upstream) : RAB9BP1 (209635 downstream)																																			---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109103631	109103631	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109103631delA	uc003kou.1	+							NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109940905	109940905	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109940905delT	uc011cvh.1	-	10	1247	c.1175delA	c.(1174-1176)AATfs	p.N392fs	TMEM232_uc003kow.1_Frame_Shift_Del_p.N200fs|TMEM232_uc003kox.2_RNA|TMEM232_uc010jbs.2_Frame_Shift_Del_p.N394fs|TMEM232_uc003koy.3_Frame_Shift_Del_p.N128fs			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;	394						integral to membrane					0																		---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111136684	111136684	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111136684delA	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947			neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111547992	111547993	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111547992_111547993delTT	uc003kpv.1	-						EPB41L4A_uc003kpp.1_Intron	NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
PGGT1B	5229	broad.mit.edu	37	5	114566819	114566819	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114566819delT	uc003kqw.3	-						PGGT1B_uc003kqx.3_Intron|PGGT1B_uc010jch.2_Intron	NM_005023	NP_005014			geranylgeranyltransferase type 1 beta						protein geranylgeranylation	CAAX-protein geranylgeranyltransferase complex	CAAX-protein geranylgeranyltransferase activity				0		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)	Pravastatin(DB00175)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	115106723	115106723	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115106723delA								TMED7-TICAM2 (144853 upstream) : CDO1 (33709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116332325	116332325	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116332325delT								SEMA6A (421774 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117825112	117825112	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117825112delA								None (None upstream) : DTWD2 (347459 downstream)																																			---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310505	118310506	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118310505_118310506delAA	uc003ksa.2	-							NM_173666	NP_775937			DTW domain containing 2												0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)														---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118320838	118320838	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118320838delC	uc003ksa.2	-							NM_173666	NP_775937			DTW domain containing 2												0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	119193718	119193718	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119193718delT								FAM170A (222202 upstream) : PRR16 (606301 downstream)																																			---	---	---	---
PRR16	51334	broad.mit.edu	37	5	119835462	119835462	+	Intron	DEL	T	-	-	rs5870893		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119835462delT	uc003ksq.2	+						PRR16_uc003ksp.2_Intron	NM_016644	NP_057728			proline rich 16											pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)														---	---	---	---
CEP120	153241	broad.mit.edu	37	5	122722368	122722368	+	Intron	DEL	T	-	-	rs34328840		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122722368delT	uc003ktk.2	-						CEP120_uc011cwq.1_Intron|CEP120_uc010jcz.1_Intron	NM_153223	NP_694955			coiled-coil domain containing 100							centrosome				ovary(1)	1																		---	---	---	---
CSNK1G3	1456	broad.mit.edu	37	5	122930883	122930883	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122930883delT	uc003ktm.2	+						CSNK1G3_uc003ktl.2_Intron|CSNK1G3_uc003ktn.2_Intron|CSNK1G3_uc003kto.2_Intron|CSNK1G3_uc011cwr.1_Intron|CSNK1G3_uc011cws.1_Intron|CSNK1G3_uc010jda.2_Intron	NM_004384	NP_004375			casein kinase 1, gamma 3 isoform 1						Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	123803929	123803929	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123803929delA								CSNK1G3 (851467 upstream) : ZNF608 (168681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126202244	126202244	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126202244delA								LMNB1 (29535 upstream) : MARCH3 (1163 downstream)																																			---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126790345	126790345	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126790345delT	uc003kuh.3	+						MEGF10_uc003kui.3_Intron	NM_032446	NP_115822			multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	127920221	127920221	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127920221delA								FBN2 (46305 upstream) : SLC27A6 (380989 downstream)																																			---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130828154	130828154	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130828154delA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130993429	130993430	+	Intron	INS	-	AA	AA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130993429_130993430insAA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131914905	131914905	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131914905delT	uc003kxi.2	+						RAD50_uc003kxg.1_Intron|RAD50_uc003kxh.2_Intron	NM_005732	NP_005723			RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131924640	131924640	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131924640delT	uc003kxi.2	+						RAD50_uc003kxh.2_Intron	NM_005732	NP_005723			RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131944382	131944382	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131944382delA	uc003kxi.2	+	17	3181	c.2794delA	c.(2794-2796)AAAfs	p.K932fs	RAD50_uc003kxh.2_Frame_Shift_Del_p.K793fs	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	932	Potential.				DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
KIF3A	11127	broad.mit.edu	37	5	132035886	132035887	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132035886_132035887insT	uc003kxo.2	-						KIF3A_uc003kxm.2_Intron|KIF3A_uc003kxn.2_Intron|KIF3A_uc011cxf.1_Intron|KIF3A_uc003kxp.2_Intron	NM_007054	NP_008985			kinesin family member 3A						blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134111122	134111122	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134111122delT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134118927	134118927	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134118927delT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	136240832	136240832	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136240832delT								TRPC7 (547759 upstream) : SPOCK1 (70156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	137930087	137930087	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137930087delT								HSPA9 (18972 upstream) : CTNNA1 (159020 downstream)																																			---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138643062	138643062	+	5'UTR	DEL	T	-	-	rs12153162	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138643062delT	uc003ldu.2	+	5					MATR3_uc003lds.2_5'UTR|MATR3_uc010jfb.2_5'UTR|MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_5'UTR|MATR3_uc003ldx.2_5'UTR|MATR3_uc010jfc.2_5'UTR|MATR3_uc003ldy.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_5'UTR|MATR3_uc003lea.2_5'UTR	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
PCDHAC2	56134	broad.mit.edu	37	5	140358994	140358994	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140358994delT	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron	NM_018899	NP_061722			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	140524070	140524070	+	IGR	DEL	A	-	-	rs143739997		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140524070delA								PCDHB5 (6367 upstream) : PCDHB6 (5613 downstream)																																			---	---	---	---
FGF1	2246	broad.mit.edu	37	5	141993498	141993498	+	Intron	DEL	G	-	-	rs41290617	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141993498delG	uc003lmm.2	-						FGF1_uc011dbi.1_Intron|FGF1_uc003lmn.3_Intron|FGF1_uc003lmp.3_Intron|FGF1_uc003lmq.2_Intron|FGF1_uc010jgj.2_Intron|FGF1_uc003lmr.2_Intron|FGF1_uc003lms.3_Intron	NM_001144892	NP_001138364			fibroblast growth factor 1 (acidic) isoform 1						angiogenesis|cellular response to heat|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of angiogenesis|positive regulation of cell division|positive regulation of cell migration|positive regulation of cholesterol biosynthetic process|positive regulation of intracellular protein kinase cascade|positive regulation of transcription from RNA polymerase II promoter	cell cortex|cytosol|extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|S100 alpha binding				0		all_neural(839;0.0416)|Ovarian(839;0.0955)|all_hematologic(541;0.1)|Prostate(461;0.157)|Lung NSC(810;0.21)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00032)	Pentosan Polysulfate(DB00686)													---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142202961	142202962	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142202961_142202962insT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	142926756	142926756	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142926756delA								NR3C1 (111679 upstream) : HMHB1 (264970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142965616	142965616	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142965616delT								NR3C1 (150539 upstream) : HMHB1 (226110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	145080130	145080138	+	IGR	DEL	AGGACCCAC	-	-	rs146802398		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145080130_145080138delAGGACCCAC								None (None upstream) : PRELID2 (58444 downstream)																																			---	---	---	---
SH3RF2	153769	broad.mit.edu	37	5	145454141	145454142	+	Intron	DEL	AA	-	-	rs72469967		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145454141_145454142delAA	uc011dbl.1	+							NM_152550	NP_689763			SH3 domain containing ring finger 2								ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
LARS	51520	broad.mit.edu	37	5	145562643	145562644	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145562643_145562644delTT	uc003lnx.1	-						LARS_uc011dbq.1_5'Flank|LARS_uc011dbr.1_5'Flank|LARS_uc011dbs.1_5'Flank	NM_020117	NP_064502			leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)													---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147503851	147503851	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147503851delT	uc003lox.2	+						SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148884875	148884875	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148884875delT	uc003lqx.1	-						CSNK1A1_uc011dcb.1_Intron|CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883			casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	149227268	149227271	+	IGR	DEL	AAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149227268_149227271delAAAA								PPARGC1B (1 upstream) : PDE6A (10249 downstream)																																			---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155204541	155204542	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155204541_155204542insT	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155351076	155351077	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155351076_155351077insA	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156381896	156381896	+	Intron	DEL	T	-	-	rs71922795		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381896delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CLINT1	9685	broad.mit.edu	37	5	157240304	157240304	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157240304delA	uc003lxj.1	-						CLINT1_uc003lxi.1_Intron|CLINT1_uc011ddv.1_Intron	NM_014666	NP_055481			epsin 4						endocytosis|post-Golgi vesicle-mediated transport	clathrin-coated vesicle|cytosol|Golgi apparatus|membrane|perinuclear region of cytoplasm	clathrin binding|lipid binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158257289	158257289	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158257289delT	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870			early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)					T	HMGA2	lipoma								---	---	---	---
Unknown	0	broad.mit.edu	37	5	159321597	159321597	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159321597delT								LOC285627 (428313 upstream) : ADRA1B (22143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162004543	162004543	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162004543delA								GABRG2 (421999 upstream) : CCNG1 (860034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163565374	163565375	+	IGR	DEL	TT	-	-	rs143690511		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163565374_163565375delTT								MAT2B (619041 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165563579	165563579	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165563579delA								None (None upstream) : None (None downstream)																																			---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167782979	167782979	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167782979delG	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168149360	168149361	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168149360_168149361delTG	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168351499	168351500	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168351499_168351500delGT	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
CCDC99	54908	broad.mit.edu	37	5	169020698	169020698	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169020698delT	uc003mae.3	+						CCDC99_uc010jjj.2_Intron|CCDC99_uc011deq.1_Intron|CCDC99_uc010jjk.2_Intron	NM_017785	NP_060255			coiled-coil domain containing 99						cell division|establishment of mitotic spindle orientation|mitotic metaphase plate congression|mitotic prometaphase|protein localization to kinetochore	condensed chromosome outer kinetochore|cytosol|microtubule organizing center|nucleus|spindle pole	kinetochore binding|protein binding			ovary(1)|liver(1)	2	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	169908871	169908872	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169908871_169908872insT	uc003map.2	+							NM_001034838	NP_001030010			Kv channel interacting protein 1 isoform 3						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
NPM1	4869	broad.mit.edu	37	5	170819655	170819655	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170819655delT	uc011dex.1	+						NPM1_uc003mbh.2_Intron|NPM1_uc003mbi.2_Intron|NPM1_uc003mbj.2_Intron	NM_002520	NP_002511			nucleophosmin 1 isoform 1						anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding		NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3109)|skin(1)	3110	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T|F 	ALK|RARA|MLF1	NHL|APL|AML								---	---	---	---
NPM1	4869	broad.mit.edu	37	5	170834815	170834815	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170834815delT	uc011dex.1	+						NPM1_uc003mbi.2_Intron|NPM1_uc003mbj.2_Intron	NM_002520	NP_002511			nucleophosmin 1 isoform 1						anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding	p.D280_E282del(1)	NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3109)|skin(1)	3110	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T|F 	ALK|RARA|MLF1	NHL|APL|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	5	171997981	171998000	+	IGR	DEL	GGAAGGAAGGAGGGAAGGAA	-	-	rs72075870		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171997981_171998000delGGAAGGAAGGAGGGAAGGAA								SH3PXD2B (116454 upstream) : NEURL1B (70276 downstream)																																			---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172512417	172512418	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172512417_172512418delTT	uc003mch.2	+						C5orf41_uc003mcg.2_Intron|C5orf41_uc003mcf.2_Intron|C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	172739962	172739962	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172739962delT								NKX2-5 (77700 upstream) : STC2 (1764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	175403350	175403350	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175403350delA								THOC3 (7805 upstream) : FAM153B (84342 downstream)																																			---	---	---	---
TSPAN17	26262	broad.mit.edu	37	5	176082910	176082912	+	Intron	DEL	AAC	-	-	rs6897431	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176082910_176082912delAAC	uc003met.2	+						TSPAN17_uc003mes.3_Intron|TSPAN17_uc003meu.2_Intron|TSPAN17_uc003mev.2_Intron|TSPAN17_uc003mew.2_Intron	NM_012171	NP_036303			transmembrane 4 superfamily member 17 isoform a							integral to membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	176208511	176208512	+	IGR	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176208511_176208512delGA								TSPAN17 (122453 upstream) : UNC5A (29048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177487095	177487096	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177487095_177487096delAA								FAM153C (11007 upstream) : N4BP3 (53460 downstream)																																			---	---	---	---
AGXT2L2	85007	broad.mit.edu	37	5	177657924	177657926	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177657924_177657926delTTT	uc003miz.2	-						AGXT2L2_uc003mjc.2_Intron|AGXT2L2_uc003mja.2_Intron|AGXT2L2_uc003mjb.2_Intron	NM_153373	NP_699204			alanine-glyoxylate aminotransferase 2-like 2							mitochondrion	pyridoxal phosphate binding|transaminase activity			pancreas(1)	1	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.181)|all cancers(165;0.235)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)													---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177812286	177812287	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177812286_177812287insC	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177869166	177869167	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177869166_177869167delAA	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179335290	179335291	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179335290_179335291delTT	uc003mlh.2	-						TBC1D9B_uc003mli.2_5'Flank|TBC1D9B_uc003mlj.2_5'Flank	NM_198868	NP_942568			TBC1 domain family, member 9B (with GRAM domain)							integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	179513203	179513205	+	IGR	DEL	TTT	-	-	rs146020552		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179513203_179513205delTTT								RNF130 (14094 upstream) : RASGEF1C (14591 downstream)																																			---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	623421	623424	+	Intron	DEL	TCTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:623421_623424delTCTT	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773			Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)														---	---	---	---
LOC285768	285768	broad.mit.edu	37	6	1025169	1025170	+	Intron	INS	-	A	A	rs77610990		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1025169_1025170insA	uc011dhp.1	-						LOC285768_uc010jnf.1_Intron|LOC285768_uc003mtj.2_Intron	NR_027115				Homo sapiens cDNA clone IMAGE:5272115.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	1117608	1117609	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1117608_1117609delAA								LOC285768 (16041 upstream) : FOXQ1 (195066 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1646947	1646947	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1646947delT	uc003mtq.2	-							NM_001500	NP_001491			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)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1876493	1876493	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1876493delA	uc003mtq.2	-							NM_001500	NP_001491			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)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	2125947	2125947	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2125947delG	uc003mtq.2	-							NM_001500	NP_001491			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2433045	2433045	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2433045delT	uc003mtu.1	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1572223.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2511218	2511218	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2511218delA								GMDS (265372 upstream) : C6orf195 (111754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	2886283	2886284	+	Intron	DEL	AA	-	-	rs74461765		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2886283_2886284delAA	uc003mue.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	3213914	3213914	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3213914delA								TUBB2A (56131 upstream) : TUBB2B (10582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4210248	4210248	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4210248delA								PECI (74417 upstream) : CDYL (496145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4285236	4285236	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4285236delA								PECI (149405 upstream) : CDYL (421157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4448504	4448507	+	IGR	DEL	TTTT	-	-	rs142948428		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4448504_4448507delTTTT								PECI (312673 upstream) : CDYL (257886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4649921	4649922	+	IGR	DEL	AA	-	-	rs67041710		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4649921_4649922delAA								PECI (514090 upstream) : CDYL (56471 downstream)																																			---	---	---	---
RPP40	10799	broad.mit.edu	37	6	5000753	5000753	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5000753delT	uc003mwl.2	-						RPP40_uc003mwm.2_Intron	NM_006638	NP_006629			ribonuclease P 40kDa subunit						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0895)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	5013403	5013404	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5013403_5013404insT	uc003mwn.1	+											Homo sapiens cDNA FLJ37615 fis, clone BRCOC2011996.																														---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5413963	5413963	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5413963delC	uc010jnv.1	+						FARS2_uc003mwr.2_Intron|FARS2_uc003mws.1_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5430451	5430451	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5430451delA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron|FARS2_uc003mws.1_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	5958381	5958381	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5958381delT								FARS2 (186565 upstream) : NRN1 (39854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6916659	6916680	+	IGR	DEL	GTGTGGGTGTGTGTGGGTGTGG	-	-	rs66783379	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6916659_6916680delGTGTGGGTGTGTGTGGGTGTGG								LY86 (261443 upstream) : RREB1 (191508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6941593	6941593	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6941593delC								LY86 (286377 upstream) : RREB1 (166595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7021104	7021104	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7021104delA								LY86 (365888 upstream) : RREB1 (87084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7437761	7437762	+	IGR	INS	-	AAAGA	AAAGA	rs148119966	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7437761_7437762insAAAGA								RIOK1 (19493 upstream) : DSP (104108 downstream)																																			---	---	---	---
DSP	1832	broad.mit.edu	37	6	7566746	7566746	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7566746delA	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
DSP	1832	broad.mit.edu	37	6	7582771	7582771	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7582771delT	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
EEF1E1	9521	broad.mit.edu	37	6	8088125	8088125	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8088125delT	uc003mxz.2	-						EEF1E1_uc011dic.1_Intron|SCARNA27_uc010jod.1_5'Flank	NM_004280	NP_004271			eukaryotic translation elongation factor 1						negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of DNA damage response, signal transduction by p53 class mediator|tRNA aminoacylation for protein translation	cytosol|nucleus					0	Ovarian(93;0.0398)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8321591	8321591	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8321591delT								EEF1E1 (218763 upstream) : SLC35B3 (90142 downstream)																																			---	---	---	---
SLC35B3	51000	broad.mit.edu	37	6	8419714	8419714	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8419714delA	uc010joe.2	-						SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron	NM_001142541	NP_001136013			solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8534657	8534657	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8534657delT	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	8868144	8868145	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8868144_8868145delAC								HULC (214067 upstream) : None (None downstream)																																			---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10622106	10622106	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10622106delT	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron|GCNT2_uc003mze.2_Intron	NM_145649	NP_663624			glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	11394829	11394830	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11394829_11394830insA								NEDD9 (12248 upstream) : TMEM170B (143681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11934909	11934909	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11934909delT								C6orf105 (155629 upstream) : HIVEP1 (77815 downstream)																																			---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12162259	12162259	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12162259delT	uc003nac.2	+						HIVEP1_uc011diq.1_Intron	NM_002114	NP_002105			human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	12193082	12193084	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12193082_12193084delTTT								HIVEP1 (27851 upstream) : EDN1 (97445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12416280	12416280	+	IGR	DEL	A	-	-	rs34318579		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12416280delA								EDN1 (118854 upstream) : PHACTR1 (300608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	12435747	12435747	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12435747delT								EDN1 (138321 upstream) : PHACTR1 (281141 downstream)																																			---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13043659	13043659	+	Intron	DEL	A	-	-	rs112014734		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13043659delA	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13071659	13071660	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13071659_13071660insA	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13273827	13273827	+	Intron	DEL	A	-	-	rs35718192		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13273827delA	uc010jpc.2	+						PHACTR1_uc003nag.1_3'UTR|PHACTR1_uc003nah.1_Intron|TBC1D7_uc003naj.2_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13571381	13571381	+	IGR	DEL	A	-	-	rs35913358		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13571381delA								GFOD1 (83594 upstream) : SIRT5 (3411 downstream)																																			---	---	---	---
CCDC90A	63933	broad.mit.edu	37	6	13809828	13809828	+	Intron	DEL	T	-	-	rs76369005		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13809828delT	uc003nbd.2	-						CCDC90A_uc010jpf.2_Intron	NM_001031713	NP_001026883			coiled-coil domain containing 90A precursor							integral to membrane|mitochondrion					0	Breast(50;0.0027)|Ovarian(93;0.0964)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	13908110	13908121	+	IGR	DEL	CCTTCCTTCCTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13908110_13908121delCCTTCCTTCCTT								CCDC90A (93321 upstream) : RNF182 (17082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14430599	14430600	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14430599_14430600insG								CD83 (293453 upstream) : JARID2 (815134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14574536	14574537	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14574536_14574537delTG								CD83 (437390 upstream) : JARID2 (671197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14823721	14823721	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14823721delA								CD83 (686575 upstream) : JARID2 (422013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14841906	14841906	+	IGR	DEL	T	-	-	rs111502428		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14841906delT								CD83 (704760 upstream) : JARID2 (403828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14967807	14967807	+	IGR	DEL	A	-	-	rs35927205		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14967807delA								CD83 (830661 upstream) : JARID2 (277927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15186378	15186378	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15186378delA								None (None upstream) : JARID2 (59356 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16679268	16679268	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16679268delA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17440838	17440839	+	Intron	DEL	TG	-	-	rs71685816		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17440838_17440839delTG	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17479783	17479783	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17479783delA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17540988	17540990	+	Intron	DEL	AAC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17540988_17540990delAAC	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18202467	18202467	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18202467delA	uc003nco.1	+						KDM1B_uc003ncn.1_Intron	NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
DEK	7913	broad.mit.edu	37	6	18250107	18250109	+	Intron	DEL	ATA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18250107_18250109delATA	uc003ncr.1	-						DEK_uc011djf.1_Intron|DEK_uc011djg.1_Intron	NM_003472	NP_003463			DEK oncogene isoform 1						chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)					T	NUP214	AML								---	---	---	---
DEK	7913	broad.mit.edu	37	6	18263751	18263751	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18263751delA	uc003ncr.1	-						DEK_uc011djf.1_Intron|DEK_uc011djg.1_Intron	NM_003472	NP_003463			DEK oncogene isoform 1						chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|histone binding			kidney(1)	1	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)					T	NUP214	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	6	18558177	18558178	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18558177_18558178delTT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	18566437	18566438	+	Intron	INS	-	TCCC	TCCC	rs147177362	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18566437_18566438insTCCC	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	18796685	18796686	+	IGR	INS	-	CTTTCTTT	CTTTCTTT	rs9383437	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18796685_18796686insCTTTCTTT								MIR548A1 (224574 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19564974	19564975	+	IGR	DEL	TA	-	-	rs2205863	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19564974_19564975delTA								MIR548A1 (992863 upstream) : ID4 (272642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19668231	19668232	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19668231_19668232insA								None (None upstream) : ID4 (169385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19932469	19932469	+	IGR	DEL	T	-	-	rs35454764		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19932469delT								ID4 (91555 upstream) : MBOAT1 (168466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19997486	19997489	+	IGR	DEL	AAGA	-	-	rs68035898	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19997486_19997489delAAGA								ID4 (156572 upstream) : MBOAT1 (103446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	21418579	21418580	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21418579_21418580delTT								CDKAL1 (185947 upstream) : SOX4 (175392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	22312058	22312058	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22312058delC								PRL (8976 upstream) : HDGFL1 (257620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	22605347	22605350	+	IGR	DEL	ACAC	-	-	rs72199416		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22605347_22605350delACAC								HDGFL1 (34598 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23639363	23639363	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23639363delT								None (None upstream) : NRSN1 (487051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24010100	24010100	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24010100delT								None (None upstream) : NRSN1 (116314 downstream)																																			---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25479028	25479028	+	Intron	DEL	A	-	-	rs111562802		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25479028delA	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron|LRRC16A_uc003nez.1_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
SLC17A3	10786	broad.mit.edu	37	6	25849897	25849898	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25849897_25849898insA	uc003nfi.3	-						SLC17A3_uc003nfk.3_Intron	NM_006632	NP_006623			solute carrier family 17 (sodium phosphate),						glucose-6-phosphate transport|urate metabolic process	apical plasma membrane|brush border membrane|endoplasmic reticulum membrane|integral to plasma membrane|perinuclear region of cytoplasm	drug transmembrane transporter activity|efflux transmembrane transporter activity|organic anion transmembrane transporter activity|sodium:phosphate symporter activity|toxin transporter activity|urate transmembrane transporter activity|voltage-gated anion channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26453811	26453812	+	IGR	DEL	TT	-	-	rs79511336		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26453811_26453812delTT								BTN3A3 (169 upstream) : BTN2A1 (4377 downstream)																																			---	---	---	---
BTN2A1	11120	broad.mit.edu	37	6	26465762	26465762	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26465762delA	uc003nib.1	+						BTN2A1_uc003nic.1_Intron|BTN2A1_uc003nid.1_Intron|BTN2A1_uc011dko.1_Intron|BTN2A1_uc010jqk.1_Intron	NM_007049	NP_008980			butyrophilin, subfamily 2, member A1 isoform 1						lipid metabolic process	integral to plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
GUSBL1	387036	broad.mit.edu	37	6	26854476	26854476	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26854476delA	uc003nim.2	-							NR_003504				Homo sapiens glucuronidase, beta-like 1, mRNA (cDNA clone IMAGE:4809612).												0																		---	---	---	---
ZNF193	7746	broad.mit.edu	37	6	28192344	28192345	+	5'Flank	DEL	AC	-	-	rs66619811		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28192344_28192345delAC	uc003nkq.1	+						ZNF193_uc003nkr.1_5'Flank|ZNF193_uc010jqz.1_5'Flank	NM_006299	NP_006290			zinc finger protein 193						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	29518208	29518209	+	IGR	INS	-	CTT	CTT	rs10534974		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29518208_29518209insCTT								MAS1L (62529 upstream) : UBD (5181 downstream)																																			---	---	---	---
MOG	4340	broad.mit.edu	37	6	29630261	29630261	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29630261delA	uc003nnf.2	+						MOG_uc003qzk.1_Intron|MOG_uc010kle.1_Intron|MOG_uc010klf.1_Intron|MOG_uc003nmy.1_Intron|MOG_uc003nmz.2_Intron|MOG_uc011dlt.1_Intron|MOG_uc003nna.2_Intron|MOG_uc011dlu.1_Intron|MOG_uc011dlv.1_Intron|MOG_uc003nnd.2_Intron|MOG_uc003nne.2_Intron|MOG_uc003nng.2_Intron|MOG_uc003nnh.2_Intron|MOG_uc003nni.2_Intron|MOG_uc003nnj.2_Intron|MOG_uc003nnk.2_Intron	NM_206809	NP_996532			myelin oligodendrocyte glycoprotein isoform						cell adhesion|central nervous system development|positive regulation of MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)	1																		---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29935541	29935541	+	Intron	DEL	A	-	-	rs147092848		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29935541delA	uc011dmb.1	+							NM_002127	NP_002118			major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
NCRNA00171	80862	broad.mit.edu	37	6	30000217	30000217	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30000217delA	uc011dme.1	-							NR_026751				Homo sapiens clone HTEX4 mRNA, complete sequence.												0																		---	---	---	---
HLA-E	3133	broad.mit.edu	37	6	30459741	30459741	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30459741delT	uc003nqg.2	+						HLA-E_uc011dmg.1_Intron|HLA-E_uc011dmh.1_Intron	NM_005516	NP_005507			major histocompatibility complex, class I, E						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5																		---	---	---	---
PPP1R10	5514	broad.mit.edu	37	6	30585435	30585435	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30585435delA	uc003nqn.1	-						PPP1R10_uc010jsc.1_5'Flank|MRPS18B_uc003nqo.2_5'Flank|MRPS18B_uc011dml.1_5'Flank|MRPS18B_uc010jsd.1_5'Flank	NM_002714	NP_002705			protein phosphatase 1, regulatory subunit 10						protein import into nucleus|transcription, DNA-dependent	PTW/PP1 phosphatase complex	DNA binding|protein phosphatase inhibitor activity|RNA binding|zinc ion binding			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30665317	30665317	+	IGR	DEL	T	-	-	rs137943555		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30665317delT								NRM (6259 upstream) : MDC1 (2268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31567419	31567419	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31567419delG								NCR3 (6657 upstream) : AIF1 (15575 downstream)																																			---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31708750	31708750	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31708750delA	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron	NM_172166	NP_751898			mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
HSPA1L	3305	broad.mit.edu	37	6	31782474	31782475	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31782474_31782475insC	uc003nxh.2	-						HSPA1L_uc010jte.2_Intron|HSPA1A_uc003nxj.2_5'Flank|HSPA1A_uc011doj.1_5'Flank|HSPA1A_uc003nxi.1_5'Flank	NM_005527	NP_005518			heat shock 70kDa protein 1-like						response to unfolded protein		ATP binding			ovary(3)|pleura(1)|kidney(1)|skin(1)	6																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32292514	32292514	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32292514delT	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32298186	32298186	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32298186delA	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32381268	32381269	+	IGR	INS	-	C	C	rs145262523	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32381268_32381269insC								BTNL2 (6368 upstream) : HLA-DRA (26378 downstream)																																			---	---	---	---
TAP1	6890	broad.mit.edu	37	6	32814594	32814595	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32814594_32814595delAA	uc003ocg.2	-						PSMB8_uc003oce.2_5'Flank|PSMB8_uc003ocf.2_5'Flank|PSMB8_uc011dqh.1_5'Flank|TAP1_uc011dqi.1_Intron	NM_000593	NP_000584			transporter 1, ATP-binding cassette, sub-family						antigen processing and presentation of endogenous peptide antigen via MHC class I|cytosol to ER transport|intracellular transport of viral proteins in host cell|positive regulation of T cell mediated cytotoxicity	cytosol|plasma membrane|TAP complex	ADP binding|ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|protein homodimerization activity|TAP1 binding|TAP2 binding|tapasin binding			skin(1)	1																		---	---	---	---
TAPBP	6892	broad.mit.edu	37	6	33280796	33280797	+	Intron	DEL	TT	-	-	rs67868917		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33280796_33280797delTT	uc003odx.1	-						TAPBP_uc010jus.1_Intron|TAPBP_uc003ody.2_Intron|TAPBP_uc003odz.2_Intron|TAPBP_uc010jut.1_Intron|TAPBP_uc011drc.1_Intron	NM_003190	NP_003181			tapasin isoform 1 precursor						antigen processing and presentation of endogenous peptide antigen via MHC class I|immune response|peptide antigen stabilization|protein complex assembly|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|MHC class I peptide loading complex|microsome	MHC class I protein binding|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33305090	33305090	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33305090delA								DAXX (14297 upstream) : LYPLA2P1 (27425 downstream)																																			---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33387880	33387882	+	5'UTR	DEL	CTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33387880_33387882delCTC	uc011dri.1	+	1					CUTA_uc003oej.1_5'Flank|CUTA_uc003oek.1_5'Flank|CUTA_uc003oel.1_5'Flank|CUTA_uc003oem.1_5'Flank|CUTA_uc003oen.1_5'Flank|SYNGAP1_uc003oeo.1_5'UTR|SYNGAP1_uc010juy.2_5'UTR	NM_006772	NP_006763			synaptic Ras GTPase activating protein 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
NUDT3	11165	broad.mit.edu	37	6	34280954	34280954	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34280954delA	uc003ojl.2	-							NM_006703	NP_006694			nudix-type motif 3						cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0																		---	---	---	---
PACSIN1	29993	broad.mit.edu	37	6	34479837	34479838	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34479837_34479838delTG	uc003ojo.2	+						PACSIN1_uc003ojp.2_5'Flank	NM_020804	NP_065855			protein kinase C and casein kinase substrate in						endocytosis		protein kinase activity				0																		---	---	---	---
SNRPC	6631	broad.mit.edu	37	6	34734348	34734348	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34734348delG	uc003ojt.1	+							NM_003093	NP_003084			small nuclear ribonucleoprotein polypeptide C						spliceosomal snRNP assembly	Cajal body|U1 snRNP	protein homodimerization activity|single-stranded RNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
SNRPC	6631	broad.mit.edu	37	6	34738000	34738000	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34738000delA	uc003ojt.1	+							NM_003093	NP_003084			small nuclear ribonucleoprotein polypeptide C						spliceosomal snRNP assembly	Cajal body|U1 snRNP	protein homodimerization activity|single-stranded RNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35216592	35216592	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35216592delA	uc003okf.1	+	22					SCUBE3_uc003okg.1_3'UTR|SCUBE3_uc003okh.1_3'UTR	NM_152753	NP_689966			signal peptide, CUB domain, EGF-like 3						protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36128965	36128966	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36128965_36128966insT	uc003olu.2	-											Homo sapiens cDNA clone IMAGE:5269446.																														---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36449071	36449072	+	Intron	INS	-	ATTT	ATTT	rs146420164	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36449071_36449072insATTT	uc003ome.2	+						KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2																		---	---	---	---
C6orf89	221477	broad.mit.edu	37	6	36846943	36846943	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36846943delT	uc003omv.2	+											SubName: Full=Chromosome 6 open reading frame 89; SubName: Full=Chromosome 6 open reading frame 89, isoform CRA_a;							integral to membrane				ovary(1)	1																		---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	37864459	37864460	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37864459_37864460delTG	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
C6orf64	55776	broad.mit.edu	37	6	39079168	39079168	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39079168delA	uc003ook.1	-						C6orf64_uc011dty.1_Intron|C6orf64_uc003oom.1_RNA	NM_018322	NP_060792			hypothetical protein LOC55776							integral to membrane					0																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40417621	40417621	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40417621delA	uc003oph.1	-							NM_020737	NP_065788			leucine rich repeat and fibronectin type III							cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	40857401	40857401	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40857401delG								LRFN2 (302275 upstream) : UNC5CL (137371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40879019	40879019	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40879019delC								LRFN2 (323893 upstream) : UNC5CL (115753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40984864	40984864	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40984864delT								LRFN2 (429738 upstream) : UNC5CL (9908 downstream)																																			---	---	---	---
TREML3	340206	broad.mit.edu	37	6	41185829	41185829	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41185829delT	uc003oqb.2	-							NR_027256				Homo sapiens TREM-like transcript 3 (TLT3) mRNA, partial cds.												0																		---	---	---	---
BYSL	705	broad.mit.edu	37	6	41891050	41891051	+	Intron	DEL	TT	-	-	rs138851543		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41891050_41891051delTT	uc003orl.2	+						MED20_uc003orj.2_5'Flank|MED20_uc003ork.2_5'Flank|MED20_uc011duh.1_5'Flank|MED20_uc011dui.1_5'Flank|MED20_uc011duj.1_5'Flank	NM_004053	NP_004044			bystin						cell adhesion|female pregnancy|ribosome biogenesis	cytoplasm|nucleolus					0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42932368	42932368	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42932368delT	uc003otf.2	-						uc003ote.1_5'Flank|PEX6_uc010jya.2_Intron	NM_000287	NP_000278			peroxisomal biogenesis factor 6						protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43161661	43161661	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43161661delT	uc003ouk.2	+						CUL9_uc003oul.2_Intron|CUL9_uc010jyk.2_Intron	NM_015089	NP_055904			p53-associated parkin-like cytoplasmic protein						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12																		---	---	---	---
XPO5	57510	broad.mit.edu	37	6	43496093	43496093	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43496093delA	uc003ovp.2	-						POLR1C_uc003ovo.1_Intron	NM_020750	NP_065801			exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44019088	44019089	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44019088_44019089insA	uc003owm.1	-											Homo sapiens cDNA: FLJ21083 fis, clone CAS03150.																														---	---	---	---
CAPN11	11131	broad.mit.edu	37	6	44150043	44150044	+	Intron	INS	-	AT	AT	rs143072463	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44150043_44150044insAT	uc003owt.1	+						CAPN11_uc011dvn.1_Intron	NM_007058	NP_008989			calpain 11						proteolysis	acrosomal vesicle	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)|breast(1)	2	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	44532143	44532143	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44532143delT								CDC5L (117364 upstream) : SUPT3H (244911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	44622775	44622778	+	IGR	DEL	GGAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44622775_44622778delGGAA								CDC5L (207996 upstream) : SUPT3H (154276 downstream)																																			---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44950417	44950419	+	Intron	DEL	CTC	-	-	rs10586449		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44950417_44950419delCTC	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_Intron	NM_181356	NP_852001			suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
ENPP5	59084	broad.mit.edu	37	6	46134984	46134984	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46134984delA	uc003oxz.1	-						ENPP5_uc003oya.1_Intron|ENPP5_uc011dvz.1_Intron|ENPP5_uc010jzc.1_Intron	NM_021572	NP_067547			ectonucleotide pyrophosphatase/phosphodiesterase							extracellular region|integral to membrane	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	46163042	46163042	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46163042delG								ENPP5 (24325 upstream) : RCAN2 (25427 downstream)																																			---	---	---	---
PLA2G7	7941	broad.mit.edu	37	6	46692974	46692974	+	Intron	DEL	T	-	-	rs113442644		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46692974delT	uc010jzf.2	-						PLA2G7_uc010jzg.1_Intron|PLA2G7_uc011dwd.1_Intron|PLA2G7_uc011dwe.1_Intron	NM_005084	NP_005075			phospholipase A2, group VII						inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)															---	---	---	---
CD2AP	23607	broad.mit.edu	37	6	47522511	47522511	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47522511delT	uc003oyw.2	+							NM_012120	NP_036252			CD2-associated protein						cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	48363422	48363422	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48363422delT								C6orf138 (284479 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	48582718	48582718	+	IGR	DEL	A	-	-	rs112829144		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48582718delA								C6orf138 (503775 upstream) : MUT (816276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49088610	49088611	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49088610_49088611delAC								None (None upstream) : MUT (310383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49638074	49638075	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49638074_49638075delAC								RHAG (33487 upstream) : CRISP2 (21997 downstream)																																			---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49701364delT	uc003ozs.2	-							NM_006061	NP_006052			cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)															---	---	---	---
TFAP2D	83741	broad.mit.edu	37	6	50689571	50689571	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50689571delA	uc003paf.2	+						TFAP2D_uc011dwt.1_Intron	NM_172238	NP_758438			transcription factor AP-2 beta-like 1								DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52450778	52450779	+	IGR	INS	-	TTG	TTG	rs150960435	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52450778_52450779insTTG								TRAM2 (8916 upstream) : LOC730101 (78420 downstream)																																			---	---	---	---
ELOVL5	60481	broad.mit.edu	37	6	53134248	53134249	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53134248_53134249insT	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron	NM_021814	NP_068586			elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	53219905	53219905	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53219905delA								ELOVL5 (5963 upstream) : GCLC (142235 downstream)																																			---	---	---	---
TINAG	27283	broad.mit.edu	37	6	54221384	54221384	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54221384delG	uc003pcj.2	+						TINAG_uc010jzt.2_Intron	NM_014464	NP_055279			tubulointerstitial nephritis antigen						cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis	basement membrane	cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)															---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55128706	55128706	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55128706delT	uc003pcl.2	+						HCRTR2_uc010jzv.2_Intron|HCRTR2_uc010jzw.1_Frame_Shift_Del_p.L218fs	NM_001526	NP_001517			orexin receptor 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	55455083	55455083	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55455083delA								HMGCLL1 (11071 upstream) : BMP5 (165157 downstream)																																			---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57058002	57058003	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57058002_57058003delAA	uc003pds.2	-						RAB23_uc003pdt.2_Intron|RAB23_uc010kac.2_Intron|RAB23_uc010kad.2_Intron	NM_183227	NP_899050			Ras-related protein Rab-23						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57358075	57358076	+	Intron	INS	-	TC	TC	rs147835952	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57358075_57358076insTC	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57370657	57370658	+	Intron	INS	-	TCTT	TCTT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57370657_57370658insTCTT	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57390108	57390114	+	Intron	DEL	ATCTGTT	-	-	rs12209515		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57390108_57390114delATCTGTT	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57400246	57400251	+	Intron	DEL	TGTGTG	-	-	rs72127011		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57400246_57400251delTGTGTG	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57413029	57413030	+	Intron	INS	-	TT	TT	rs145147559		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57413029_57413030insTT	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57417986	57417986	+	Intron	DEL	A	-	-	rs111693016		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57417986delA	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57440623	57440624	+	Intron	INS	-	A	A	rs146803092		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57440623_57440624insA	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57445155	57445155	+	Intron	DEL	C	-	-	rs71309377		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57445155delC	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57472011	57472011	+	Intron	DEL	A	-	-	rs67396455		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57472011delA	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57484549	57484549	+	Intron	DEL	C	-	-	rs113067659		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57484549delC	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57489835	57489837	+	Intron	DEL	CTC	-	-	rs146019828		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57489835_57489837delCTC	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57504529	57504529	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57504529delA	uc003pdx.2	+							NM_000947	NP_000938			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	57554978	57554979	+	IGR	INS	-	AC	AC	rs146629400		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57554978_57554979insAC								PRIM2 (41603 upstream) : GUSBL2 (691180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57557095	57557095	+	IGR	DEL	T	-	-	rs79478192		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57557095delT								PRIM2 (43720 upstream) : GUSBL2 (689064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57559053	57559053	+	IGR	DEL	T	-	-	rs143848127		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57559053delT								PRIM2 (45678 upstream) : GUSBL2 (687106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57566096	57566096	+	IGR	DEL	C	-	-	rs112517932		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57566096delC								PRIM2 (52721 upstream) : GUSBL2 (680063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57607196	57607197	+	IGR	INS	-	C	C	rs139289610	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57607196_57607197insC								PRIM2 (93821 upstream) : GUSBL2 (638962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57687687	57687688	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57687687_57687688insC								PRIM2 (174312 upstream) : GUSBL2 (558471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57924514	57924514	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57924514delG								PRIM2 (411139 upstream) : GUSBL2 (321645 downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62506564	62506565	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62506564_62506565insA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62796849	62796849	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62796849delA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	64200873	64200873	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64200873delT								LGSN (170991 upstream) : PTP4A1 (30778 downstream)																																			---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64383018	64383018	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64383018delT	uc003pep.1	+						PHF3_uc010kaf.1_Intron|PHF3_uc003pem.2_Intron|PHF3_uc010kag.1_Intron|PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Intron|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Intron	NM_015153	NP_055968			PHD finger protein 3						multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64410483	64410483	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64410483delT	uc003pep.1	+						PHF3_uc010kah.1_Intron|PHF3_uc003pen.2_Intron|PHF3_uc011dxs.1_Intron	NM_015153	NP_055968			PHD finger protein 3						multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	64457599	64457599	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64457599delT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	64717514	64717514	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64717514delT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	64843369	64843370	+	Intron	INS	-	CACA	CACA	rs10546360		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64843369_64843370insCACA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	67352847	67352853	+	IGR	DEL	TTTTTTT	-	-	rs72203171		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67352847_67352853delTTTTTTT								MCART3P (853472 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68368133	68368133	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68368133delA								None (None upstream) : BAI3 (977499 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69810839	69810839	+	Intron	DEL	A	-	-	rs138343850	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69810839delA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70840125	70840125	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70840125delT	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	71679433	71679433	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71679433delT								B3GAT2 (12645 upstream) : OGFRL1 (319044 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72674999	72674999	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72674999delT	uc003pga.2	+							NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73607277	73607277	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73607277delA	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73787656	73787656	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73787656delT	uc003pgk.2	+						KCNQ5_uc003pgj.3_Intron|KCNQ5_uc011dyh.1_Intron|KCNQ5_uc011dyi.1_Intron|KCNQ5_uc010kat.2_Intron|KCNQ5_uc011dyj.1_Intron|KCNQ5_uc011dyk.1_Intron	NM_019842	NP_062816			potassium voltage-gated channel, KQT-like						protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
OOEP	441161	broad.mit.edu	37	6	74101571	74101571	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74101571delT	uc003pgv.3	-						DDX43_uc011dyn.1_5'Flank|DDX43_uc003pgw.2_5'Flank	NM_001080507	NP_001073976			oocyte expressed protein homolog							cytoplasm					0																		---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74149208	74149209	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74149208_74149209delAA	uc003pgx.1	-							NM_138441	NP_612450			hypothetical protein LOC115004												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74666942	74666943	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74666942_74666943delTT								CD109 (128902 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75758956	75758957	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75758956_75758957insT								None (None upstream) : COL12A1 (35086 downstream)																																			---	---	---	---
COX7A2	1347	broad.mit.edu	37	6	75949818	75949818	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75949818delA	uc003phv.1	-							NM_001865	NP_001856			cytochrome c oxidase subunit VIIa polypeptide 2							mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76046224	76046224	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76046224delA	uc003pia.2	-						FILIP1_uc003phy.1_Intron|FILIP1_uc003phz.2_Intron|FILIP1_uc010kbe.2_Intron|FILIP1_uc003pib.1_5'Flank	NM_015687	NP_056502			filamin A interacting protein 1											skin(3)|ovary(1)	4																		---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76072773	76072773	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76072773delT	uc003pia.2	-						FILIP1_uc003phy.1_Intron|FILIP1_uc003phz.2_5'Flank|FILIP1_uc010kbe.2_Intron	NM_015687	NP_056502			filamin A interacting protein 1											skin(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	77413892	77413892	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77413892delA								IMPG1 (631557 upstream) : HTR1B (758056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78075901	78075901	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78075901delC								None (None upstream) : HTR1B (96047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78159731	78159731	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78159731delT								None (None upstream) : HTR1B (12217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79344480	79344480	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79344480delA								None (None upstream) : IRAK1BP1 (232709 downstream)																																			---	---	---	---
IRAK1BP1	134728	broad.mit.edu	37	6	79598238	79598238	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79598238delT	uc003pim.2	+						IRAK1BP1_uc010kbg.1_Intron|IRAK1BP1_uc003pin.2_Intron	NM_001010844	NP_001010844			interleukin-1 receptor-associated kinase 1						I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus					0		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	80125188	80125188	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80125188delT								HMGN3 (180733 upstream) : LCA5 (69521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	81081891	81081891	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81081891delT								BCKDHB (25904 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82656164	82656164	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82656164delT								FAM46A (193736 upstream) : IBTK (223792 downstream)																																			---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84368820	84368820	+	Intron	DEL	A	-	-	rs7770662		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84368820delA	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_Intron	NM_014841	NP_055656			synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	84429213	84429214	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84429213_84429214delAA								SNAP91 (10086 upstream) : RIPPLY2 (133771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85879666	85879666	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85879666delA								TBX18 (405767 upstream) : NT5E (279636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87643835	87643836	+	IGR	INS	-	AGTT	AGTT	rs139749093	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87643835_87643836insAGTT								None (None upstream) : HTR1E (3188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	88519505	88519505	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88519505delT	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
CNR1	1268	broad.mit.edu	37	6	88853531	88853531	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88853531delA	uc011dzq.1	-	2					CNR1_uc010kbz.2_3'UTR|CNR1_uc011dzr.1_3'UTR|CNR1_uc011dzs.1_3'UTR|CNR1_uc003pmq.3_3'UTR|CNR1_uc011dzt.1_3'UTR|CNR1_uc010kca.2_3'UTR	NM_001160260	NP_001153732			cannabinoid receptor 1 isoform a						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	cannabinoid receptor activity|protein binding			skin(2)	2		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Marinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	89149357	89149358	+	IGR	DEL	TT	-	-	rs113745184		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89149357_89149358delTT								CNR1 (273590 upstream) : RNGTT (170631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	89302920	89302921	+	IGR	INS	-	A	A	rs142080868	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89302920_89302921insA								CNR1 (427153 upstream) : RNGTT (17068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	89846397	89846397	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89846397delA								SFRS13B (18597 upstream) : PM20D2 (9372 downstream)																																			---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90827183	90827183	+	Intron	DEL	T	-	-	rs72095831		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90827183delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91226170	91226170	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91226170delA	uc003pnz.1	-	17					MAP3K7_uc003pny.1_3'UTR|MAP3K7_uc003poa.1_3'UTR|MAP3K7_uc003pob.1_3'UTR|MAP3K7_uc003poc.1_3'UTR	NM_145331	NP_663304			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|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|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	92424335	92424335	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92424335delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92535448	92535448	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92535448delA								None (None upstream) : None (None downstream)																																			---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	93954897	93954897	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93954897delT	uc003poe.2	-						EPHA7_uc003pof.2_Intron|EPHA7_uc011eac.1_Intron	NM_004440	NP_004431			ephrin receptor EphA7 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)														---	---	---	---
MANEA	79694	broad.mit.edu	37	6	96041937	96041937	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96041937delA	uc003poo.1	+							NM_024641	NP_078917			mannosidase, endo-alpha						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	96096701	96096701	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96096701delG								MANEA (39375 upstream) : FUT9 (367144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	96148562	96148577	+	IGR	DEL	AAAGAAGAGGAAGAAC	-	-	rs10456968	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96148562_96148577delAAAGAAGAGGAAGAAC								MANEA (91236 upstream) : FUT9 (315268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	96701351	96701351	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96701351delA								FUT9 (37864 upstream) : KIAA0776 (268351 downstream)																																			---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97044490	97044490	+	Intron	DEL	T	-	-	rs68183767		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97044490delT	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97491610	97491610	+	Intron	DEL	T	-	-	rs138742569		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97491610delT	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97532863	97532863	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97532863delT	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	99565663	99565663	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99565663delC								FBXL4 (169814 upstream) : C6orf168 (155131 downstream)																																			---	---	---	---
C6orf168	84553	broad.mit.edu	37	6	99785133	99785134	+	Intron	DEL	AA	-	-	rs140382166		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99785133_99785134delAA	uc003ppj.3	-						C6orf168_uc003ppi.3_Intron	NM_032511	NP_115900			hypothetical protein LOC84553											ovary(2)|central_nervous_system(1)	3		all_cancers(76;1.63e-06)|Acute lymphoblastic leukemia(125;5.12e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00898)|Colorectal(196;0.0699)|Lung NSC(302;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.073)														---	---	---	---
COQ3	51805	broad.mit.edu	37	6	99817820	99817820	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99817820delA	uc003ppk.2	-							NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)														---	---	---	---
MCHR2	84539	broad.mit.edu	37	6	100426684	100426684	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100426684delA	uc003pqh.1	-						MCHR2_uc003pqi.1_Intron	NM_001040179	NP_001035269			melanin-concentrating hormone receptor 2							integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101215315	101215315	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101215315delA	uc003pqk.2	-						ASCC3_uc011eai.1_Intron|ASCC3_uc003pql.2_Intron	NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101800262	101800263	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101800262_101800263delAA								ASCC3 (471038 upstream) : GRIK2 (46642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103773127	103773127	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103773127delA								None (None upstream) : None (None downstream)																																			---	---	---	---
LIN28B	389421	broad.mit.edu	37	6	105439946	105439947	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105439946_105439947delTT	uc003pqv.1	+						LIN28B_uc010kda.1_Intron	NM_001004317	NP_001004317			lin-28 homolog B						miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)																---	---	---	---
PREP	5550	broad.mit.edu	37	6	105836060	105836060	+	Intron	DEL	A	-	-	rs67304405		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105836060delA	uc003prc.2	-							NM_002726	NP_002717			prolyl endopeptidase						proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	105892738	105892738	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105892738delA								PREP (41769 upstream) : PRDM1 (641457 downstream)																																			---	---	---	---
PRDM1	639	broad.mit.edu	37	6	106534485	106534485	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106534485delT	uc003prd.2	+							NM_001198	NP_001189			PR domain containing 1, with ZNF domain isoform						negative regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(54)|ovary(1)|skin(1)	56	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)				D|N|Mis|F|S		DLBCL								---	---	---	---
Unknown	0	broad.mit.edu	37	6	107178396	107178397	+	Intron	INS	-	AAAAA	AAAAA	rs2024741	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107178396_107178397insAAAAA	uc003pro.1	-						uc003prn.1_Intron					Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1534000.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	107223784	107223785	+	Intron	INS	-	T	T	rs117147700	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107223784_107223785insT	uc003pro.1	-						uc003prp.2_5'Flank					Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1534000.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	108012215	108012215	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108012215delA								SOBP (29707 upstream) : SCML4 (11150 downstream)																																			---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108687358	108687358	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108687358delA	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	109655410	109655411	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109655410_109655411delTT								C6orf182 (170297 upstream) : CD164 (32307 downstream)																																			---	---	---	---
FIG4	9896	broad.mit.edu	37	6	110113940	110113946	+	Intron	DEL	TTTTTTT	-	-	rs72243181		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110113940_110113946delTTTTTTT	uc003ptt.2	+						FIG4_uc011eau.1_Intron	NM_014845	NP_055660			Sac domain-containing inositol phosphatase 3						cell death	endosome membrane	protein binding			ovary(1)	1		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	110288754	110288754	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110288754delG								FIG4 (142120 upstream) : GPR6 (10755 downstream)																																			---	---	---	---
AMD1	262	broad.mit.edu	37	6	111185169	111185169	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111185169delT	uc011eay.1	+							NM_001033059	NP_001028231			adenosylmethionine decarboxylase 1 isoform 2						spermidine biosynthetic process|spermine biosynthetic process	cytosol	adenosylmethionine decarboxylase activity			upper_aerodigestive_tract(1)	1		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)													---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111665249	111665249	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111665249delA	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron|REV3L_uc003pva.1_Intron	NM_002912	NP_002903			DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	6	112279532	112279533	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112279532_112279533delTT								FYN (84905 upstream) : WISP3 (95745 downstream)																																			---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112462354	112462354	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112462354delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676			laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114455136	114455137	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114455136_114455137delGA	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114490457	114490458	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114490457_114490458delAC	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	114703568	114703569	+	IGR	INS	-	TG	TG	rs139132418	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114703568_114703569insTG								HS3ST5 (40028 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114735242	114735242	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114735242delA								HS3ST5 (71702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115877067	115877068	+	IGR	INS	-	TG	TG	rs137884104	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115877067_115877068insTG								None (None upstream) : FRK (385625 downstream)																																			---	---	---	---
KPNA5	3841	broad.mit.edu	37	6	117026119	117026119	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117026119delT	uc003pxh.2	+							NM_002269	NP_002260			karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	117543099	117543101	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117543099_117543101delTTT								RFX6 (289791 upstream) : VGLL2 (43620 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118365543	118365543	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118365543delT	uc003pxx.3	+							NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	118885507	118885507	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118885507delT	uc003pxz.1	-						C6orf204_uc003pya.1_Intron|C6orf204_uc003pyb.2_Intron|C6orf204_uc011ebj.1_Intron|C6orf204_uc003pyc.2_Intron	NM_001042475	NP_001035940			chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119283390	119283391	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119283390_119283391delGA	uc003pyj.2	-						FAM184A_uc003pyk.3_Intron|FAM184A_uc003pyl.3_Intron|FAM184A_uc003pyi.2_Intron	NM_024581	NP_078857			hypothetical protein LOC79632 isoform 1											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
MAN1A1	4121	broad.mit.edu	37	6	119589600	119589600	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119589600delT	uc003pym.1	-						MAN1A1_uc010kei.1_Intron	NM_005907	NP_005898			mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119907667	119907667	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119907667delT								MAN1A1 (236741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122356376	122356376	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122356376delA								GJA1 (585504 upstream) : HSF2 (364320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122404474	122404474	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122404474delA								GJA1 (633602 upstream) : HSF2 (316222 downstream)																																			---	---	---	---
SERINC1	57515	broad.mit.edu	37	6	122775652	122775652	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122775652delA	uc003pyy.1	-							NM_020755	NP_065806			serine incorporator 1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	L-serine transmembrane transporter activity|protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.126)														---	---	---	---
FABP7	2173	broad.mit.edu	37	6	123101679	123101679	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123101679delT	uc003pzf.2	+						FABP7_uc003pzd.2_Intron|FABP7_uc003pze.1_3'UTR	NM_001446	NP_001437			fatty acid binding protein 7, brain						negative regulation of cell proliferation	cytoplasm	lipid binding|transporter activity				0				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|gamma-Homolinolenic acid(DB00154)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	124086540	124086540	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124086540delT								TRDN (128598 upstream) : NKAIN2 (38529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	126030881	126030881	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126030881delT								HDDC2 (407599 upstream) : HEY2 (37899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127384124	127384125	+	Intron	DEL	GT	-	-	rs146490292		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127384124_127384125delGT	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
ECHDC1	55862	broad.mit.edu	37	6	127636215	127636215	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127636215delA	uc003qax.2	-						ECHDC1_uc003qaz.3_Intron|ECHDC1_uc010key.2_Intron|ECHDC1_uc003qay.3_Intron|ECHDC1_uc010kez.2_Intron|ECHDC1_uc010kex.2_Intron	NM_001139510	NP_001132982			enoyl Coenzyme A hydratase domain containing 1								catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)														---	---	---	---
THEMIS	387357	broad.mit.edu	37	6	128065988	128065989	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128065988_128065989delAC	uc003qbi.2	-						THEMIS_uc010kfa.2_Intron|THEMIS_uc011ebt.1_Intron|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923			thymocyte selection pathway associated isoform						negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4																		---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128321487	128321487	+	Intron	DEL	A	-	-	rs113113294		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128321487delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron|PTPRK_uc010kfd.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	129125173	129125175	+	IGR	DEL	TCA	-	-	rs5879910		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129125173_129125175delTCA								PTPRK (283303 upstream) : LAMA2 (79111 downstream)																																			---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129573211	129573211	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129573211delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129626966	129626966	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129626966delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130074981	130074981	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130074981delT								ARHGAP18 (43611 upstream) : C6orf191 (77410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130273487	130273487	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130273487delA								C6orf191 (91071 upstream) : L3MBTL3 (66247 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131188114	131188115	+	Intron	INS	-	TG	TG	rs138332627	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131188114_131188115insTG	uc003qch.2	-						EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc003qcd.1_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131941945	131941947	+	Intron	DEL	TTT	-	-	rs114412536	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131941945_131941947delTTT	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc003qct.1_Intron|MED23_uc011ecb.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
SLC2A12	154091	broad.mit.edu	37	6	134312046	134312046	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134312046delT	uc003qem.1	-	5						NM_145176	NP_660159			solute carrier family 2 (facilitated glucose							endomembrane system|integral to membrane|perinuclear region of cytoplasm|plasma membrane	D-glucose transmembrane transporter activity			ovary(1)	1	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)														---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135889023	135889023	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135889023delT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
FAM54A	113115	broad.mit.edu	37	6	136566111	136566111	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136566111delT	uc010kgp.1	-						FAM54A_uc003qgt.1_Intron|FAM54A_uc003qgu.1_Intron	NM_001099286	NP_001092756			DUF729 domain containing 1											skin(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00228)|OV - Ovarian serous cystadenocarcinoma(155;0.00504)														---	---	---	---
IL20RA	53832	broad.mit.edu	37	6	137350507	137350507	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137350507delG	uc003qhj.2	-						IL20RA_uc011edl.1_Intron|IL20RA_uc003qhk.2_Intron|IL20RA_uc010kgy.1_Intron	NM_014432	NP_055247			interleukin 20 receptor, alpha precursor							integral to membrane	receptor activity			ovary(2)|skin(2)	4	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	137844056	137844057	+	IGR	DEL	AA	-	-	rs78352809		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137844056_137844057delAA								OLIG3 (28525 upstream) : TNFAIP3 (344524 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138628599	138628599	+	Intron	DEL	A	-	-	rs80147113		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138628599delA	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	138956216	138956216	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138956216delA								NHSL1 (62548 upstream) : CCDC28A (138441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140306772	140306773	+	Intron	DEL	TC	-	-	rs71562529		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140306772_140306773delTC	uc003qis.2	+											Homo sapiens, clone IMAGE:3451765, mRNA.																														---	---	---	---
LOC153910	153910	broad.mit.edu	37	6	142860299	142860299	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142860299delT	uc003qjc.1	-						LOC153910_uc010khg.1_Intron	NR_027312				Homo sapiens cDNA FLJ31371 fis, clone NB9N42000196.												0																		---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143082717	143082717	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143082717delA	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143166698	143166698	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143166698delC	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143392900	143392900	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143392900delT	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron|AIG1_uc011edw.1_Intron|AIG1_uc003qjg.2_Intron	NM_016108	NP_057192			androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143548770	143548770	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143548770delT	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron	NM_016108	NP_057192			androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796037	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144935181	144935181	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144935181delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	145273702	145273703	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145273702_145273703delTC								UTRN (99534 upstream) : EPM2A (672743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148494724	148494726	+	IGR	DEL	AGG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148494724_148494726delAGG								SAMD5 (603567 upstream) : SASH1 (169003 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148810987	148810992	+	Intron	DEL	TGTGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148810987_148810992delTGTGTG	uc003qme.1	+							NM_015278	NP_056093			SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)														---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149637765	149637765	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149637765delT	uc003qmj.2	+						TAB2_uc011eec.1_Intron|TAB2_uc010kia.1_5'Flank|TAB2_uc010kib.1_5'Flank	NM_015093	NP_055908			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|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|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149669751	149669751	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149669751delA	uc003qmj.2	+						TAB2_uc011eec.1_Intron|TAB2_uc010kia.1_Intron|TAB2_uc010kib.1_Intron|TAB2_uc003qmk.3_Intron	NM_015093	NP_055908			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|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|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149808515	149808516	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149808515_149808516delAA	uc010kic.2	-						ZC3H12D_uc003qmm.2_5'Flank|ZC3H12D_uc010kid.2_5'Flank	NM_139126				peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PPP1R14C	81706	broad.mit.edu	37	6	150489100	150489101	+	Intron	DEL	CT	-	-	rs74508153		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150489100_150489101delCT	uc003qnt.2	+							NM_030949	NP_112211			protein phosphatase 1, regulatory (inhibitor)						regulation of phosphorylation	cytoplasm|membrane					0		Ovarian(120;0.0284)	BRCA - Breast invasive adenocarcinoma(37;0.215)	OV - Ovarian serous cystadenocarcinoma(155;9.14e-12)														---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	150998421	150998422	+	Intron	INS	-	AC	AC	rs145781581	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150998421_150998422insAC	uc003qny.1	+						PLEKHG1_uc011eel.1_Intron	NM_001029884	NP_001025055			pleckstrin homology domain containing, family G						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151413789	151413789	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151413789delT	uc003qob.2	+						MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255			methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152456138	152456138	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152456138delA	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc003qop.3_Intron|SYNE1_uc011eez.1_Intron|SYNE1_uc003qoq.3_Intron|SYNE1_uc003qor.3_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153308092	153308092	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153308092delA								FBXO5 (3352 upstream) : MTRF1L (309 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155490959	155490959	+	Intron	DEL	T	-	-	rs112991074		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155490959delT	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	156463761	156463762	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156463761_156463762delTC								MIR1202 (195748 upstream) : ARID1B (635324 downstream)																																			---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158313078	158313079	+	Intron	INS	-	AAG	AAG	rs146970264	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158313078_158313079insAAG	uc003qqv.1	+							NM_016224	NP_057308			sorting nexin 9						cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)														---	---	---	---
DYNLT1	6993	broad.mit.edu	37	6	159062373	159062375	+	In_Frame_Del	DEL	TCA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159062373_159062375delTCA	uc003qrn.1	-	2	45_47	c.45_47delTGA	c.(43-48)GATGAA>GAA	p.D15del		NM_006519	NP_006510	P63172	DYLT1_HUMAN	dynein, light chain, Tctex-type 1	15					cell division|establishment of mitotic spindle orientation|intracellular transport of viral proteins in host cell|mitosis|negative regulation of neurogenesis|regulation of G-protein coupled receptor protein signaling pathway	cytoplasmic dynein complex|Golgi apparatus|microtubule|spindle	identical protein binding|motor activity				0		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;4.02e-18)|BRCA - Breast invasive adenocarcinoma(81;9.53e-06)														---	---	---	---
TCP1	6950	broad.mit.edu	37	6	160200861	160200861	+	Intron	DEL	A	-	-	rs147097290	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160200861delA	uc003qsr.2	-						TCP1_uc003qss.2_Intron|TCP1_uc010kjz.2_Intron|TCP1_uc003qst.2_Intron	NM_030752	NP_110379			T-complex protein 1 isoform a						'de novo' posttranslational protein folding|tubulin complex assembly	cell junction|Golgi apparatus	ATP binding|unfolded protein binding			breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160524765	160524765	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160524765delT	uc003qta.2	+							NM_000876	NP_000867			insulin-like growth factor 2 receptor precursor						receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
SLC22A1	6580	broad.mit.edu	37	6	160559117	160559117	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160559117delC	uc003qtc.2	+						SLC22A1_uc003qtd.2_Intron	NM_003057	NP_003048			solute carrier family 22 member 1 isoform a							basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160694708	160694708	+	IGR	DEL	G	-	-	rs67868908		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160694708delG								SLC22A2 (14749 upstream) : SLC22A3 (74717 downstream)																																			---	---	---	---
LPAL2	80350	broad.mit.edu	37	6	160907117	160907117	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160907117delT	uc003qtj.2	-						LPAL2_uc011efy.1_Intron	NR_028093				Homo sapiens cDNA FLJ43922 fis, clone TESTI4012406.												0		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162075037	162075037	+	Intron	DEL	T	-	-	rs68037466		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162075037delT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162792760	162792760	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162792760delT	uc003qtx.3	-						PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	163098299	163098299	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163098299delA	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	163792298	163792299	+	IGR	INS	-	G	G	rs146375470	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163792298_163792299insG								LOC285796 (46804 upstream) : QKI (43376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164663076	164663076	+	IGR	DEL	G	-	-	rs11300557		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164663076delG								QKI (668184 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165266670	165266670	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165266670delA								None (None upstream) : C6orf118 (426485 downstream)																																			---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165906065	165906066	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165906065_165906066insA	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	166639661	166639663	+	IGR	DEL	AAG	-	-	rs113533629		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166639661_166639663delAAG								T (57530 upstream) : PRR18 (79505 downstream)																																			---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166952429	166952429	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166952429delT	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|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|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167268853	167268854	+	Intron	INS	-	GAA	GAA	rs142771541	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167268853_167268854insGAA	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|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|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167368476	167368476	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167368476delA	uc003qve.2	-						RNASET2_uc003qvh.2_Intron|RNASET2_uc003qvf.2_Intron|RNASET2_uc003qvg.2_Intron|RNASET2_uc003qvi.1_Intron	NM_003730	NP_003721			ribonuclease T2 precursor						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)														---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167376681	167376681	+	Intron	DEL	T	-	-	rs78702284		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167376681delT	uc003qvh.2	-											Homo sapiens mRNA for extra-cellular ribonuclease (RNASE6PL gene).						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168325544	168325544	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168325544delT	uc003qwd.2	+						MLLT4_uc003qwb.1_Intron|MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168959486	168959487	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168959486_168959487delTG	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	169038584	169038601	+	Intron	DEL	GCTGTATGCTGAGCTGGA	-	-	rs138260239		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169038584_169038601delGCTGTATGCTGAGCTGGA	uc003qws.1	+						SMOC2_uc003qwr.1_Intron|SMOC2_uc011egu.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170118766	170118766	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170118766delA	uc011egy.1	-						PHF10_uc011egz.1_Intron|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758			PHD finger protein 10 isoform a						nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	npBAF complex	zinc ion binding			urinary_tract(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)														---	---	---	---
C6orf70	55780	broad.mit.edu	37	6	170153638	170153638	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170153638delT	uc003qxg.1	+						TCTE3_uc003qxe.1_5'Flank|TCTE3_uc003qxf.2_5'Flank|C6orf70_uc011ehb.1_Intron|C6orf70_uc003qxh.1_Intron|C6orf70_uc010kky.1_5'Flank	NM_018341	NP_060811			hypothetical protein LOC55780							integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)														---	---	---	---
C7orf50	84310	broad.mit.edu	37	7	1167118	1167119	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1167118_1167119delAA	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726			hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	1371285	1371285	+	IGR	DEL	G	-	-	rs75030330	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1371285delG								UNCX (94673 upstream) : MICALL2 (102711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1735797	1735798	+	5'Flank	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1735797_1735798delAG	uc003slc.1	-											SubName: Full=LOC401296 protein;																														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2301677	2301677	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2301677delT	uc003slw.2	-							NM_013321	NP_037453			sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)														---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2690213	2690213	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2690213delA	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526			tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2975132	2975132	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2975132delA	uc003smv.2	-							NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
KIAA0415	9907	broad.mit.edu	37	7	4827515	4827515	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4827515delC	uc003sne.2	+						KIAA0415_uc010ksp.2_Intron|KIAA0415_uc003snf.2_5'Flank	NM_014855	NP_055670			hypothetical protein LOC9907						cell death|double-strand break repair via homologous recombination	cytoplasm|nucleus	protein binding			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.091)|OV - Ovarian serous cystadenocarcinoma(56;8.35e-15)														---	---	---	---
LOC389458	389458	broad.mit.edu	37	7	5076994	5076994	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5076994delT	uc003snr.2	+											Synthetic construct DNA, clone: pF1KB3788, Homo sapiens RBAK gene for RB-associated KRAB repressor, complete cds, without stop codon, in Flexi system.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	5124161	5124161	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5124161delA								LOC389458 (11308 upstream) : WIPI2 (105674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	5273845	5273846	+	IGR	DEL	AA	-	-	rs66510751		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5273845_5273846delAA								WIPI2 (360 upstream) : SLC29A4 (48715 downstream)																																			---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5449942	5449944	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5449942_5449944delAAA	uc003soi.3	-						TNRC18_uc010ksx.1_Intron|TNRC18_uc003sok.1_Intron	NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5714099	5714101	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5714099_5714101delAAA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron|RNF216_uc003spa.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
RSPH10B2	728194	broad.mit.edu	37	7	5968562	5968562	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5968562delT	uc003sph.1	-						RSPH10B2_uc003spg.1_Intron|RSPH10B2_uc010ktd.1_Intron|RSPH10B2_uc011jwk.1_Intron	NM_173565	NP_775836			radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
PMS2	5395	broad.mit.edu	37	7	6031470	6031470	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6031470delA	uc003spl.2	-						PMS2_uc003spj.2_Intron|PMS2_uc003spk.2_Intron|PMS2_uc011jwl.1_Intron|PMS2_uc010ktg.2_Intron|PMS2_uc010kte.2_Intron|PMS2_uc010ktf.1_Intron	NM_000535	NP_000526			PMS2 postmeiotic segregation increased 2 isoform						mismatch repair|reciprocal meiotic recombination|somatic hypermutation of immunoglobulin genes	MutLalpha complex	ATP binding|ATPase activity|endonuclease activity|protein binding|single base insertion or deletion binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)				Mis|N|F			colorectal|endometrial|ovarian|medulloblastoma|glioma		Direct_reversal_of_damage|MMR	Lynch_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
USP42	84132	broad.mit.edu	37	7	6184962	6184962	+	Intron	DEL	A	-	-	rs72151157		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6184962delA	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_Intron|USP42_uc011jwr.1_Intron	NM_032172	NP_115548			ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
GRID2IP	392862	broad.mit.edu	37	7	6541864	6541864	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6541864delT	uc011jwx.1	-							NM_001145118	NP_001138590			glutamate receptor, ionotropic, delta 2 (Grid2)						actin cytoskeleton organization	cell junction|postsynaptic membrane	actin binding				0																		---	---	---	---
C1GALT1	56913	broad.mit.edu	37	7	7226886	7226886	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7226886delT	uc010ktn.2	+						C1GALT1_uc010ktm.1_Intron	NM_020156	NP_064541			core 1 synthase,						angiogenesis|cell differentiation|kidney development	integral to membrane	glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity|metal ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
RPA3	6119	broad.mit.edu	37	7	7722081	7722081	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7722081delT	uc003sri.2	-						uc011jxf.1_Intron	NM_002947	NP_002938			replication protein A3, 14kDa						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|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	cytoplasm|DNA replication factor A complex|nucleoplasm	protein binding|single-stranded DNA binding			large_intestine(1)	1		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)									Direct_reversal_of_damage|NER					---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8183660	8183660	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8183660delA	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron	NM_022307	NP_071682			islet cell autoantigen 1						neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	8324823	8324823	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8324823delT	uc003srt.1	+											full-length cDNA clone CS0DC002YA18 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8651759	8651759	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8651759delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958			neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)														---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8692748	8692748	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8692748delT	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958			neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	9145785	9145785	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9145785delA								NXPH1 (353193 upstream) : PER4 (528115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9325942	9325942	+	IGR	DEL	C	-	-	rs6963740	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9325942delC								NXPH1 (533350 upstream) : PER4 (347958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10608142	10608142	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10608142delA								PER4 (932695 upstream) : NDUFA4 (364673 downstream)																																			---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11042583	11042583	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11042583delT	uc003sry.1	+						PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Intron|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475			PHD finger protein 14 isoform 2								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11441364	11441364	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11441364delT	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11822409	11822409	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11822409delT	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12887708	12887709	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12887708_12887709delAG								ARL4A (157152 upstream) : None (None downstream)																																			---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14225984	14225984	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14225984delA	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron	NM_004080	NP_004071			diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15556604	15556605	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15556604_15556605delTT	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	15942222	15942222	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15942222delT								MEOX2 (215914 upstream) : ISPD (184930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	15972611	15972611	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15972611delT								MEOX2 (246303 upstream) : ISPD (154541 downstream)																																			---	---	---	---
SOSTDC1	25928	broad.mit.edu	37	7	16503625	16503626	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16503625_16503626delAA	uc003stg.2	-						SOSTDC1_uc003sth.2_Intron	NM_015464	NP_056279			sclerostin domain containing 1 precursor						Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	17756762	17756762	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17756762delT								AHR (370987 upstream) : SNX13 (73624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17818205	17818205	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17818205delA								AHR (432430 upstream) : SNX13 (12181 downstream)																																			---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18126136	18126136	+	5'Flank	DEL	A	-	-	rs4721693		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18126136delA	uc011jya.1	+							NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18796501	18796503	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18796501_18796503delTTT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	19153797	19153798	+	RNA	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19153797_19153798insG	uc003sul.2	+	2		c.1614_1615insG								full-length cDNA clone CS0DA003YM21 of Neuroblastoma of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	22054482	22054483	+	IGR	DEL	AA	-	-	rs139660162		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22054482_22054483delAA								CDCA7L (68940 upstream) : RAPGEF5 (103426 downstream)																																			---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22196602	22196602	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22196602delT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426			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																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22295046	22295046	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22295046delA	uc003svg.2	-							NM_012294	NP_036426			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																		---	---	---	---
TOMM7	54543	broad.mit.edu	37	7	22857031	22857031	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22857031delT	uc003svk.2	-							NM_019059	NP_061932			translocase of outer mitochondrial membrane 7						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity				0																		---	---	---	---
C7orf46	340277	broad.mit.edu	37	7	23730803	23730803	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23730803delT	uc003swo.3	+						C7orf46_uc003swq.3_Intron|C7orf46_uc003swr.3_Intron|C7orf46_uc003swp.3_Intron|C7orf46_uc010kup.2_Intron	NM_199136	NP_954587			hypothetical protein LOC340277 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	24291468	24291469	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24291468_24291469insA								STK31 (347103 upstream) : NPY (32340 downstream)																																			---	---	---	---
OSBPL3	26031	broad.mit.edu	37	7	24903320	24903320	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24903320delT	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron|OSBPL3_uc003sxj.1_5'Flank|OSBPL3_uc003sxk.1_5'Flank	NM_015550	NP_056365			oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25226820	25226820	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25226820delT								C7orf31 (7003 upstream) : NPVF (37373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25417784	25417791	+	IGR	DEL	CCCTTCCC	-	-	rs75017634		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25417784_25417791delCCCTTCCC								NPVF (149679 upstream) : MIR148A (571748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25459682	25459684	+	IGR	DEL	AAA	-	-	rs34378094		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25459682_25459684delAAA								NPVF (191577 upstream) : MIR148A (529855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25729106	25729106	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25729106delT								NPVF (461001 upstream) : MIR148A (260433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26006125	26006125	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26006125delT								MIR148A (16519 upstream) : NFE2L3 (185722 downstream)																																			---	---	---	---
NFE2L3	9603	broad.mit.edu	37	7	26226399	26226399	+	3'UTR	DEL	A	-	-	rs35180301		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26226399delA	uc003sxq.2	+	4						NM_004289	NP_004280			nuclear factor erythroid 2-like 3						transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27308926	27308926	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27308926delT								EVX1 (22734 upstream) : HIBADH (256137 downstream)																																			---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28661875	28661878	+	Intron	DEL	CTCA	-	-	rs74638346	by1000genomes;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28661875_28661878delCTCA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron	NM_182898	NP_878901			cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	28988555	28988555	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28988555delA								CREB5 (123046 upstream) : TRIL (4421 downstream)																																			---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29148937	29148937	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29148937delC	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29160776	29160776	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29160776delA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	29610159	29610159	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29610159delG								PRR15 (3248 upstream) : LOC646762 (75380 downstream)																																			---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30080362	30080362	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30080362delT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028			pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30291392	30291393	+	IGR	INS	-	ACAC	ACAC	rs137885088	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30291392_30291393insACAC								C7orf41 (89011 upstream) : ZNRF2 (32530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	30528175	30528178	+	IGR	DEL	TTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30528175_30528178delTTTT								NOD1 (9782 upstream) : GGCT (8061 downstream)																																			---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30699565	30699565	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30699565delT	uc003tbn.2	-						CRHR2_uc010kvw.1_Intron|CRHR2_uc010kvx.1_Intron|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Intron|CRHR2_uc003tbp.2_Intron	NM_001883	NP_001874			corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30981121	30981121	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30981121delT								AQP1 (15990 upstream) : GHRHR (22515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	32366305	32366305	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32366305delG								PDE1C (27364 upstream) : LSM5 (158640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	33670507	33670507	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33670507delG								BBS9 (24827 upstream) : BMPER (274605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	33784304	33784304	+	IGR	DEL	C	-	-	rs10246905	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33784304delC								BBS9 (138624 upstream) : BMPER (160808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	34304266	34304267	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34304266_34304267insA								BMPER (110155 upstream) : AAA1 (85768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	34363042	34363042	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34363042delT								BMPER (168931 upstream) : AAA1 (26993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36093586	36093587	+	IGR	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36093586_36093587delCT								SEPT7 (148671 upstream) : EEPD1 (99249 downstream)																																			---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36333573	36333573	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36333573delA	uc003tfa.2	+							NM_030636	NP_085139			endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	36521582	36521583	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36521582_36521583insT								ANLN (28184 upstream) : AOAH (31027 downstream)																																			---	---	---	---
AOAH	313	broad.mit.edu	37	7	36711255	36711256	+	Intron	DEL	TG	-	-	rs34363257		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36711255_36711256delTG	uc003tfh.3	-						AOAH_uc010kxf.2_Intron|AOAH_uc011kba.1_Intron	NM_001637	NP_001628			acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	36955791	36955791	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36955791delG	uc003tfk.1	-						ELMO1_uc003tfi.1_Intron|ELMO1_uc003tfj.1_Intron|ELMO1_uc011kbb.1_Intron|ELMO1_uc011kbc.1_Intron|ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615			engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38673658	38673659	+	5'Flank	INS	-	C	C	rs150406009	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38673658_38673659insC	uc003tgu.2	-						AMPH_uc003tgv.2_5'Flank	NM_001635	NP_001626			amphiphysin isoform 1						endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39200478	39200478	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39200478delT	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	39994109	39994109	+	Intron	DEL	T	-	-	rs34424227		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39994109delT	uc003thh.3	+						CDK13_uc003thi.3_Intron	NM_003718	NP_003709			cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40356555	40356556	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40356555_40356556delTT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42254059	42254059	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42254059delA	uc011kbh.1	-							NM_000168	NP_000159			GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	42511802	42511802	+	IGR	DEL	T	-	-	rs74674111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42511802delT								GLI3 (235184 upstream) : C7orf25 (437072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42754998	42754998	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42754998delA								GLI3 (478380 upstream) : C7orf25 (193876 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43256261	43256261	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43256261delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43293510	43293510	+	Intron	DEL	A	-	-	rs74779735		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43293510delA	uc003tid.1	+						HECW1_uc011kbi.1_Intron|HECW1_uc003tie.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43533027	43533027	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43533027delG	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44066097	44066098	+	IGR	INS	-	TTTG	TTTG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44066097_44066098insTTTG								POLR2J4 (7349 upstream) : RASA4P (2388 downstream)																																			---	---	---	---
RAMP3	10268	broad.mit.edu	37	7	45203975	45203976	+	Intron	DEL	AA	-	-	rs67711715		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45203975_45203976delAA	uc003tnb.2	+							NM_005856	NP_005847			receptor activity modifying protein 3 precursor						intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)													---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45747744	45747745	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45747744_45747745insC	uc003tne.3	+							NM_021116	NP_066939			adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
C7orf69	80099	broad.mit.edu	37	7	47859242	47859242	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47859242delA	uc003tnz.3	+	3					PKD1L1_uc003tny.1_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	NM_025031	NP_079307			hypothetical protein LOC80099 precursor							extracellular region					0																		---	---	---	---
ZPBP	11055	broad.mit.edu	37	7	50107670	50107670	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50107670delT	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940			zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)																	---	---	---	---
DDC	1644	broad.mit.edu	37	7	50602859	50602859	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50602859delT	uc003tpf.3	-						DDC_uc010kza.2_Intron|DDC_uc003tpg.3_Intron	NM_000790	NP_000781			dopa decarboxylase (aromatic L-amino acid						cellular amino acid metabolic process|hormone biosynthetic process|neurotransmitter secretion	cytosol	aromatic-L-amino-acid decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(2)	2	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Flupenthixol(DB00875)|L-Tryptophan(DB00150)|Levodopa(DB01235)|Pimozide(DB01100)|Pyridoxal Phosphate(DB00114)|Remoxipride(DB00409)													---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50737185	50737185	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50737185delA	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	50924758	50924758	+	IGR	DEL	C	-	-	rs113548983		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50924758delC								GRB10 (63599 upstream) : COBL (159152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	51695622	51695623	+	IGR	INS	-	A	A	rs146600417	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51695622_51695623insA								COBL (311107 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52386501	52386504	+	IGR	DEL	TCCT	-	-	rs72422842		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52386501_52386504delTCCT								None (None upstream) : POM121L12 (716845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52390633	52390633	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52390633delT								None (None upstream) : POM121L12 (712716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52527452	52527455	+	IGR	DEL	GCCA	-	-	rs5884256		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52527452_52527455delGCCA								None (None upstream) : POM121L12 (575894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52774618	52774618	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52774618delT								None (None upstream) : POM121L12 (328731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53554546	53554546	+	IGR	DEL	T	-	-	rs62451925		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53554546delT								POM121L12 (449929 upstream) : HPVC1 (714371 downstream)																																			---	---	---	---
VSTM2A	222008	broad.mit.edu	37	7	54613415	54613415	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54613415delG	uc010kzf.2	+						VSTM2A_uc010kze.2_Intron|VSTM2A_uc003tqc.3_Intron	NM_182546	NP_872352			V-set and transmembrane domain containing 2							extracellular region					0			STAD - Stomach adenocarcinoma(5;0.0525)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	54685119	54685120	+	IGR	DEL	AA	-	-	rs78376059		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54685119_54685120delAA								VSTM2A (46932 upstream) : SEC61G (134821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54790015	54790016	+	IGR	DEL	TC	-	-	rs71804993	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54790015_54790016delTC								VSTM2A (151828 upstream) : SEC61G (29925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54916965	54916965	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54916965delT								SEC61G (90026 upstream) : EGFR (169760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55009831	55009831	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55009831delG								SEC61G (182892 upstream) : EGFR (76894 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55085288	55085288	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55085288delT	uc003tqk.2	+						EGFR_uc003tqh.2_5'Flank|EGFR_uc003tqi.2_5'Flank|EGFR_uc003tqj.2_5'Flank|EGFR_uc010kzg.1_5'Flank	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55309641	55309641	+	IGR	DEL	T	-	-	rs60403897		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55309641delT								EGFR (34611 upstream) : LANCL2 (123500 downstream)																																			---	---	---	---
LANCL2	55915	broad.mit.edu	37	7	55438940	55438941	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55438940_55438941insT	uc003tqp.2	+							NM_018697	NP_061167			LanC lantibiotic synthetase component C-like 2						negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)															---	---	---	---
PSPH	5723	broad.mit.edu	37	7	56094332	56094333	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56094332_56094333delAA	uc003trg.2	-						PSPH_uc003trh.2_Intron|PSPH_uc003tri.2_Intron|PSPH_uc003trj.2_Intron	NM_004577	NP_004568			phosphoserine phosphatase						L-serine biosynthetic process	cytoplasm	calcium ion binding|magnesium ion binding|phosphoserine phosphatase activity|protein homodimerization activity			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56545058	56545058	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56545058delA								PSPH (360968 upstream) : DKFZp434L192 (18858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56699457	56699457	+	IGR	DEL	A	-	-	rs78077053		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56699457delA								DKFZp434L192 (134480 upstream) : ZNF479 (487871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57625723	57625723	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57625723delA								ZNF716 (92458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57638257	57638258	+	IGR	INS	-	T	T	rs148699362		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57638257_57638258insT								ZNF716 (104992 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57768869	57768869	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57768869delT								ZNF716 (235604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57910844	57910844	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57910844delA								ZNF716 (377579 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61788545	61788546	+	IGR	INS	-	ATTGAATGGA	ATTGAATGGA	rs58897813		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61788545_61788546insATTGAATGGA								None (None upstream) : LOC643955 (963126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61823842	61823843	+	IGR	INS	-	T	T	rs113647649		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61823842_61823843insT								None (None upstream) : LOC643955 (927829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62027477	62027477	+	IGR	DEL	C	-	-	rs76773165		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62027477delC								None (None upstream) : LOC643955 (724195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62028591	62028592	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62028591_62028592insA								None (None upstream) : LOC643955 (723080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62191720	62191720	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62191720delA								None (None upstream) : LOC643955 (559952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62984752	62984752	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62984752delA								LOC100287704 (172601 upstream) : ZNF727 (521069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63032004	63032005	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63032004_63032005delAA								LOC100287704 (219853 upstream) : ZNF727 (473816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63857702	63857702	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63857702delA								ZNF679 (130402 upstream) : ZNF680 (122553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64426891	64426891	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64426891delT								ZNF273 (34938 upstream) : ZNF117 (7939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64570704	64570704	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64570704delC								ZNF117 (103583 upstream) : INTS4L1 (30899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65271987	65271988	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65271987_65271988delAG								CCT6P1 (43326 upstream) : VKORC1L1 (66269 downstream)																																			---	---	---	---
RABGEF1	27342	broad.mit.edu	37	7	66177811	66177811	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66177811delT	uc003tvf.2	+						RABGEF1_uc003tvg.2_Intron	NM_014504	NP_055319			RAB guanine nucleotide exchange factor (GEF) 1						endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66551452	66551453	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66551452_66551453delGA	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	67799304	67799306	+	IGR	DEL	TTT	-	-	rs36042868		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67799304_67799306delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68206477	68206477	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68206477delC								None (None upstream) : AUTS2 (857428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68223724	68223727	+	IGR	DEL	GAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68223724_68223727delGAAG								None (None upstream) : AUTS2 (840178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68964783	68964783	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68964783delT								None (None upstream) : AUTS2 (99122 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69216370	69216370	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69216370delG	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69253903	69253904	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69253903_69253904insG	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69729697	69729697	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69729697delT	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70601781	70601781	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70601781delT	uc003tvy.2	+							NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70786948	70786948	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786948delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	71186480	71186480	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71186480delT								WBSCR17 (7897 upstream) : CALN1 (57997 downstream)																																			---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71695496	71695496	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71695496delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71806535	71806538	+	Intron	DEL	AAAT	-	-	rs149774149		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71806535_71806538delAAAT	uc003twb.3	-						CALN1_uc003twc.3_Intron	NM_031468	NP_113656			calneuron 1 isoform 1							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72195500	72195500	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72195500delA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron|TYW1B_uc011kek.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72869194	72869194	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72869194delT	uc003tyc.2	-							NM_032408	NP_115784			bromodomain adjacent to zinc finger domain, 1B						ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
MLXIPL	51085	broad.mit.edu	37	7	73010315	73010315	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73010315delG	uc003tyn.1	-						MLXIPL_uc003tyj.1_Intron|MLXIPL_uc003tyk.1_Intron|MLXIPL_uc003tyl.1_Intron|MLXIPL_uc003tym.1_Intron|MLXIPL_uc003tyo.1_Intron|MLXIPL_uc003typ.1_Intron	NM_032951	NP_116569			Williams Beuren syndrome chromosome region 14						anatomical structure morphogenesis|energy reserve metabolic process|glucose mediated signaling pathway|intracellular protein kinase cascade|negative regulation of cell cycle arrest|negative regulation of oxidative phosphorylation|negative regulation of peptidyl-serine phosphorylation|positive regulation of cell proliferation|positive regulation of fatty acid biosynthetic process|positive regulation of glycolysis|positive regulation of transcription from RNA polymerase II promoter|triglyceride homeostasis	cytosol|transcription factor complex	carbohydrate response element binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
WBSCR22	114049	broad.mit.edu	37	7	73112327	73112327	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73112327delA	uc003tyt.2	+	12					WBSCR22_uc003tyu.2_3'UTR|WBSCR22_uc003tyv.2_3'UTR|WBSCR22_uc003tyw.1_Intron	NM_017528	NP_059998			Williams Beuren syndrome chromosome region 22							nucleus	methyltransferase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
ELN	2006	broad.mit.edu	37	7	73466911	73466911	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73466911delA	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224			elastin isoform a precursor						blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73931346	73931347	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73931346_73931347insT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74073725	74073725	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74073725delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
WBSCR16	81554	broad.mit.edu	37	7	74470293	74470293	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74470293delT	uc003ubr.2	-						WBSCR16_uc010lca.2_Intron|WBSCR16_uc010lcb.1_Intron	NM_030798	NP_110425			Williams-Beuren syndrome chromosome region 16												0																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75096018	75096018	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75096018delA	uc003udk.3	-						POM121C_uc003udl.1_Intron	NM_001099415	NP_001092885			POM121 membrane glycoprotein (rat)-like						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75777783	75777784	+	IGR	INS	-	G	G	rs141337270	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75777783_75777784insG								MDH2 (81855 upstream) : SRRM3 (53432 downstream)																																			---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76627201	76627202	+	Intron	INS	-	TGT	TGT	rs138040684		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76627201_76627202insTGT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76655246	76655246	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76655246delA	uc011kgn.1	+											Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77164106	77164107	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77164106_77164107delTT	uc003ugh.2	+							NM_002835	NP_002826			protein tyrosine phosphatase, non-receptor type							soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77652725	77652725	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77652725delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77973759	77973759	+	Intron	DEL	T	-	-	rs75038338		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77973759delT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.1_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron|RPL13AP17_uc010ldz.2_5'Flank	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78374849	78374849	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78374849delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc011kgr.1_Intron|MAGI2_uc011kgs.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	79316815	79316816	+	IGR	DEL	TG	-	-	rs111943642		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79316815_79316816delTG								MAGI2 (233925 upstream) : GNAI1 (447324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79905748	79905748	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79905748delA								GNAI1 (57023 upstream) : CD36 (93143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	81170130	81170130	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81170130delT								SEMA3C (618455 upstream) : HGF (161315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	81303878	81303878	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81303878delT	uc003uhk.1	-											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	82186387	82186387	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82186387delA								CACNA2D1 (113356 upstream) : PCLO (196934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	82219160	82219160	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82219160delT								CACNA2D1 (146129 upstream) : PCLO (164161 downstream)																																			---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82622885	82622885	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82622885delT	uc003uhx.2	-						PCLO_uc003uhv.2_Intron	NM_033026	NP_149015			piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
SEMA3A	10371	broad.mit.edu	37	7	83773011	83773011	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83773011delA	uc003uhz.2	-							NM_006080	NP_006071			semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4																		---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86554624	86554624	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86554624delA	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron|KIAA1324L_uc003uie.2_Intron	NM_001142749	NP_001136221			hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	86746275	86746275	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86746275delG								KIAA1324L (57261 upstream) : DMTF1 (35402 downstream)																																			---	---	---	---
DMTF1	9988	broad.mit.edu	37	7	86823978	86823978	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86823978delT	uc003uih.2	+						DMTF1_uc003uii.2_Intron|DMTF1_uc003uij.2_Intron|DMTF1_uc011khb.1_Intron|DMTF1_uc003uik.2_Intron|DMTF1_uc003uil.2_Intron|DMTF1_uc003uin.2_Intron	NM_001142327	NP_001135799			cyclin D binding myb-like transcription factor 1						cell cycle	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(14;0.0058)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	87987859	87987863	+	IGR	DEL	AAAAA	-	-	rs9692222		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87987859_87987863delAAAAA								STEAP4 (51650 upstream) : ZNF804B (400890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	88010958	88010958	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88010958delT								STEAP4 (74749 upstream) : ZNF804B (377795 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88608116	88608117	+	Intron	INS	-	CCTC	CCTC	rs147121548	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88608116_88608117insCCTC	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89381581	89381581	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89381581delA								ZNF804B (415237 upstream) : DPY19L2P4 (367133 downstream)																																			---	---	---	---
DPY19L2P4	442523	broad.mit.edu	37	7	89751362	89751363	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89751362_89751363insT	uc003ujw.1	+							NR_003551				Homo sapiens dpy-19-like 2 pseudogene 4 (C. elegans), mRNA (cDNA clone IMAGE:5295327).												0																		---	---	---	---
STEAP2	261729	broad.mit.edu	37	7	89859613	89859613	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89859613delA	uc003ujz.2	+						STEAP2_uc010len.2_Intron|STEAP2_uc003uka.2_Intron|STEAP2_uc003ukb.2_Intron|STEAP2_uc003ukc.2_Intron|STEAP2_uc003ukd.2_Intron	NM_152999	NP_694544			six transmembrane epithelial antigen of the						electron transport chain|endocytosis|Golgi to plasma membrane transport|ion transport|iron ion homeostasis|regulated secretory pathway|response to hormone stimulus	cytosol|early endosome|endosome membrane|integral to Golgi membrane|plasma membrane|trans-Golgi network transport vesicle|vesicular fraction	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity|transporter activity			ovary(2)	2	all_hematologic(106;0.112)																	---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90097095	90097104	+	Intron	DEL	TGTTTTGTTT	-	-	rs67247028		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90097095_90097104delTGTTTTGTTT	uc003ukt.1	+							NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90133635	90133635	+	Intron	DEL	A	-	-	rs79106222		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90133635delA	uc003ukt.1	+							NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90376819	90376819	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90376819delT	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90742138	90742139	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90742138_90742139delGT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	91009609	91009610	+	IGR	DEL	AC	-	-	rs66827661		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91009609_91009610delAC								FZD1 (111478 upstream) : MTERF (421850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91516140	91516141	+	IGR	INS	-	CCTCTC	CCTCTC	rs10628334		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91516140_91516141insCCTCTC								MTERF (6124 upstream) : AKAP9 (54048 downstream)																																			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91697914	91697914	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91697914delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_5'Flank	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
KRIT1	889	broad.mit.edu	37	7	91864653	91864653	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91864653delA	uc003ulq.1	-						KRIT1_uc010lev.1_Intron|KRIT1_uc003ulr.1_Intron|KRIT1_uc003uls.1_Intron|KRIT1_uc003ult.1_Intron|KRIT1_uc003ulu.1_Intron|KRIT1_uc003ulv.1_Intron	NM_194456	NP_919438			krev interaction trapped 1 isoform 1						angiogenesis|cell redox homeostasis|negative regulation of angiogenesis|negative regulation of endothelial cell apoptosis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|regulation of establishment of cell polarity|small GTPase mediated signal transduction	cell-cell junction|cytoskeleton	protein binding|small GTPase regulator activity			ovary(2)|lung(1)	3	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)											Familial_Cerebral_Cavernous_Angioma				---	---	---	---
C7orf64	84060	broad.mit.edu	37	7	92166147	92166147	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92166147delT	uc003ulz.2	+						C7orf64_uc003uma.2_3'UTR|MGC16142_uc011khv.1_5'Flank	NM_032120	NP_115496			hypothetical protein LOC84060								nucleotide binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	92694020	92694021	+	IGR	INS	-	C	C	rs149998373	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92694020_92694021insC								CDK6 (228079 upstream) : SAMD9 (34811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	92723439	92723440	+	IGR	DEL	TG	-	-	rs72422892		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92723439_92723440delTG								CDK6 (257498 upstream) : SAMD9 (5392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	95080334	95080334	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95080334delT								PON2 (15950 upstream) : ASB4 (34950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96115478	96115479	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96115478_96115479delTT	uc003uoh.1	-						uc011kil.1_Intron					RecName: Full=Putative uncharacterized protein FLJ42280;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96217666	96217679	+	IGR	DEL	ACACACACACACAC	-	-	rs71716104		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96217666_96217679delACACACACACACAC								SLC25A13 (266207 upstream) : SHFM1 (84558 downstream)																																			---	---	---	---
DLX5	1749	broad.mit.edu	37	7	96654673	96654676	+	5'Flank	DEL	TTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96654673_96654676delTTTT	uc003uon.2	-						DLX5_uc011kim.1_5'Flank	NM_005221	NP_005212			distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	97370467	97370467	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97370467delA								TAC1 (685 upstream) : ASNS (110976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97624103	97624104	+	IGR	DEL	AA	-	-	rs113620608		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97624103_97624104delAA								OCM2 (4687 upstream) : LMTK2 (112093 downstream)																																			---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97942070	97942071	+	Intron	INS	-	TG	TG	rs145529341	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97942070_97942071insTG	uc003upj.2	-							NM_018842	NP_061330			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98118662	98118662	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98118662delA								BAIAP2L1 (88235 upstream) : NPTX2 (127935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98385782	98385782	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98385782delT								NPTX2 (126601 upstream) : TMEM130 (58330 downstream)																																			---	---	---	---
MYH16	84176	broad.mit.edu	37	7	98893001	98893001	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98893001delA	uc003upw.2	+							NR_002147				SubName: Full=cDNA: FLJ22037 fis, clone HEP08868; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	99178594	99178594	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99178594delT								ZNF655 (4520 upstream) : ZNF498 (35977 downstream)																																			---	---	---	---
CYP3A5	1577	broad.mit.edu	37	7	99271824	99271824	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99271824delC	uc003urq.2	-						ZNF498_uc003urn.2_Intron|CYP3A5_uc003urr.2_Intron|CYP3A5_uc011kiy.1_Intron|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron|CYP3A5_uc003urt.2_Intron	NM_000777	NP_000768			cytochrome P450, family 3, subfamily A,						alkaloid catabolic process|drug catabolic process|oxidative demethylation|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				Alfentanil(DB00802)|Clopidogrel(DB00758)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Indinavir(DB00224)|Irinotecan(DB00762)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Mephenytoin(DB00532)|Midazolam(DB00683)|Mifepristone(DB00834)|Phenytoin(DB00252)|Quinine(DB00468)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Troleandomycin(DB01361)|Verapamil(DB00661)|Vincristine(DB00541)													---	---	---	---
ZNF3	7551	broad.mit.edu	37	7	99673916	99673917	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99673916_99673917delTT	uc003usq.2	-						ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Intron|ZNF3_uc010lgj.2_Intron|ZNF3_uc003uss.2_Intron|ZNF3_uc003ust.3_Intron	NM_032924	NP_116313			zinc finger protein 3 isoform 2						cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99687409	99687409	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99687409delA	uc003usu.2	+						COPS6_uc011kjf.1_Frame_Shift_Del_p.*125fs	NM_006833	NP_006824			COP9 signalosome subunit 6						cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99687973	99687974	+	Intron	DEL	AA	-	-	rs75914464		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99687973_99687974delAA	uc003usu.2	+							NM_006833	NP_006824			COP9 signalosome subunit 6						cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99782538	99782538	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99782538delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
SPDYE3	441272	broad.mit.edu	37	7	99911897	99911897	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99911897delA	uc003uug.1	+							NM_001004351	NP_001004351			speedy homolog E3												0																		---	---	---	---
PILRB	29990	broad.mit.edu	37	7	99950298	99950298	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99950298delG	uc003uuk.2	+						PILRB_uc003uul.2_5'UTR|PILRB_uc003uum.1_Intron	NM_013440	NP_038468			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)																	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100342493	100342493	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100342493delT	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron	NM_003386	NP_003377			zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
TRIP6	7205	broad.mit.edu	37	7	100470475	100470475	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100470475delT	uc003uww.2	+						SRRT_uc010lhl.1_5'Flank|SRRT_uc003uwy.2_5'Flank|SRRT_uc003uxa.2_5'Flank|SRRT_uc003uwz.2_5'Flank	NM_003302	NP_003293			thyroid receptor-interacting protein 6						focal adhesion assembly|positive regulation of cell migration|regulation of transcription, DNA-dependent|release of cytoplasmic sequestered NF-kappaB|transcription, DNA-dependent	cytoplasm|cytoskeleton|focal adhesion|nucleus	identical protein binding|interleukin-1 receptor binding|kinase binding|thyroid hormone receptor binding|zinc ion binding			central_nervous_system(2)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
MYL10	93408	broad.mit.edu	37	7	101259142	101259142	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101259142delT	uc003uyr.2	-							NM_138403	NP_612412			myosin, light chain 10, regulatory							mitochondrion	calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	101372321	101372321	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101372321delT								MYL10 (99745 upstream) : CUX1 (86971 downstream)																																			---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101803458	101803460	+	Intron	DEL	AAA	-	-	rs71806379		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101803458_101803460delAAA	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			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																		---	---	---	---
LRWD1	222229	broad.mit.edu	37	7	102107608	102107609	+	Intron	DEL	GT	-	-	rs71922776		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102107608_102107609delGT	uc003uzn.2	+						ALKBH4_uc003uzl.2_5'Flank|ALKBH4_uc003uzm.2_5'Flank|LRWD1_uc003uzo.2_Intron	NM_152892	NP_690852			leucine-rich repeats and WD repeat domain						chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102627428	102627428	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102627428delA	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|FBXL13_uc003vav.2_Intron	NM_145032	NP_659469			F-box and leucine-rich repeat protein 13 isoform												0																		---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104420362	104420363	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104420362_104420363delTT	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	104604738	104604739	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104604738_104604739delTG								LOC723809 (37646 upstream) : LOC100216545 (46250 downstream)																																			---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104884188	104884188	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104884188delA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182691	NP_872633			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105302458	105302461	+	Intron	DEL	TTTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105302458_105302461delTTTC	uc003vde.2	-						ATXN7L1_uc003vdf.2_Intron|ATXN7L1_uc003vdh.3_Intron|ATXN7L1_uc011klr.1_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105772458	105772458	+	IGR	DEL	A	-	-	rs75809190		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105772458delA								SYPL1 (19401 upstream) : NAMPT (116276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106349101	106349101	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106349101delG	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
BCAP29	55973	broad.mit.edu	37	7	107262674	107262674	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107262674delA	uc003vej.2	+	8					BCAP29_uc011kly.1_3'UTR|BCAP29_uc011kma.1_3'UTR	NM_018844	NP_061332			B-cell receptor-associated protein BAP29 isoform						apoptosis|intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane				large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	107368057	107368057	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107368057delT								SLC26A4 (9807 upstream) : CBLL1 (16222 downstream)																																			---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107832102	107832102	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107832102delT	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209			neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108745043	108745043	+	IGR	DEL	A	-	-	rs77304252		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108745043delA								C7orf66 (220406 upstream) : EIF3IP1 (854241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109187538	109187538	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109187538delT								C7orf66 (662901 upstream) : EIF3IP1 (411746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109625943	109625943	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109625943delA								EIF3IP1 (25673 upstream) : IMMP2L (677167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110285973	110285973	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110285973delA								EIF3IP1 (685703 upstream) : IMMP2L (17137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110302574	110302574	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110302574delA								EIF3IP1 (702304 upstream) : IMMP2L (536 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110703297	110703297	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110703297delG	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111383766	111383766	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111383766delG	uc003vfx.2	-						DOCK4_uc011kml.1_Intron|DOCK4_uc011kmm.1_Intron|DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.2_Intron	NM_014705	NP_055520			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)																---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111423075	111423075	+	Intron	DEL	A	-	-	rs35825505		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111423075delA	uc003vfx.2	-						DOCK4_uc011kml.1_Intron|DOCK4_uc011kmm.1_Intron|DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.2_Intron	NM_014705	NP_055520			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)																---	---	---	---
TMEM168	64418	broad.mit.edu	37	7	112415656	112415656	+	Intron	DEL	A	-	-	rs10256800	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112415656delA	uc003vgn.2	-						TMEM168_uc010lju.2_Intron|TMEM168_uc011kmr.1_Intron	NM_022484	NP_071929			transmembrane protein 168							integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	114972522	114972523	+	IGR	INS	-	GT	GT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114972522_114972523insGT								MDFIC (313259 upstream) : TFEC (602679 downstream)																																			---	---	---	---
ST7	7982	broad.mit.edu	37	7	116747998	116747998	+	Intron	DEL	C	-	-	rs11764503	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116747998delC	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	NM_021908	NP_068708			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)														---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117200700	117200700	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117200700delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron|CFTR_uc003vje.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
Unknown	0	broad.mit.edu	37	7	117936654	117936654	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117936654delT								ANKRD7 (53872 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118517115	118517115	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118517115delA								ANKRD7 (634333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	120566361	120566361	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120566361delT								TSPAN12 (68184 upstream) : ING3 (24456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121435728	121435728	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121435728delT								FAM3C (399306 upstream) : PTPRZ1 (77431 downstream)																																			---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121616732	121616732	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121616732delT	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron	NM_002851	NP_002842			protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122000789	122000789	+	Intron	DEL	T	-	-	rs66913253		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122000789delT	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			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																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122204902	122204907	+	Intron	DEL	CACACA	-	-	rs71161307		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122204902_122204907delCACACA	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	122647940	122647940	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122647940delG								TAS2R16 (12186 upstream) : SLC13A1 (105649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	122904091	122904092	+	IGR	DEL	TT	-	-	rs10556500		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122904091_122904092delTT								SLC13A1 (64066 upstream) : IQUB (188146 downstream)																																			---	---	---	---
WASL	8976	broad.mit.edu	37	7	123388031	123388031	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123388031delG	uc003vkz.2	-						uc003vla.2_5'Flank	NM_003941	NP_003932			Wiskott-Aldrich syndrome gene-like protein						actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|cytosol|nucleolus|plasma membrane	actin binding|small GTPase regulator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	124191714	124191714	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124191714delA								TMEM229A (518191 upstream) : GPR37 (194402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124250068	124250068	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124250068delG								TMEM229A (576545 upstream) : GPR37 (136048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125164590	125164591	+	IGR	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125164590_125164591delGA								POT1 (594553 upstream) : GRM8 (914061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125588300	125588301	+	IGR	INS	-	GAAG	GAAG	rs10215505	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125588300_125588301insGAAG								None (None upstream) : GRM8 (490351 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126759571	126759572	+	Intron	DEL	TG	-	-	rs71977682		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126759571_126759572delTG	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
SND1	27044	broad.mit.edu	37	7	127302170	127302170	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127302170delA	uc003vmi.2	+							NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SND1	27044	broad.mit.edu	37	7	127309055	127309056	+	Intron	DEL	TT	-	-	rs72181011		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127309055_127309056delTT	uc003vmi.2	+							NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SND1	27044	broad.mit.edu	37	7	127481321	127481321	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127481321delT	uc003vmi.2	+						SND1_uc010lle.2_Intron	NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	127794664	127794664	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127794664delA								SND1 (62006 upstream) : MIR129-1 (53261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128148560	128148560	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128148560delA								METTL2B (5583 upstream) : FLJ45340 (132735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128162511	128162515	+	IGR	DEL	TTTCT	-	-	rs113681597		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128162511_128162515delTTTCT								METTL2B (19534 upstream) : FLJ45340 (118780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128186134	128186134	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128186134delT								METTL2B (43157 upstream) : FLJ45340 (95161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128703727	128703728	+	IGR	DEL	AA	-	-	rs75339887		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128703727_128703728delAA								TPI1P2 (6434 upstream) : LOC407835 (62597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	128815756	128815757	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128815756_128815757insC								TSPAN33 (7085 upstream) : SMO (12956 downstream)																																			---	---	---	---
TSGA14	95681	broad.mit.edu	37	7	130039661	130039662	+	Intron	DEL	AA	-	-	rs34927892		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130039661_130039662delAA	uc003vpz.2	-						TSGA14_uc003vpy.2_Intron|TSGA14_uc010lmf.2_Intron|TSGA14_uc003vqa.2_Intron|TSGA14_uc011kpg.1_Intron	NM_018718	NP_061188			testis specific, 14						G2/M transition of mitotic cell cycle	centrosome|cytosol					0	Melanoma(18;0.0435)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	130605177	130605177	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130605177delT	uc003vql.1	+											full-length cDNA clone CS0DI009YJ20 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131122491	131122491	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131122491delT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131134410	131134411	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131134410_131134411delTT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131958764	131958764	+	Intron	DEL	A	-	-	rs34036409		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131958764delA	uc003vra.3	-							NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132520880	132520882	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132520880_132520882delTTT	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron	NM_017812	NP_060282			coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0																		---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133568074	133568078	+	Intron	DEL	TTTTT	-	-	rs72085311		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133568074_133568078delTTTTT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133674291	133674291	+	Intron	DEL	A	-	-	rs34032888		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133674291delA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron|EXOC4_uc011kpq.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	133809040	133809041	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133809040_133809041insA								EXOC4 (58529 upstream) : LRGUK (3064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	134118183	134118183	+	IGR	DEL	A	-	-	rs72330328		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134118183delA								SLC35B4 (116356 upstream) : AKR1B1 (8924 downstream)																																			---	---	---	---
SLC13A4	26266	broad.mit.edu	37	7	135399441	135399442	+	Intron	INS	-	C	C	rs114438497	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135399441_135399442insC	uc003vta.2	-						SLC13A4_uc003vtb.2_Intron|SLC13A4_uc003vtc.1_Intron	NM_012450	NP_036582			solute carrier family 13 (sodium/sulfate							integral to plasma membrane	sodium:sulfate symporter activity				0																		---	---	---	---
FAM180A	389558	broad.mit.edu	37	7	135429842	135429842	+	Intron	DEL	T	-	-	rs35535059		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135429842delT	uc003vtd.2	-						FAM180A_uc010lmt.2_Intron|FAM180A_uc010lmu.2_Intron	NM_205855	NP_995327			hypothetical protein LOC389558 precursor							extracellular region				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	136298732	136298733	+	IGR	INS	-	T	T	rs147412675	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136298732_136298733insT								LUZP6 (636528 upstream) : CHRM2 (254666 downstream)																																			---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137198583	137198583	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137198583delT	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	138039764	138039764	+	IGR	DEL	T	-	-	rs357408	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138039764delT								AKR1D1 (236714 upstream) : TRIM24 (105315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	138809125	138809125	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138809125delA								ZC3HAV1 (14660 upstream) : TTC26 (9365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	138895327	138895327	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138895327delA								TTC26 (20777 upstream) : UBN2 (20904 downstream)																																			---	---	---	---
LUC7L2	51631	broad.mit.edu	37	7	139094952	139094952	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139094952delA	uc003vux.2	+						LUC7L2_uc011kqs.1_Intron|LUC7L2_uc011kqt.1_Intron|LUC7L2_uc003vuy.2_Intron|LUC7L2_uc003vuz.1_Intron|LUC7L2_uc003vva.2_Intron	NM_016019	NP_057103			LUC7-like 2								enzyme binding|metal ion binding				0	Melanoma(164;0.242)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	139132147	139132148	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139132147_139132148delTC								LUC7L2 (23949 upstream) : KLRG2 (5941 downstream)																																			---	---	---	---
CLEC2L	154790	broad.mit.edu	37	7	139209325	139209329	+	Intron	DEL	AGGGC	-	-	rs72035971		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139209325_139209329delAGGGC	uc010lnd.2	+							NM_001080511	NP_001073980			C-type lectin domain family 2, member L							integral to membrane	sugar binding				0	Melanoma(164;0.233)																	---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139309227	139309228	+	Intron	DEL	TT	-	-	rs71170905		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139309227_139309228delTT	uc003vvf.3	-						HIPK2_uc003vvd.3_Intron	NM_022740	NP_073577			homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139483151	139483152	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139483151_139483152delAA	uc003vvh.2	+						TBXAS1_uc010lne.2_Intron	NM_001130966	NP_001124438			thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)																	---	---	---	---
PARP12	64761	broad.mit.edu	37	7	139738671	139738671	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139738671delA	uc003vvl.1	-						PARP12_uc003vvk.1_Intron|PARP12_uc010lnf.1_Intron	NM_022750	NP_073587			poly ADP-ribose polymerase 12							nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
PARP12	64761	broad.mit.edu	37	7	139758300	139758300	+	Intron	DEL	A	-	-	rs75849660		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139758300delA	uc003vvl.1	-						PARP12_uc003vvk.1_5'Flank|PARP12_uc010lnf.1_Intron	NM_022750	NP_073587			poly ADP-ribose polymerase 12							nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	139972021	139972022	+	IGR	DEL	AA	-	-	rs35182412		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139972021_139972022delAA								LOC100134229 (92582 upstream) : SLC37A3 (61532 downstream)																																			---	---	---	---
BRAF	673	broad.mit.edu	37	7	140507736	140507736	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140507736delA	uc003vwc.3	-							NM_004333	NP_004324			B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	140782015	140782015	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140782015delC								MRPS33 (67234 upstream) : AGK (469063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	140868572	140868572	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140868572delA								MRPS33 (153791 upstream) : AGK (382506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	142465101	142465102	+	Intron	INS	-	AG	AG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142465101_142465102insAG	uc011krr.1	+						uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|uc003wan.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142597211	142597211	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142597211delT								TRPV6 (13734 upstream) : TRPV5 (8437 downstream)																																			---	---	---	---
FAM115C	285966	broad.mit.edu	37	7	143417881	143417881	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143417881delT	uc003wdf.2	+						FAM115C_uc003wdg.2_Intron|FAM115C_uc011ktk.1_Intron|FAM115C_uc003wdh.2_Intron|FAM115C_uc011ktm.1_Intron|uc011ktn.1_Intron|uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|FAM115C_uc011ktt.1_Intron|FAM115C_uc003wdi.1_Intron	NM_001130025	NP_001123497			hypothetical protein LOC285966 isoform A												0																		---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144437377	144437377	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144437377delA	uc003weq.2	-						TPK1_uc003wep.2_5'Flank|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	144628479	144628479	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144628479delT								TPK1 (95333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145557011	145557011	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145557011delA								None (None upstream) : CNTNAP2 (256442 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146320076	146320076	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146320076delA	uc003weu.1	+							NM_014141	NP_054860			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)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147343680	147343680	+	Intron	DEL	T	-	-	rs34100873		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147343680delT	uc003weu.1	+							NM_014141	NP_054860			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)												HNSCC(39;0.1)			---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148538274	148538274	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148538274delT	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447			enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148556598	148556600	+	Intron	DEL	AAC	-	-	rs72092401		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148556598_148556600delAAC	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447			enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
ZNF425	155054	broad.mit.edu	37	7	148819798	148819798	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148819798delT	uc003wfj.2	-							NM_001001661	NP_001001661			zinc finger protein 425						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)															---	---	---	---
LRRC61	65999	broad.mit.edu	37	7	150012920	150012920	+	Intron	DEL	T	-	-	rs111902608		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150012920delT	uc003wgv.2	+							NM_023942	NP_076431			leucine rich repeat containing 61												0			OV - Ovarian serous cystadenocarcinoma(82;0.011)															---	---	---	---
GIMAP8	155038	broad.mit.edu	37	7	150148464	150148476	+	Intron	DEL	GGGTTGAATGGCA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150148464_150148476delGGGTTGAATGGCA	uc003whj.2	+							NM_175571	NP_783161			GTPase, IMAP family member 8							endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)														---	---	---	---
GIMAP8	155038	broad.mit.edu	37	7	150168925	150168926	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150168925_150168926delAA	uc003whj.2	+							NM_175571	NP_783161			GTPase, IMAP family member 8							endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)														---	---	---	---
KCNH2	3757	broad.mit.edu	37	7	150656368	150656369	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150656368_150656369insT	uc003wic.2	-						KCNH2_uc011kux.1_Intron|KCNH2_uc003wie.2_Intron	NM_000238	NP_000229			voltage-gated potassium channel, subfamily H,						blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)													---	---	---	---
ATG9B	285973	broad.mit.edu	37	7	150719079	150719080	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150719079_150719080delTT	uc011kvc.1	-						ATG9B_uc003wig.3_Intron	NM_173681	NP_775952			ATG9 autophagy related 9 homolog B						autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ATG9B	285973	broad.mit.edu	37	7	150719924	150719925	+	Intron	DEL	AA	-	-	rs5888425		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150719924_150719925delAA	uc011kvc.1	-						ATG9B_uc003wig.3_Intron	NM_173681	NP_775952			ATG9 autophagy related 9 homolog B						autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	151010529	151010530	+	IGR	INS	-	GT	GT	rs145069407	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151010529_151010530insGT								SMARCD3 (36298 upstream) : NUB1 (28328 downstream)																																			---	---	---	---
GALNTL5	168391	broad.mit.edu	37	7	151656318	151656318	+	Intron	DEL	T	-	-	rs141762572		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151656318delT	uc003wkp.2	+						GALNTL5_uc003wkq.2_Intron	NM_145292	NP_660335			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)														---	---	---	---
GALNTL5	168391	broad.mit.edu	37	7	151716998	151716998	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151716998delA	uc003wkp.2	+	9					GALNTL5_uc003wkq.2_3'UTR|GALNTL5_uc003wkr.2_RNA|GALNTL5_uc003wks.2_RNA|GALNTL5_uc010lqf.2_3'UTR	NM_145292	NP_660335			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152103923	152103924	+	Intron	INS	-	G	G	rs62845260		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152103923_152103924insG	uc003wla.2	-							NM_170606	NP_733751			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)				N		medulloblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	7	152849671	152849672	+	IGR	INS	-	A	A	rs144050610	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152849671_152849672insA								ACTR3B (297208 upstream) : DPP6 (734747 downstream)																																			---	---	---	---
INSIG1	3638	broad.mit.edu	37	7	155093907	155093907	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155093907delT	uc003wly.2	+						INSIG1_uc011kvu.1_Intron|INSIG1_uc003wlz.2_Intron	NM_005542	NP_005533			insulin induced gene 1 isoform 1						cell proliferation|ER-nuclear sterol response pathway	endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155585275	155585276	+	IGR	DEL	CT	-	-	rs111286890		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155585275_155585276delCT								RBM33 (11096 upstream) : SHH (7460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155613989	155613989	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155613989delT								SHH (9022 upstream) : C7orf4 (719196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155907140	155907140	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155907140delA								SHH (302173 upstream) : C7orf4 (426045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155997691	155997691	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155997691delC								SHH (392724 upstream) : C7orf4 (335494 downstream)																																			---	---	---	---
UBE3C	9690	broad.mit.edu	37	7	156991227	156991227	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156991227delT	uc010lqs.2	+						UBE3C_uc003wng.2_Intron	NM_014671	NP_055486			ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)														---	---	---	---
UBE3C	9690	broad.mit.edu	37	7	157046464	157046465	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157046464_157046465delCT	uc010lqs.2	+						UBE3C_uc003wni.3_Intron	NM_014671	NP_055486			ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157921105	157921105	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157921105delT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			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)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157928431	157928432	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157928431_157928432insT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			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)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157995918	157995928	+	Intron	DEL	AAAAAAAAAAA	-	-	rs72286934		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157995918_157995928delAAAAAAAAAAA	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158400681	158400681	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158400681delA								PTPRN2 (20199 upstream) : NCAPG2 (23322 downstream)																																			---	---	---	---
C8orf42	157695	broad.mit.edu	37	8	446071	446071	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:446071delA	uc003wpd.2	-						C8orf42_uc011kwg.1_Intron	NM_175075	NP_778250			hypothetical protein LOC157695												0		Ovarian(12;0.0481)|Colorectal(14;0.0815)|Hepatocellular(245;0.0968)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;5.16e-14)|OV - Ovarian serous cystadenocarcinoma(5;7.35e-07)|BRCA - Breast invasive adenocarcinoma(11;4.17e-06)|COAD - Colon adenocarcinoma(149;0.0255)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1177502	1177502	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1177502delT								ERICH1 (496276 upstream) : DLGAP2 (272067 downstream)																																			---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1623995	1623996	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1623995_1623996delTT	uc003wpl.2	+						DLGAP2_uc003wpm.2_Intron	NM_004745	NP_004736			discs large-associated protein 2						neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
CLN8	2055	broad.mit.edu	37	8	1720793	1720794	+	Intron	DEL	TG	-	-	rs71686906		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1720793_1720794delTG	uc003wpo.3	+							NM_018941	NP_061764			ceroid-lipofuscinosis, neuronal 8						cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)														---	---	---	---
CLN8	2055	broad.mit.edu	37	8	1724686	1724687	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1724686_1724687delAC	uc003wpo.3	+							NM_018941	NP_061764			ceroid-lipofuscinosis, neuronal 8						cell death|ceramide biosynthetic process|cholesterol metabolic process|lipid transport|negative regulation of proteolysis|phospholipid metabolic process	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.67e-05)|READ - Rectum adenocarcinoma(644;0.0913)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1958441	1958441	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1958441delT								KBTBD11 (3333 upstream) : MYOM2 (34717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2160893	2160894	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2160893_2160894delTC								MYOM2 (67514 upstream) : CSMD1 (631982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2224942	2224943	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2224942_2224943delAA								MYOM2 (131563 upstream) : CSMD1 (567933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2233184	2233185	+	IGR	INS	-	A	A	rs146202510	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2233184_2233185insA								MYOM2 (139805 upstream) : CSMD1 (559691 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3360526	3360526	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3360526delG	uc011kwk.1	-							NM_033225	NP_150094			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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	4496774	4496777	+	Intron	DEL	TTTT	-	-	rs143203307		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4496774_4496777delTTTT	uc011kwk.1	-							NM_033225	NP_150094			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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	4671719	4671720	+	Intron	DEL	TG	-	-	rs35824182		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4671719_4671720delTG	uc011kwk.1	-							NM_033225	NP_150094			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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	4760943	4760943	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4760943delT	uc011kwk.1	-							NM_033225	NP_150094			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	5466120	5466121	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5466120_5466121delTG								CSMD1 (613792 upstream) : MCPH1 (798000 downstream)																																			---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6601294	6601294	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6601294delT	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
DEFB1	1672	broad.mit.edu	37	8	6731668	6731669	+	Intron	DEL	CG	-	-	rs71214966		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6731668_6731669delCG	uc003wqs.2	-							NM_005218	NP_005209			defensin, beta 1 preproprotein						chemotaxis|defense response to bacterium|G-protein coupled receptor protein signaling pathway|innate immune response	extracellular region					0			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	6964631	6964650	+	IGR	DEL	CATCCATCCATGCATCCATC	-	-	rs59555794	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6964631_6964650delCATCCATCCATGCATCCATC								DEFA5 (50372 upstream) : LOC349196 (153492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8367919	8367920	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8367919_8367920delAA								SGK223 (128662 upstream) : CLDN23 (191746 downstream)																																			---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8715270	8715270	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8715270delA	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
ERI1	90459	broad.mit.edu	37	8	8884658	8884659	+	Intron	DEL	TA	-	-	rs140641752	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8884658_8884659delTA	uc011kwu.1	+						ERI1_uc003wsk.2_Intron	NM_153332	NP_699163			three prime histone mRNA exonuclease 1						gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	9312815	9312815	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9312815delA								PPP1R3B (303731 upstream) : TNKS (100630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9747184	9747185	+	IGR	DEL	AC	-	-	rs72236600		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9747184_9747185delAC								TNKS (107329 upstream) : LOC157627 (10389 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	10181255	10181256	+	Intron	INS	-	GTGTGTGTGT	GTGTGTGTGT	rs145723947	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10181255_10181256insGTGTGTGTGT	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463			methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10501796	10501796	+	Intron	DEL	A	-	-	rs35056017		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10501796delA	uc003wtc.2	-							NM_178857	NP_849188			retinitis pigmentosa 1-like 1						intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10593063	10593064	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10593063_10593064insC	uc011kwz.1	-						uc003wtg.1_Intron	NM_031439	NP_113627			SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11136213	11136214	+	IGR	INS	-	AG	AG	rs149636132	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11136213_11136214insAG								XKR6 (77338 upstream) : MTMR9 (5786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	11809297	11809298	+	IGR	INS	-	TTCC	TTCC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11809297_11809298insTTCC								CTSB (83651 upstream) : DEFB136 (22150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	12439870	12439870	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12439870delA	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12450124	12450124	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12450124delC	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12499226	12499226	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12499226delG	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
LONRF1	91694	broad.mit.edu	37	8	12581290	12581290	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12581290delA	uc003wwd.1	-						LONRF1_uc011kxv.1_Intron|LONRF1_uc010lsp.1_Intron	NM_152271	NP_689484			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14858326	14858326	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14858326delT	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14988122	14988122	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14988122delT	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	15079953	15079954	+	Intron	INS	-	A	A	rs144434219	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15079953_15079954insA	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	15136786	15136787	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15136786_15136787insT								SGCZ (40994 upstream) : TUSC3 (260943 downstream)																																			---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15424111	15424111	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15424111delT	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756			tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	16242699	16242699	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16242699delT								MSR1 (192399 upstream) : FGF20 (607635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16455387	16455388	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16455387_16455388insA								MSR1 (405087 upstream) : FGF20 (394946 downstream)																																			---	---	---	---
EFHA2	286097	broad.mit.edu	37	8	16915923	16915923	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16915923delT	uc003wxd.2	+							NM_181723	NP_859074			EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)														---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17120083	17120084	+	Intron	DEL	TG	-	-	rs34185941		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17120083_17120084delTG	uc003wxj.2	+						VPS37A_uc003wxk.2_Intron	NM_152415	NP_689628			hepatocellular carcinoma related protein 1						cellular membrane organization|endosome transport|protein transport	centrosome|late endosome membrane|nucleus					0				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17701043	17701044	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17701043_17701044delGT								MTUS1 (42617 upstream) : FGL1 (20858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	17891350	17891350	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17891350delA								PCM1 (3895 upstream) : ASAH1 (22575 downstream)																																			---	---	---	---
ASAH1	427	broad.mit.edu	37	8	17914872	17914872	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17914872delA	uc003wyl.2	-	14					ASAH1_uc010ltb.1_RNA|ASAH1_uc003wym.2_3'UTR|ASAH1_uc003wyn.2_3'UTR|ASAH1_uc003wyo.2_3'UTR	NM_177924	NP_808592			N-acylsphingosine amidohydrolase 1 isoform a						ceramide metabolic process	lysosome	ceramidase activity				0				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	18014259	18014259	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18014259delA								ASAH1 (71752 upstream) : NAT1 (13712 downstream)																																			---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18432469	18432469	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18432469delT	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19001026	19001027	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19001026_19001027insA								PSD3 (129830 upstream) : SH2D4A (170180 downstream)																																			---	---	---	---
INTS10	55174	broad.mit.edu	37	8	19680155	19680155	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19680155delT	uc003wzj.2	+							NM_018142	NP_060612			integrator complex subunit 10						snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20415033	20415033	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20415033delT								LZTS1 (302230 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20574923	20574924	+	IGR	INS	-	TG	TG	rs150413246	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20574923_20574924insTG								LZTS1 (462120 upstream) : GFRA2 (974606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20927256	20927256	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20927256delC								LZTS1 (814453 upstream) : GFRA2 (622274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21204636	21204637	+	IGR	INS	-	A	A	rs149625960	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21204636_21204637insA								None (None upstream) : GFRA2 (344893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21546618	21546619	+	IGR	INS	-	CGCACACA	CGCACACA	rs141618944	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21546618_21546619insCGCACACA								None (None upstream) : GFRA2 (2911 downstream)																																			---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21848180	21848180	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21848180delA	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltk.2_Intron	NM_015024	NP_055839			exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	21963500	21963500	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21963500delT								FAM160B2 (1610 upstream) : NUDT18 (883 downstream)																																			---	---	---	---
BMP1	649	broad.mit.edu	37	8	22053641	22053641	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22053641delT	uc003xbg.2	+						BMP1_uc003xba.2_Intron|BMP1_uc003xbb.2_Intron|BMP1_uc003xbe.2_Intron|BMP1_uc003xbc.2_Intron|BMP1_uc003xbd.2_Intron|BMP1_uc003xbf.2_Intron|BMP1_uc011kzc.1_Intron|BMP1_uc003xbh.2_Intron|BMP1_uc003xbi.2_Intron	NM_006129	NP_006120			bone morphogenetic protein 1 isoform 3						cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22095384	22095384	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22095384delT								PHYHIP (5533 upstream) : MIR320A (7091 downstream)																																			---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22173618	22173618	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22173618delT	uc003xbn.2	+						PIWIL2_uc011kzf.1_Intron|PIWIL2_uc010ltv.2_Intron	NM_018068	NP_060538			piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22175837	22175837	+	Intron	DEL	T	-	-	rs112432255		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22175837delT	uc003xbn.2	+						PIWIL2_uc011kzf.1_Intron|PIWIL2_uc010ltv.2_Intron	NM_018068	NP_060538			piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22248227	22248227	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22248227delT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903			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)														---	---	---	---
SORBS3	10174	broad.mit.edu	37	8	22426860	22426860	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22426860delT	uc003xbv.2	+						SORBS3_uc003xbw.3_Intron	NM_005775	NP_005766			sorbin and SH3 domain containing 3 isoform 1						muscle contraction|positive regulation of stress fiber assembly	cytoskeleton|cytosol|nucleus	protein binding|structural constituent of cytoskeleton|vinculin binding				0		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22638965	22638965	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22638965delT	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22753129	22753130	+	Intron	INS	-	TTC	TTC	rs145171635	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22753129_22753130insTTC	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23026117	23026118	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23026117_23026118insT								TNFRSF10D (4577 upstream) : TNFRSF10A (22853 downstream)																																			---	---	---	---
CHMP7	91782	broad.mit.edu	37	8	23116145	23116145	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23116145delA	uc003xdc.2	+						CHMP7_uc011kzs.1_Intron|CHMP7_uc003xdd.2_Intron|CHMP7_uc003xde.2_Intron	NM_152272	NP_689485			CHMP family, member 7						cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
LOXL2	4017	broad.mit.edu	37	8	23215082	23215082	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23215082delT	uc003xdh.1	-						uc003xdj.2_Intron	NM_002318	NP_002309			lysyl oxidase-like 2 precursor						aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23664792	23664792	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23664792delA								NKX2-6 (100870 upstream) : STC1 (34642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23808549	23808551	+	IGR	DEL	AGA	-	-	rs79027723		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23808549_23808551delAGA								STC1 (96229 upstream) : ADAM28 (343029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23854090	23854090	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23854090delT								STC1 (141770 upstream) : ADAM28 (297490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23952732	23952733	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23952732_23952733insA								STC1 (240412 upstream) : ADAM28 (198847 downstream)																																			---	---	---	---
ADAM28	10863	broad.mit.edu	37	8	24157704	24157705	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24157704_24157705delTG	uc003xdy.2	+						ADAM28_uc003xdx.2_Intron|ADAM28_uc011kzz.1_Intron|ADAM28_uc011laa.1_Intron	NM_014265	NP_055080			ADAM metallopeptidase domain 28 isoform 1						proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24408914	24408914	+	IGR	DEL	T	-	-	rs111990300		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24408914delT								ADAM7 (24433 upstream) : NEFM (362360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24440679	24440681	+	IGR	DEL	AAA	-	-	rs72318535		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24440679_24440681delAAA								ADAM7 (56198 upstream) : NEFM (330593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24522777	24522777	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24522777delT								ADAM7 (138296 upstream) : NEFM (248497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24672433	24672449	+	IGR	DEL	CACCTGTCAGTCCTGGC	-	-	rs66852414		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24672433_24672449delCACCTGTCAGTCCTGGC								ADAM7 (287952 upstream) : NEFM (98825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24964989	24964990	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24964989_24964990delAC								NEFL (150858 upstream) : DOCK5 (77297 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25156246	25156246	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25156246delA	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xef.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25240127	25240127	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25240127delT	uc003xeg.2	+						PPP2R2A_uc003xek.2_Intron|DOCK5_uc003xei.2_Intron|DOCK5_uc003xej.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25537519	25537520	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25537519_25537520insC	uc003xek.2	+							NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25761243	25761243	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25761243delA	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron	NM_022659	NP_073150			early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25938084	25938084	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25938084delA	uc003xek.2	+							NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26427758	26427758	+	Intron	DEL	G	-	-	rs67266423		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26427758delG	uc003xfa.2	+							NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26465301	26465301	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26465301delA	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26514038	26514039	+	3'UTR	INS	-	TC	TC	rs144398185	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26514038_26514039insTC	uc003xfb.1	+	14					DPYSL2_uc003xfa.2_3'UTR|DPYSL2_uc010luk.1_RNA|DPYSL2_uc011lah.1_3'UTR	NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27387143	27387143	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27387143delA	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron	NM_001979	NP_001970			epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
SCARA5	286133	broad.mit.edu	37	8	27822477	27822477	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27822477delA	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194			scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)														---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27928112	27928112	+	Intron	DEL	T	-	-	rs71945009		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27928112delT	uc003xgm.3	-							NM_001010906	NP_001010906			speckled-like pattern in the germinal center							nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)														---	---	---	---
ELP3	55140	broad.mit.edu	37	8	27981461	27981462	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27981461_27981462delTT	uc003xgo.3	+						ELP3_uc003xgn.3_Intron|ELP3_uc011laq.1_Intron|ELP3_uc011lar.1_Intron|ELP3_uc011las.1_Intron|ELP3_uc011lat.1_Intron	NM_018091	NP_060561			elongation protein 3 homolog						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	histone acetyltransferase activity|iron-sulfur cluster binding|metal ion binding|phosphorylase kinase regulator activity|protein binding				0		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.151)|Colorectal(74;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28201278	28201278	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28201278delA								PNOC (412 upstream) : ZNF395 (1826 downstream)																																			---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28247372	28247372	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28247372delA	uc003xgt.2	-							NM_018660	NP_061130			zinc finger protein 395						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
FZD3	7976	broad.mit.edu	37	8	28362877	28362878	+	Intron	INS	-	T	T	rs111513017		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28362877_28362878insT	uc003xgx.2	+						FZD3_uc010lvb.2_Intron|hsa-mir-4288|MI0015896_5'Flank	NM_017412	NP_059108			frizzled 3 precursor						canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)														---	---	---	---
INTS9	55756	broad.mit.edu	37	8	28635058	28635058	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28635058delT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron	NM_018250	NP_060720			integrator complex subunit 9 isoform 1						snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)														---	---	---	---
HMBOX1	79618	broad.mit.edu	37	8	28908874	28908875	+	3'UTR	INS	-	AACC	AACC	rs147395804	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28908874_28908875insAACC	uc003xhd.3	+	10					HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_RNA|HMBOX1_uc003xhe.2_3'UTR|HMBOX1_uc011lay.1_3'UTR|HMBOX1_uc003xhf.2_3'UTR|HMBOX1_uc003xhg.2_3'UTR	NM_001135726	NP_001129198			homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	28940645	28940645	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28940645delA	uc003xhh.3	-						KIF13B_uc011laz.1_Intron	NM_015254	NP_056069			kinesin family member 13B						microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
DUSP4	1846	broad.mit.edu	37	8	29194242	29194242	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29194242delA	uc003xhm.2	-	4					DUSP4_uc003xhl.2_3'UTR	NM_001394	NP_001385			dual specificity phosphatase 4 isoform 1						endoderm formation|inactivation of MAPK activity|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	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/threonine phosphatase activity			lung(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29251285	29251285	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29251285delT								DUSP4 (43100 upstream) : C8orf75 (327493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29610452	29610452	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29610452delT	uc003xho.2	+						uc003xhp.2_Intron					Homo sapiens, clone IMAGE:4861097, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29916291	29916291	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29916291delA								LOC286135 (105170 upstream) : TMEM66 (4341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30228442	30228445	+	IGR	DEL	ACAC	-	-	rs112948312		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30228442_30228445delACAC								DCTN6 (187383 upstream) : RBPMS (13499 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30268260	30268260	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30268260delT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30374421	30374422	+	Intron	DEL	AC	-	-	rs67437122		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30374421_30374422delAC	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc003xif.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron|RBPMS_uc010lvh.1_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30472065	30472065	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30472065delA	uc003xig.2	-							NM_002095	NP_002086			general transcription factor IIE, polypeptide 2,						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)														---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30498005	30498005	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30498005delA	uc003xig.2	-							NM_002095	NP_002086			general transcription factor IIE, polypeptide 2,						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)														---	---	---	---
GSR	2936	broad.mit.edu	37	8	30538569	30538569	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30538569delA	uc003xih.1	-							NM_000637	NP_000628			glutathione reductase precursor						cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)													---	---	---	---
WRN	7486	broad.mit.edu	37	8	30957063	30957063	+	Intron	DEL	T	-	-	rs114173587	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30957063delT	uc003xio.3	+						WRN_uc010lvk.2_Intron	NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	31174463	31174463	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31174463delA								WRN (143187 upstream) : NRG1 (322805 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32096837	32096838	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32096837_32096838delAA	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32432112	32432113	+	Intron	INS	-	TC	TC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32432112_32432113insTC	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33075837	33075839	+	IGR	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33075837_33075839delAAA								NRG1 (453279 upstream) : FUT10 (152507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33225237	33225237	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33225237delT								NRG1 (602679 upstream) : FUT10 (3109 downstream)																																			---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33362833	33362833	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33362833delC	uc003xjl.3	-						C8orf41_uc003xjk.3_Intron|C8orf41_uc010lvv.2_Intron|C8orf41_uc003xjm.3_Intron|C8orf41_uc003xjn.1_Intron	NM_025115	NP_079391			hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33445941	33445941	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33445941delT								RNF122 (21298 upstream) : DUSP26 (2915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33866130	33866130	+	IGR	DEL	A	-	-	rs66919887		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33866130delA								DUSP26 (408691 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34376884	34376885	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34376884_34376885delGT								DUSP26 (919445 upstream) : UNC5D (716090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34551766	34551766	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34551766delT								None (None upstream) : UNC5D (541209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34946942	34946942	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34946942delT								None (None upstream) : UNC5D (146033 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35175882	35175882	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35175882delA	uc003xjr.1	+							NM_080872	NP_543148			unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	35723466	35723467	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35723466_35723467insA								UNC5D (71286 upstream) : KCNU1 (918375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35740564	35740564	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35740564delA								UNC5D (88384 upstream) : KCNU1 (901278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36064368	36064368	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36064368delT								UNC5D (412188 upstream) : KCNU1 (577474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36321057	36321057	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36321057delA								UNC5D (668877 upstream) : KCNU1 (320785 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36716517	36716518	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36716517_36716518insA	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006			potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)														---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36785559	36785559	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36785559delA	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006			potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	36895072	36895072	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36895072delA								KCNU1 (101431 upstream) : ZNF703 (658229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37337195	37337195	+	IGR	DEL	C	-	-	rs10808344	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37337195delC								KCNU1 (543554 upstream) : ZNF703 (216106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37487537	37487537	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37487537delA								KCNU1 (693896 upstream) : ZNF703 (65764 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37731434	37731435	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37731434_37731435delAA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	37832578	37832578	+	IGR	DEL	T	-	-	rs111260524		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37832578delT								ADRB3 (8394 upstream) : EIF4EBP1 (55442 downstream)																																			---	---	---	---
EIF4EBP1	1978	broad.mit.edu	37	8	37913547	37913547	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37913547delT	uc003xks.2	+							NM_004095	NP_004086			eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|positive regulation of mitotic cell cycle|TOR signaling cascade|translation	cytosol					0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)																---	---	---	---
ASH2L	9070	broad.mit.edu	37	8	37986672	37986672	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37986672delT	uc003xkt.3	+						ASH2L_uc011lbk.1_Intron|ASH2L_uc003xku.3_Intron|ASH2L_uc010lwa.2_Intron	NM_004674	NP_004665			ash2-like isoform a						hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)																---	---	---	---
BAG4	9530	broad.mit.edu	37	8	38050110	38050110	+	Intron	DEL	T	-	-	rs77367699		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38050110delT	uc003xky.1	+						BAG4_uc003xkz.1_Intron	NM_004874	NP_004865			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)																---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38147731	38147733	+	Intron	DEL	AAA	-	-	rs33956434		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38147731_38147733delAAA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38306625	38306625	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38306625delA	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598			fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	8	38339200	38339200	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38339200delT								FGFR1 (12848 upstream) : C8orf86 (29152 downstream)																																			---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38626179	38626180	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38626179_38626180delGT	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38637154	38637156	+	Intron	DEL	ATT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38637154_38637156delATT	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38804679	38804680	+	Intron	DEL	AG	-	-	rs10555385		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38804679_38804680delAG	uc003xmi.3	+						PLEKHA2_uc011lce.1_Intron	NM_021623	NP_067636			pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38880852	38880852	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38880852delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron	NM_003816	NP_003807			ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39014993	39014993	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39014993delT	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron	NM_145004	NP_659441			a disintegrin and metalloprotease domain 32						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
ADAM3A	1587	broad.mit.edu	37	8	39351833	39351833	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39351833delT	uc003xnf.2	-						ADAM3A_uc003xne.2_Intron|ADAM3A_uc003xnd.2_Intron|ADAM3A_uc011lci.1_Intron|ADAM3A_uc011lcj.1_Intron|ADAM3A_uc003xng.3_Intron	NR_001569				SubName: Full=Putative uncharacterized protein ENSP00000328747;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	40191351	40191351	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40191351delT								C8orf4 (178530 upstream) : ZMAT4 (196765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40266042	40266043	+	IGR	INS	-	CTTT	CTTT	rs142186427	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40266042_40266043insCTTT								C8orf4 (253221 upstream) : ZMAT4 (122073 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40622520	40622520	+	Intron	DEL	A	-	-	rs67110607		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40622520delA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	40840990	40840991	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40840990_40840991delAA								ZMAT4 (85647 upstream) : SFRP1 (278488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41286593	41286593	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41286593delT								SFRP1 (119613 upstream) : GOLGA7 (61488 downstream)																																			---	---	---	---
ANK1	286	broad.mit.edu	37	8	41560505	41560506	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41560505_41560506delTT	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209			ankyrin 1 isoform 1						axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41792805	41792805	+	Intron	DEL	T	-	-	rs79547054		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41792805delT	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41948292	41948292	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41948292delT								MYST3 (38787 upstream) : AP3M2 (62172 downstream)																																			---	---	---	---
PLAT	5327	broad.mit.edu	37	8	42042793	42042793	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42042793delT	uc003xos.2	-						PLAT_uc010lxf.1_Intron|PLAT_uc010lxg.1_Intron|PLAT_uc003xot.2_Intron|PLAT_uc011lcm.1_Intron|PLAT_uc011lcn.1_Intron	NM_000930	NP_000921			plasminogen activator, tissue isoform 1						blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis	cell surface|cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			breast(1)|skin(1)	2	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)													---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42126092	42126092	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42126092delT	uc003xow.1	+						IKBKB_uc003xov.2_5'Flank|IKBKB_uc010lxh.1_5'Flank|IKBKB_uc011lco.1_5'Flank|IKBKB_uc010lxj.1_5'Flank|IKBKB_uc003xox.1_5'Flank|IKBKB_uc011lcp.1_5'Flank|IKBKB_uc011lcq.1_5'Flank|IKBKB_uc010lxi.1_5'Flank|IKBKB_uc011lcr.1_5'Flank	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42136515	42136515	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42136515delA	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|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	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42279385	42279387	+	Intron	DEL	TTT	-	-	rs75198947		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42279385_42279387delTTT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	42450987	42450987	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42450987delC								C8orf40 (42848 upstream) : CHRNB3 (101575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42596347	42596347	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42596347delA								CHRNB3 (4138 upstream) : CHRNA6 (11435 downstream)																																			---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42619491	42619491	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42619491delT	uc003xpj.2	-						CHRNA6_uc011lcw.1_Intron	NM_004198	NP_004189			cholinergic receptor, nicotinic, alpha 6							cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	43672222	43672222	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43672222delA								POTEA (453894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43754778	43754779	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43754778_43754779delTT								POTEA (536450 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46918864	46918864	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46918864delA								None (None upstream) : BEYLA (833644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47545976	47545976	+	IGR	DEL	A	-	-	rs78926432		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47545976delA								None (None upstream) : BEYLA (206532 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48240852	48240852	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48240852delT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48306239	48306248	+	Intron	DEL	TTTCCTTTCC	-	-	rs150623579		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48306239_48306248delTTTCCTTTCC	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48395691	48395691	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48395691delT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48586205	48586205	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48586205delT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_5'UTR|KIAA0146_uc010lxv.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48612124	48612124	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48612124delT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron|KIAA0146_uc010lxv.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48812834	48812834	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48812834delA	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			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)											NHEJ					---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48953734	48953736	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48953734_48953736delTTT	uc003xqm.2	+							NM_003350	NP_003341			ubiquitin-conjugating enzyme E2v2						cell proliferation|DNA double-strand break processing|protein polyubiquitination|regulation of DNA repair	cytoplasm|nucleus|UBC13-MMS2 complex	acid-amino acid ligase activity|protein binding				0		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)											Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
Unknown	0	broad.mit.edu	37	8	49267464	49267464	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49267464delA								UBE2V2 (293012 upstream) : EFCAB1 (355887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49941904	49941911	+	IGR	DEL	CCTTCCTT	-	-	rs58975536	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49941904_49941911delCCTTCCTT								SNAI2 (107916 upstream) : C8orf22 (42992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50211773	50211773	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50211773delA								C8orf22 (223132 upstream) : SNTG1 (610576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50716917	50716918	+	IGR	INS	-	GT	GT	rs149566946	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50716917_50716918insGT								C8orf22 (728276 upstream) : SNTG1 (105431 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51362183	51362183	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51362183delT	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840			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)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51453803	51453804	+	Intron	INS	-	TG	TG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51453803_51453804insTG	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840			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)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52656468	52656469	+	Intron	INS	-	AAGG	AAGG	rs67558657		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52656468_52656469insAAGG	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
RB1CC1	9821	broad.mit.edu	37	8	53615269	53615269	+	Intron	DEL	A	-	-	rs111945832		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53615269delA	uc003xre.3	-						RB1CC1_uc003xrf.3_Intron	NM_014781	NP_055596			Rb1-inducible coiled coil protein 1 isoform 1						autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53976543	53976544	+	IGR	INS	-	TC	TC	rs71967732		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53976543_53976544insTC								NPBWR1 (123090 upstream) : OPRK1 (161732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54081348	54081348	+	IGR	DEL	T	-	-	rs731239	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54081348delT								NPBWR1 (227895 upstream) : OPRK1 (56928 downstream)																																			---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54884542	54884542	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54884542delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc010lyg.2_Intron	NM_006756	NP_006747			transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)					T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	55396600	55396600	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55396600delA								SOX17 (23145 upstream) : RP1 (132027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55765909	55765910	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55765909_55765910delAG								RP1 (83378 upstream) : XKR4 (249107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55884651	55884651	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55884651delT								RP1 (202120 upstream) : XKR4 (130366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55991632	55991632	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55991632delA								RP1 (309101 upstream) : XKR4 (23385 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56168766	56168766	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56168766delG	uc003xsf.2	+							NM_052898	NP_443130			XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
C8orf71	26138	broad.mit.edu	37	8	58197154	58197154	+	RNA	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58197154delG	uc003xtg.2	+	4		c.1739delG				NR_026772				Homo sapiens mRNA; cDNA DKFZp434F122 (from clone DKFZp434F122).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	58312483	58312483	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58312483delT								C8orf71 (115195 upstream) : FAM110B (594630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58379580	58379580	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58379580delT								C8orf71 (182292 upstream) : FAM110B (527533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60266762	60266763	+	IGR	INS	-	T	T	rs146658363	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60266762_60266763insT								TOX (234995 upstream) : CA8 (834660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60672252	60672252	+	IGR	DEL	A	-	-	rs34318367		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60672252delA								TOX (640485 upstream) : CA8 (429171 downstream)																																			---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61440295	61440295	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61440295delT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61583417	61583417	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61583417delG								RAB2A (49788 upstream) : CHD7 (7922 downstream)																																			---	---	---	---
ASPH	444	broad.mit.edu	37	8	62596444	62596446	+	Intron	DEL	CTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62596444_62596446delCTT	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Intron|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron|ASPH_uc011lel.1_Intron|ASPH_uc011lem.1_Intron|ASPH_uc003xur.2_Intron|ASPH_uc003xus.2_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	62714646	62714646	+	IGR	DEL	C	-	-	rs34861663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62714646delC								ASPH (87447 upstream) : NKAIN3 (446855 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63774857	63774857	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63774857delA	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
TTPA	7274	broad.mit.edu	37	8	64001326	64001327	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64001326_64001327delTT	uc003xux.1	-							NM_000370	NP_000361			tocopherol (alpha) transfer protein						lipid metabolic process		transporter activity|vitamin E binding				0	Breast(64;0.0716)	all_cancers(86;0.145)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.123)			Vitamin E(DB00163)													---	---	---	---
YTHDF3	253943	broad.mit.edu	37	8	64106584	64106585	+	Intron	DEL	TT	-	-	rs34053682		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64106584_64106585delTT	uc003xuy.2	+						YTHDF3_uc010lys.2_Intron|YTHDF3_uc003xuz.2_Intron|YTHDF3_uc003xva.2_Intron|YTHDF3_uc011len.1_Intron	NM_152758	NP_689971			YTH domain family, member 3												0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	64445796	64445796	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64445796delT								YTHDF3 (320451 upstream) : MIR124-2 (845910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64536047	64536047	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64536047delT								YTHDF3 (410702 upstream) : MIR124-2 (755659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65106994	65106994	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65106994delT								YTHDF3 (981649 upstream) : MIR124-2 (184712 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528843	65528843	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528843delA	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	65742588	65742589	+	IGR	INS	-	TG	TG	rs141900528	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65742588_65742589insTG								CYP7B1 (31240 upstream) : ARMC1 (772483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66494596	66494598	+	IGR	DEL	GGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66494596_66494598delGGA								CYP7B1 (783248 upstream) : ARMC1 (20474 downstream)																																			---	---	---	---
DNAJC5B	85479	broad.mit.edu	37	8	66939804	66939805	+	Intron	INS	-	A	A	rs138629539	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66939804_66939805insA	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096			DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)															---	---	---	---
C8orf46	254778	broad.mit.edu	37	8	67408175	67408175	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67408175delC	uc003xwg.2	+						C8orf46_uc003xwh.2_Intron|C8orf46_uc011let.1_Intron	NM_152765	NP_689978			hypothetical protein LOC254778											skin(2)	2			Epithelial(68;0.0224)|BRCA - Breast invasive adenocarcinoma(89;0.0508)|all cancers(69;0.0558)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67733753	67733753	+	Intron	DEL	T	-	-	rs76076671		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67733753delT	uc003xwr.2	+						SGK3_uc003xwp.2_Intron|SGK3_uc003xwt.2_Intron|SGK3_uc003xwu.2_Intron	NM_001033578	NP_001028750			serum/glucocorticoid regulated kinase 3 isoform						cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67853827	67853827	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67853827delT								SNHG6 (16050 upstream) : LRRC67 (46541 downstream)																																			---	---	---	---
LRRC67	286187	broad.mit.edu	37	8	67923224	67923224	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67923224delT	uc003xxc.2	-							NM_001013626	NP_001013648			leucine rich repeat containing 67												0																		---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68011197	68011198	+	Intron	DEL	TT	-	-	rs74385209		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68011197_68011198delTT	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68043622	68043622	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68043622delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68044403	68044403	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68044403delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69048041	69048041	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69048041delA	uc003xxv.1	+							NM_024870	NP_079146			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																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69334782	69334782	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69334782delC	uc010lyz.2	+						C8orf34_uc010lyx.1_Intron|C8orf34_uc010lyy.1_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70516968	70516969	+	Intron	DEL	AG	-	-	rs76379305	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70516968_70516969delAG	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron|SULF1_uc003xyh.1_Intron	NM_015170	NP_055985			sulfatase 1 precursor						apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	70574256	70574257	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70574256_70574257insC								SULF1 (1109 upstream) : SLCO5A1 (10313 downstream)																																			---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71117842	71117842	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71117842delA	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
NCOA2	10499	broad.mit.edu	37	8	71282946	71282946	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71282946delA	uc003xyn.1	-							NM_006540	NP_006531			nuclear receptor coactivator 2						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	histone acetyltransferase activity|ligand-dependent nuclear receptor binding|nuclear hormone receptor binding|signal transducer activity		PAX3/NCOA2(4)	lung(6)|soft_tissue(4)|breast(2)|skin(2)|ovary(1)|pancreas(1)	16	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)					T	RUNXBP2	AML								---	---	---	---
TRAM1	23471	broad.mit.edu	37	8	71487027	71487027	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71487027delA	uc003xyo.1	-	11					TRAM1_uc011lfc.1_3'UTR	NM_014294	NP_055109			translocation associated membrane protein 1						cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)															---	---	---	---
TRAM1	23471	broad.mit.edu	37	8	71507193	71507193	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71507193delA	uc003xyo.1	-						TRAM1_uc011lfc.1_Intron	NM_014294	NP_055109			translocation associated membrane protein 1						cotranslational protein targeting to membrane|transmembrane transport	endoplasmic reticulum membrane|integral to membrane	protein binding|receptor activity			ovary(1)	1			Epithelial(68;0.00679)|all cancers(69;0.0324)|OV - Ovarian serous cystadenocarcinoma(28;0.0509)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	71931376	71931376	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71931376delT								XKR9 (283200 upstream) : EYA1 (178294 downstream)																																			---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72127508	72127508	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72127508delT	uc003xys.3	-						EYA1_uc003xyr.3_Intron|EYA1_uc003xyt.3_Intron|EYA1_uc010lzf.2_Intron|EYA1_uc003xyu.2_Intron|EYA1_uc011lfe.1_Intron|EYA1_uc003xyv.2_Intron	NM_172058	NP_742055			eyes absent 1 isoform b						double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|protein sumoylation|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74316940	74316940	+	IGR	DEL	T	-	-	rs111504470		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74316940delT								RDH10 (79426 upstream) : STAU2 (15666 downstream)																																			---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74338405	74338406	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74338405_74338406delTT	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|uc003xzl.2_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74341836	74341836	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74341836delT	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|uc003xzl.2_Intron	NM_014393	NP_055208			staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74676257	74676257	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74676257delT								STAU2 (16314 upstream) : UBE2W (16075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74835942	74835943	+	IGR	DEL	TT	-	-	rs112744545		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74835942_74835943delTT								UBE2W (44832 upstream) : TCEB1 (22691 downstream)																																			---	---	---	---
GDAP1	54332	broad.mit.edu	37	8	75275006	75275007	+	Intron	INS	-	CT	CT	rs140955331	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75275006_75275007insCT	uc003yah.2	+						GDAP1_uc011lfj.1_Intron|GDAP1_uc003yai.2_Intron	NM_018972	NP_061845			ganglioside-induced differentiation-associated							cytoplasm					0	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	75394354	75394356	+	IGR	DEL	TGG	-	-	rs5892459		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75394354_75394356delTGG								GDAP1 (115021 upstream) : MIR2052 (223572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76778527	76778528	+	IGR	DEL	AA	-	-	rs75583938		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76778527_76778528delAA								HNF4G (299468 upstream) : LOC100192378 (744587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77262356	77262356	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77262356delA								HNF4G (783297 upstream) : LOC100192378 (260759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77884002	77884002	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77884002delT								ZFHX4 (104482 upstream) : PEX2 (8494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77930835	77930835	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77930835delA								PEX2 (18311 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78685063	78685063	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78685063delT								PEX2 (772539 upstream) : PKIA (743273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78913659	78913659	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78913659delT								None (None upstream) : PKIA (514677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78936308	78936308	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78936308delT								None (None upstream) : PKIA (492028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79196731	79196731	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79196731delT								None (None upstream) : PKIA (231605 downstream)																																			---	---	---	---
PKIA	5569	broad.mit.edu	37	8	79482966	79482966	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79482966delT	uc003yba.2	+						PKIA_uc003ybb.2_Intron	NM_006823	NP_006814			cAMP-dependent protein kinase inhibitor alpha								cAMP-dependent protein kinase inhibitor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
PKIA	5569	broad.mit.edu	37	8	79511033	79511033	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79511033delT	uc003yba.2	+						PKIA_uc003ybb.2_Intron|PKIA_uc010lzo.2_Intron	NM_006823	NP_006814			cAMP-dependent protein kinase inhibitor alpha								cAMP-dependent protein kinase inhibitor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	79780253	79780255	+	IGR	DEL	TTT	-	-	rs149549411		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79780253_79780255delTTT								IL7 (62495 upstream) : STMN2 (743125 downstream)																																			---	---	---	---
STMN2	11075	broad.mit.edu	37	8	80523941	80523941	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80523941delG	uc003ybj.2	+						STMN2_uc010lzp.2_Intron|STMN2_uc011lfn.1_Intron	NM_007029	NP_008960			superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	80781379	80781379	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80781379delA	uc003ybn.2	-											Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	80784117	80784118	+	5'Flank	INS	-	T	T	rs140641341		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80784117_80784118insT	uc003ybn.2	-											Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																														---	---	---	---
TPD52	7163	broad.mit.edu	37	8	80951656	80951656	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80951656delT	uc003ybr.1	-						TPD52_uc010lzr.2_Intron|TPD52_uc010lzs.1_Intron|TPD52_uc003ybs.1_Intron|TPD52_uc003ybt.1_Intron|TPD52_uc003ybq.1_Intron|TPD52_uc003ybu.1_Intron	NM_001025252	NP_001020423			tumor protein D52 isoform 1						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)															---	---	---	---
TPD52	7163	broad.mit.edu	37	8	80964536	80964536	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80964536delA	uc003ybr.1	-						TPD52_uc010lzr.2_Intron|TPD52_uc010lzs.1_Intron|TPD52_uc003ybs.1_Intron|TPD52_uc003ybt.1_Intron|TPD52_uc003ybq.1_Intron|TPD52_uc003ybu.1_Intron	NM_001025252	NP_001020423			tumor protein D52 isoform 1						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81213788	81213788	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81213788delC								TPD52 (129952 upstream) : ZBTB10 (184066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82402440	82402440	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82402440delA								FABP4 (6967 upstream) : FABP12 (34843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82530375	82530375	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82530375delT								FABP12 (86825 upstream) : IMPA1 (38776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82917914	82917914	+	IGR	DEL	A	-	-	rs79507462		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82917914delA								SNX16 (163393 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83248979	83248979	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83248979delT								SNX16 (494458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84221162	84221162	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84221162delT								None (None upstream) : RALYL (874291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84372019	84372020	+	IGR	DEL	CC	-	-	rs60051271		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84372019_84372020delCC								None (None upstream) : RALYL (723433 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85446970	85446970	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85446970delG	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85801420	85801421	+	Intron	INS	-	TAGAG	TAGAG	rs144068711	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85801420_85801421insTAGAG	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron|RALYL_uc003ycu.3_Intron|RALYL_uc003ycv.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	86931509	86931510	+	IGR	DEL	CA	-	-	rs113841846		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86931509_86931510delCA								REXO1L1 (356241 upstream) : PSKH2 (129183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87264830	87264830	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87264830delT								SLC7A13 (22221 upstream) : WWP1 (90164 downstream)																																			---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87476590	87476590	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87476590delT	uc003ydt.2	+							NM_007013	NP_008944			WW domain containing E3 ubiquitin protein ligase						central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2																		---	---	---	---
CNGB3	54714	broad.mit.edu	37	8	87758201	87758201	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87758201delT	uc003ydx.2	-							NM_019098	NP_061971			cyclic nucleotide gated channel beta 3						signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87859835	87859836	+	IGR	INS	-	AGGA	AGGA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87859835_87859836insAGGA								CNGB3 (103934 upstream) : CNBD1 (18840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88878068	88878068	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88878068delT								CNBD1 (483113 upstream) : DCAF4L2 (4905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89640020	89640020	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89640020delT								MMP16 (300303 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89690441	89690441	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89690441delT								MMP16 (350724 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90084530	90084530	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90084530delA								MMP16 (744813 upstream) : RIPK2 (685445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90645008	90645008	+	IGR	DEL	C	-	-	rs72135793		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90645008delC								None (None upstream) : RIPK2 (124967 downstream)																																			---	---	---	---
DECR1	1666	broad.mit.edu	37	8	91056917	91056917	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91056917delT	uc003yek.1	+						DECR1_uc011lgc.1_Intron|DECR1_uc011lgd.1_Intron	NM_001359	NP_001350			2,4-dienoyl CoA reductase 1 precursor						fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
OTUD6B	51633	broad.mit.edu	37	8	92096993	92096993	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92096993delT	uc003yeu.3	+						OTUD6B_uc011lgh.1_Intron	NM_016023	NP_057107			OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)															---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92301876	92301877	+	Intron	DEL	AA	-	-	rs111279250		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92301876_92301877delAA	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_Intron|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897			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)															---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92365352	92365353	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92365352_92365353insT	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_Intron|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897			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)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93008015	93008015	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93008015delA	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfb.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93088475	93088475	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93088475delA	uc003yfd.2	-						RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94068557	94068557	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94068557delT								C8orf83 (38656 upstream) : FAM92A1 (644216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94456323	94456323	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94456323delA								C8orf83 (426422 upstream) : FAM92A1 (256450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94994084	94994084	+	IGR	DEL	A	-	-	rs34721591		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94994084delA								PDP1 (55790 upstream) : CDH17 (145310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95101650	95101651	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95101650_95101651insT								PDP1 (163356 upstream) : CDH17 (37743 downstream)																																			---	---	---	---
CDH17	1015	broad.mit.edu	37	8	95141822	95141822	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95141822delA	uc003ygh.2	-						CDH17_uc011lgo.1_Intron|CDH17_uc011lgp.1_Intron	NM_004063	NP_004054			cadherin 17 precursor							integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)															---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95405072	95405072	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95405072delT	uc003ygk.2	-						RAD54B_uc010may.1_Intron|RAD54B_uc003ygl.1_Intron	NM_012415	NP_036547			RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95479469	95479469	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95479469delA	uc003ygk.2	-						RAD54B_uc003ygl.1_Intron|RAD54B_uc003ygn.1_Intron	NM_012415	NP_036547			RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	8	95596322	95596323	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95596322_95596323delTT								KIAA1429 (30634 upstream) : ESRP1 (57041 downstream)																																			---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95681940	95681940	+	Intron	DEL	A	-	-	rs1820418	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95681940delA	uc003ygq.3	+						ESRP1_uc003ygr.3_Intron|ESRP1_uc003ygs.3_Intron|ESRP1_uc003ygt.3_Intron|ESRP1_uc003ygu.3_Intron|ESRP1_uc003ygv.2_Intron|ESRP1_uc003ygw.2_Intron	NM_017697	NP_060167			RNA binding motif protein 35A isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4																		---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95713517	95713518	+	Intron	DEL	AG	-	-	rs59557867		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95713517_95713518delAG	uc003ygq.3	+						ESRP1_uc003ygr.3_Intron|ESRP1_uc003ygs.3_Intron|ESRP1_uc003ygt.3_Intron|ESRP1_uc003ygu.3_Intron|ESRP1_uc003ygv.2_Intron|ESRP1_uc003ygw.2_Intron	NM_017697	NP_060167			RNA binding motif protein 35A isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4																		---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96050048	96050048	+	Intron	DEL	A	-	-	rs72329200		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96050048delA	uc003yhj.2	+						C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron|C8orf38_uc011lgs.1_Intron|C8orf38_uc003yhi.2_Intron|C8orf38_uc003yhk.2_Intron|C8orf38_uc003yhl.2_Intron	NM_152416	NP_689629			hypothetical protein LOC137682 precursor						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96903588	96903588	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96903588delA								C8orf37 (622151 upstream) : GDF6 (250972 downstream)																																			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97313355	97313355	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97313355delT	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569			phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)													---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97757536	97757536	+	Intron	DEL	A	-	-	rs112851967		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97757536delA	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97811686	97811686	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97811686delT	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	98237422	98237422	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98237422delA								PGCP (81701 upstream) : TSPYL5 (48293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98467220	98467220	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98467220delT								TSPYL5 (177044 upstream) : MTDH (189187 downstream)																																			---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98698791	98698791	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98698791delT	uc003yhz.2	+							NM_178812	NP_848927			metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)															---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98704098	98704098	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98704098delT	uc003yhz.2	+						MTDH_uc010mbf.2_Intron	NM_178812	NP_848927			metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98920486	98920486	+	Intron	DEL	A	-	-	rs75561324		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98920486delA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98922015	98922017	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98922015_98922017delTTT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
STK3	6788	broad.mit.edu	37	8	99697978	99697979	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99697978_99697979insA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100591942	100591942	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100591942delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100606313	100606313	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100606313delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100778982	100778982	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100778982delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100833442	100833442	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100833442delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
RGS22	26166	broad.mit.edu	37	8	100995444	100995444	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100995444delT	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron	NM_015668	NP_056483			regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)															---	---	---	---
SPAG1	6674	broad.mit.edu	37	8	101223060	101223060	+	Intron	DEL	T	-	-	rs72052734		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101223060delT	uc003yjh.1	+						SPAG1_uc003yji.1_Intron	NM_172218	NP_757367			sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
SNX31	169166	broad.mit.edu	37	8	101615974	101615975	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101615974_101615975delTT	uc003yjr.2	-						SNX31_uc011lha.1_Intron|SNX31_uc011lhb.1_Intron	NM_152628	NP_689841			sorting nexin 31						cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101979901	101979901	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101979901delT								YWHAZ (14278 upstream) : ZNF706 (229367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101991184	101991184	+	IGR	DEL	A	-	-	rs67680329		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101991184delA								YWHAZ (25561 upstream) : ZNF706 (218084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102286032	102286032	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102286032delT								ZNF706 (68072 upstream) : NACAP1 (87990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102396897	102396897	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102396897delA								NACAP1 (11962 upstream) : GRHL2 (107771 downstream)																																			---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102845839	102845841	+	Intron	DEL	TTT	-	-	rs13271806		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102845839_102845841delTTT	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103158948	103158948	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103158948delA								NCALD (21813 upstream) : RRM2B (57784 downstream)																																			---	---	---	---
RRM2B	50484	broad.mit.edu	37	8	103221378	103221378	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103221378delA	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528			ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)										Direct_reversal_of_damage|Modulation_of_nucleotide_pools					---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103289349	103289349	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103289349delT	uc003ykr.1	-	45	6393	c.6360delA	c.(6358-6360)AAAfs	p.K2120fs	UBR5_uc003yks.1_Frame_Shift_Del_p.K2120fs	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2120					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103483485	103483485	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103483485delA								UBR5 (58990 upstream) : ODF1 (80363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103738835	103738835	+	IGR	DEL	T	-	-	rs113661111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103738835delT								KLF10 (70852 upstream) : AZIN1 (99702 downstream)																																			---	---	---	---
BAALC	79870	broad.mit.edu	37	8	104210405	104210405	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104210405delT	uc003yld.2	+						BAALC_uc003yle.2_Intron|uc003ylf.2_Intron	NM_024812	NP_079088			brain and acute leukemia, cytoplasmic isoform 1							centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	104295855	104295855	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104295855delT	uc003ylf.2	-											Homo sapiens cDNA FLJ43745 fis, clone TESTI2019648.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	104404181	104404182	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104404181_104404182delTT								CTHRC1 (8966 upstream) : SLC25A32 (6685 downstream)																																			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104932408	104932408	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104932408delT	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_Intron|RIMS2_uc003ylv.1_Intron	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	105261141	105261144	+	Intron	DEL	TTCC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105261141_105261144delTTCC	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105276112	105276112	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105276112delT								RIMS2 (10661 upstream) : TM7SF4 (75942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105642112	105642114	+	IGR	DEL	TTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105642112_105642114delTTG								LRP12 (40892 upstream) : ZFPM2 (689033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106304701	106304701	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106304701delA								LRP12 (703481 upstream) : ZFPM2 (26446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107229568	107229568	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107229568delA								ZFPM2 (412803 upstream) : OXR1 (52905 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107442256	107442257	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107442256_107442257delTG	uc003ymf.2	+							NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107651421	107651421	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107651421delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc003ymg.1_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107708415	107708415	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107708415delT	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc003ymg.1_Intron|OXR1_uc003ymi.1_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107738389	107738389	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107738389delA	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc010mch.2_Intron|OXR1_uc003ymk.2_5'UTR|OXR1_uc003yml.2_5'UTR	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	108091447	108091447	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108091447delT								ABRA (308975 upstream) : ANGPT1 (170264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108208086	108208086	+	IGR	DEL	T	-	-	rs78581330		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108208086delT								ABRA (425614 upstream) : ANGPT1 (53625 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108296808	108296808	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108296808delT	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_3'UTR	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	108685555	108685556	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108685555_108685556delAC								ANGPT1 (175301 upstream) : RSPO2 (225989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109140114	109140133	+	IGR	DEL	AAGGAAGGAAGGAAGGAAGG	-	-	rs71947791	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109140114_109140133delAAGGAAGGAAGGAAGGAAGG								RSPO2 (44201 upstream) : EIF3E (73840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109277511	109277513	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109277511_109277513delTTT								EIF3E (16552 upstream) : TTC35 (178340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109832864	109832864	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109832864delT								TMEM74 (33094 upstream) : TRHR (266875 downstream)																																			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110445693	110445694	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110445693_110445694insC	uc003yne.2	+							NM_177531	NP_803875			fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110460728	110460728	+	Intron	DEL	G	-	-	rs1673406		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110460728delG	uc003yne.2	+							NM_177531	NP_803875			fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
EBAG9	9166	broad.mit.edu	37	8	110573290	110573290	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110573290delT	uc003ynf.2	+						EBAG9_uc003yng.2_Intron	NM_198120	NP_936056			estrogen receptor binding site associated						apoptosis|regulation of cell growth	focal adhesion|Golgi membrane|integral to membrane|soluble fraction	apoptotic protease activator activity				0			OV - Ovarian serous cystadenocarcinoma(57;1.39e-14)															---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110664623	110664623	+	Intron	DEL	T	-	-	rs111759751		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110664623delT	uc010mct.2	-						SYBU_uc010mcs.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099745	NP_001093215			Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	110790905	110790905	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110790905delA								SYBU (86885 upstream) : KCNV1 (188330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110964705	110964705	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110964705delT								SYBU (260685 upstream) : KCNV1 (14530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111029546	111029547	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111029546_111029547delTT								KCNV1 (41470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111535345	111535345	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111535345delT								KCNV1 (547269 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111824238	111824238	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111824238delT								KCNV1 (836162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112374752	112374753	+	IGR	INS	-	ACAG	ACAG	rs142997585	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112374752_112374753insACAG								None (None upstream) : CSMD3 (860408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112388617	112388617	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112388617delT								None (None upstream) : CSMD3 (846544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	113171571	113171571	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113171571delA								None (None upstream) : CSMD3 (63590 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113693269	113693269	+	Intron	DEL	T	-	-	rs66829385		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113693269delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113702411	113702411	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113702411delT	uc003ynu.2	-						CSMD3_uc003yns.2_5'Flank|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113845920	113845921	+	Intron	DEL	TG	-	-	rs34246089		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113845920_113845921delTG	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115149056	115149056	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115149056delT								CSMD3 (699814 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115760385	115760385	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115760385delA								None (None upstream) : TRPS1 (660340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116009798	116009798	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116009798delA								None (None upstream) : TRPS1 (410927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116266134	116266134	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116266134delA								None (None upstream) : TRPS1 (154591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116310992	116310992	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116310992delT								None (None upstream) : TRPS1 (109733 downstream)																																			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116490031	116490031	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116490031delT	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831			zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	116888843	116888844	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116888843_116888844delAA								TRPS1 (207615 upstream) : EIF3H (768212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116893083	116893085	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116893083_116893085delTTT								TRPS1 (211855 upstream) : EIF3H (763971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118300889	118300890	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118300889_118300890insT								SLC30A8 (111937 upstream) : MED30 (232075 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118820106	118820107	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118820106_118820107delAA	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118946496	118946496	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118946496delA	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119251364	119251366	+	Intron	DEL	TGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119251364_119251366delTGA	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119498654	119498654	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119498654delA	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	119900279	119900279	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119900279delA								SAMD12 (266045 upstream) : TNFRSF11B (35518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119920765	119920765	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119920765delT								SAMD12 (286531 upstream) : TNFRSF11B (15032 downstream)																																			---	---	---	---
COLEC10	10584	broad.mit.edu	37	8	120102330	120102331	+	Intron	DEL	TT	-	-	rs3214976		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120102330_120102331delTT	uc003yoo.2	+							NM_006438	NP_006429			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)															---	---	---	---
MAL2	114569	broad.mit.edu	37	8	120238864	120238881	+	Intron	DEL	TGAAGGCAATTAAGAAAG	-	-	rs71836418		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120238864_120238881delTGAAGGCAATTAAGAAAG	uc003yop.2	+							NM_052886	NP_443118			MAL2 proteolipid protein							apical plasma membrane|endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding				0	all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)															---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120642354	120642354	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120642354delT	uc003yot.1	-						ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120805739	120805739	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120805739delT	uc003you.2	-							NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	120873967	120873967	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120873967delA								DSCC1 (5797 upstream) : DEPDC6 (11933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121867399	121867399	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121867399delT								SNTB1 (43090 upstream) : HAS2 (757872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121896325	121896325	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121896325delT								SNTB1 (72016 upstream) : HAS2 (728946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122087642	122087642	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122087642delA								SNTB1 (263333 upstream) : HAS2 (537629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122241134	122241135	+	IGR	INS	-	AC	AC	rs146382111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122241134_122241135insAC								SNTB1 (416825 upstream) : HAS2 (384136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122312149	122312150	+	IGR	INS	-	TGTC	TGTC	rs144138057	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122312149_122312150insTGTC								SNTB1 (487840 upstream) : HAS2 (313121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122570044	122570044	+	IGR	DEL	T	-	-	rs112325363		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122570044delT								SNTB1 (745735 upstream) : HAS2 (55227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123030709	123030709	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123030709delT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123557442	123557443	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123557442_123557443insG								HAS2AS (900509 upstream) : ZHX2 (236458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123781249	123781250	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123781249_123781250insA								None (None upstream) : ZHX2 (12651 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123981401	123981401	+	Intron	DEL	A	-	-	rs77758101		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123981401delA	uc003ypk.1	+							NM_014943	NP_055758			zinc fingers and homeoboxes 2							cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124110541	124110542	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124110541_124110542insT	uc003ypp.1	+						WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003yps.1_5'Flank|WDR67_uc003ypo.1_Intron|WDR67_uc003ypr.2_Intron	NM_145647	NP_663622			WD repeat domain 67 isoform 1							centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124413834	124413834	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124413834delC	uc003yqi.3	-						uc003yqk.2_5'Flank					Homo sapiens PRO2000 mRNA, complete cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124489272	124489272	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124489272delA								WDYHV1 (35012 upstream) : FBXO32 (26087 downstream)																																			---	---	---	---
FBXO32	114907	broad.mit.edu	37	8	124535874	124535874	+	Intron	DEL	C	-	-	rs13268187	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124535874delC	uc003yqr.2	-						FBXO32_uc003yqq.2_Intron|FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136			F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
FBXO32	114907	broad.mit.edu	37	8	124547489	124547489	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124547489delA	uc003yqr.2	-						FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136			F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
FAM91A1	157769	broad.mit.edu	37	8	124790387	124790387	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124790387delT	uc003yqv.2	+						FAM91A1_uc011lik.1_Intron|FAM91A1_uc011lil.1_Intron	NM_144963	NP_659400			hypothetical protein LOC157769											ovary(1)|central_nervous_system(1)	2	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124926079	124926080	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124926079_124926080insA	uc003yqw.2	+							NM_001039112	NP_001034201			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)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124946644	124946645	+	Intron	INS	-	G	G	rs140974505	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124946644_124946645insG	uc003yqw.2	+							NM_001039112	NP_001034201			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)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124946774	124946775	+	Intron	DEL	TT	-	-	rs34039461		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124946774_124946775delTT	uc003yqw.2	+							NM_001039112	NP_001034201			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125288690	125288691	+	IGR	INS	-	T	T	rs28504585		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125288690_125288691insT								FER1L6 (156389 upstream) : TMEM65 (34470 downstream)																																			---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126193433	126193434	+	Intron	INS	-	C	C	rs138360631	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126193433_126193434insC	uc003yrw.2	+						NSMCE2_uc003yrv.2_Intron	NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	126467360	126467361	+	IGR	DEL	AG	-	-	rs60408359		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126467360_126467361delAG								TRIB1 (16718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126518502	126518505	+	IGR	DEL	AAAA	-	-	rs34865156		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126518502_126518505delAAAA								TRIB1 (67860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126970575	126970576	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126970575_126970576delAC								TRIB1 (519933 upstream) : FAM84B (594111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127888868	127888868	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127888868delT								FAM84B (318402 upstream) : LOC727677 (413194 downstream)																																	OREG0018977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	8	128099579	128099579	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128099579delT								FAM84B (529113 upstream) : LOC727677 (202483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128699866	128699867	+	RNA	INS	-	A	A	rs138818064	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128699866_128699867insA	uc003ysg.2	-	3		c.2019_2020insT								Homo sapiens, clone IMAGE:5554747, mRNA.																														---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128901383	128901383	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128901383delT	uc010mdq.2	+						PVT1_uc003ysl.2_5'Flank|PVT1_uc010mdp.1_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	130107018	130107018	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130107018delA								MIR1208 (944584 upstream) : GSDMC (653425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	131049066	131049067	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131049066_131049067delAA								FAM49B (20169 upstream) : ASAP1 (15286 downstream)																																			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131812181	131812181	+	Intron	DEL	C	-	-	rs34976647		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131812181delC	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	132055594	132055594	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132055594delA	uc003ytd.3	-						ADCY8_uc010mds.2_5'Flank	NM_001115	NP_001106			adenylate cyclase 8						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132529651	132529651	+	IGR	DEL	C	-	-	rs2915016	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132529651delC								ADCY8 (476816 upstream) : EFR3A (386708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132740371	132740371	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132740371delT								ADCY8 (687536 upstream) : EFR3A (175988 downstream)																																			---	---	---	---
OC90	729330	broad.mit.edu	37	8	133040898	133040899	+	Intron	INS	-	AAGA	AAGA	rs142271215	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133040898_133040899insAAGA	uc003ytg.2	-						OC90_uc011lix.1_Intron	NM_001080399	NP_001073868			otoconin 90						lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)															---	---	---	---
HHLA1	10086	broad.mit.edu	37	8	133081603	133081603	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133081603delT	uc011liy.1	-						HHLA1_uc003yth.2_Intron	NM_001145095	NP_001138567			HERV-H LTR-associating 1							extracellular region					0																		---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133141659	133141659	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133141659delC	uc003ytj.2	-	15	2694	c.2469delG	c.(2467-2469)GGGfs	p.G823fs	KCNQ3_uc010mdt.2_Frame_Shift_Del_p.G811fs|uc003yti.2_5'Flank	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	823					axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133160502	133160503	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133160502_133160503insC	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133421708	133421710	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133421708_133421710delAAA	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133968816	133968817	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133968816_133968817delAA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron	NM_003235	NP_003226			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)														---	---	---	---
TG	7038	broad.mit.edu	37	8	134052224	134052225	+	Intron	DEL	AT	-	-	rs34759687		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134052224_134052225delAT	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc011ljd.1_Intron	NM_003235	NP_003226			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)														---	---	---	---
TG	7038	broad.mit.edu	37	8	134125651	134125651	+	Intron	DEL	T	-	-	rs72433148		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134125651delT	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron	NM_003235	NP_003226			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)														---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134207325	134207326	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134207325_134207326delTT	uc003yub.2	+						WISP1_uc003yuc.2_Intron|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron	NM_003882	NP_003873			WNT1 inducible signaling pathway protein 1						cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134903550	134903550	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134903550delT								ST3GAL1 (319367 upstream) : ZFAT (586483 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135602974	135602976	+	Intron	DEL	CAA	-	-	rs146800539		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135602974_135602976delCAA	uc003yup.2	-						ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	135857141	135857141	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135857141delT								MIR30D (39953 upstream) : LOC286094 (389233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136068865	136068877	+	IGR	DEL	AAAAAAAAAAAAC	-	-	rs140413857		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136068865_136068877delAAAAAAAAAAAAC								MIR30D (251677 upstream) : LOC286094 (177497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136184402	136184402	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136184402delG								MIR30D (367214 upstream) : LOC286094 (61972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136209457	136209458	+	IGR	INS	-	T	T	rs143366630	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136209457_136209458insT								MIR30D (392269 upstream) : LOC286094 (36916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136716899	136716899	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136716899delC								KHDRBS3 (57053 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137255029	137255029	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137255029delA								KHDRBS3 (595183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137658113	137658114	+	IGR	INS	-	GTGT	GTGT	rs148855151	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137658113_137658114insGTGT								KHDRBS3 (998267 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137893275	137893276	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137893275_137893276delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138939125	138939126	+	IGR	INS	-	A	A	rs146492080	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138939125_138939126insA								None (None upstream) : FAM135B (203142 downstream)																																			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139727809	139727809	+	Intron	DEL	T	-	-	rs5895555		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139727809delT	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	NM_152888	NP_690848			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)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139817035	139817036	+	Intron	INS	-	TA	TA	rs113949514		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139817035_139817036insTA	uc003yvd.2	-							NM_152888	NP_690848			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)												HNSCC(7;0.00092)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140230241	140230241	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140230241delC								COL22A1 (304005 upstream) : KCNK9 (382841 downstream)																																			---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140677169	140677169	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140677169delA	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron	NM_016601	NP_057685			potassium channel, subfamily K, member 9							integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	140939499	140939499	+	Intron	DEL	T	-	-	rs111550323		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140939499delT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141337343	141337343	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141337343delA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	141530800	141530800	+	IGR	DEL	A	-	-	rs33974530		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141530800delA								CHRAC1 (3548 upstream) : EIF2C2 (10465 downstream)																																			---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141688098	141688100	+	Intron	DEL	AGG	-	-	rs148764887		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141688098_141688100delAGG	uc003yvu.2	-						PTK2_uc011ljp.1_Intron|PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141810338	141810338	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141810338delT	uc003yvu.2	-						PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142026658	142026658	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142026658delG								PTK2 (15326 upstream) : DENND3 (112062 downstream)																																			---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142510285	142510285	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142510285delA	uc003ywi.2	-							NM_207414	NP_997297			hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142944566	142944566	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142944566delC								MIR1302-7 (76892 upstream) : NCRNA00051 (335151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143667057	143667057	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143667057delG								BAI1 (40690 upstream) : ARC (25353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143797840	143797840	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143797840delC								LY6K (12258 upstream) : C8orf55 (10781 downstream)																																			---	---	---	---
GLI4	2738	broad.mit.edu	37	8	144351008	144351009	+	Intron	INS	-	TGC	TGC	rs35029485		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144351008_144351009insTGC	uc003yxx.2	+						ZFP41_uc003yxv.2_Intron	NM_138465	NP_612474			GLI-Kruppel family member GLI4							nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)															---	---	---	---
GSDMD	79792	broad.mit.edu	37	8	144639483	144639524	+	Intron	DEL	TGGCGAAGGATGCTGCCGCTATGGTGAAGGATGCTGCCGCTT	-	-	rs71316898		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144639483_144639524delTGGCGAAGGATGCTGCCGCTATGGTGAAGGATGCTGCCGCTT	uc010mfe.2	+						uc003yye.2_RNA|GSDMD_uc003yyf.2_5'Flank|GSDMD_uc003yyi.2_5'Flank|GSDMD_uc003yyg.2_5'Flank|GSDMD_uc003yyh.2_5'Flank	NM_024736	NP_079012			gasdermin D												0																		---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144673074	144673074	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144673074delA	uc011lki.1	-						EEF1D_uc003yyp.1_5'Flank|EEF1D_uc003yyq.1_5'Flank|EEF1D_uc011lkj.1_Intron|EEF1D_uc003yyr.2_Intron|EEF1D_uc003yyt.2_Intron|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144940081	144940081	+	Intron	DEL	C	-	-	rs60421625		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940081delC	uc003zaa.1	-							NM_031308	NP_112598			epiplakin 1							cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145003563	145003563	+	Intron	DEL	G	-	-	rs140068101		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145003563delG	uc003zaf.1	-						PLEC_uc003zab.1_Intron|PLEC_uc003zac.1_Intron|PLEC_uc003zad.2_Intron|PLEC_uc003zae.1_Intron|PLEC_uc003zag.1_Intron|PLEC_uc003zah.2_Intron|PLEC_uc003zaj.2_Intron	NM_201380	NP_958782			plectin isoform 1						cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145098201	145098202	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145098201_145098202delTT	uc011lkw.1	+						SPATC1_uc011lkx.1_Intron	NM_198572	NP_940974			spermatogenesis and centriole associated 1											ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145099521	145099521	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145099521delT	uc011lkw.1	+						SPATC1_uc011lkx.1_Intron	NM_198572	NP_940974			spermatogenesis and centriole associated 1											ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145253520	145253520	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145253520delT	uc003zbk.3	+						HEATR7A_uc003zbh.3_Intron|HEATR7A_uc003zbi.3_Intron|HEATR7A_uc011lla.1_Intron|HEATR7A_uc010mft.2_Intron	NM_032450	NP_115826			HEAT repeat containing 7A isoform 1								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	145572743	145572743	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145572743delT								SCRT1 (12800 upstream) : C8ORFK29 (4144 downstream)																																			---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145886370	145886370	+	Intron	DEL	A	-	-	rs76400904		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145886370delA	uc011llk.1	-							NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
ZNF7	7553	broad.mit.edu	37	8	146058113	146058113	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146058113delA	uc003zeg.3	+						ZNF7_uc010mge.2_Intron|ZNF7_uc011lln.1_Intron|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zej.2_Intron|ZNF7_uc003zek.3_5'Flank	NM_003416	NP_003407			zinc finger protein 7						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	1102692	1102692	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1102692delC								DMRT2 (45139 upstream) : SMARCA2 (912650 downstream)																																			---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2047084	2047085	+	Intron	DEL	TT	-	-	rs113139565		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2047084_2047085delTT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	3029132	3029132	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3029132delT								KIAA0020 (185002 upstream) : RFX3 (195517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	3223161	3223161	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3223161delT								KIAA0020 (379031 upstream) : RFX3 (1488 downstream)																																			---	---	---	---
SLC1A1	6505	broad.mit.edu	37	9	4567629	4567629	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4567629delT	uc003zij.1	+						C9orf68_uc003zik.2_Intron	NM_004170	NP_004161			solute carrier family 1, member 1						D-aspartate import|L-glutamate import|synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)													---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5025539	5025539	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5025539delT	uc010mhm.2	+						JAK2_uc003ziw.2_Intron	NM_004972	NP_004963			Janus kinase 2						actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5066768	5066768	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5066768delT	uc010mhm.2	+	9	1418	c.1305delT	c.(1303-1305)TATfs	p.Y435fs	JAK2_uc003ziw.2_Frame_Shift_Del_p.Y435fs	NM_004972	NP_004963	O60674	JAK2_HUMAN	Janus kinase 2	435	SH2; atypical.				actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
KIAA2026	158358	broad.mit.edu	37	9	5988333	5988333	+	Intron	DEL	C	-	-	rs2291055	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5988333delC	uc003zjq.3	-							NM_001017969	NP_001017969			hypothetical protein LOC158358											ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)														---	---	---	---
IL33	90865	broad.mit.edu	37	9	6254567	6254568	+	Intron	DEL	AT	-	-	rs60420792		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6254567_6254568delAT	uc003zjt.2	+						IL33_uc011lmg.1_Intron|IL33_uc011lmh.1_Intron|IL33_uc003zju.1_Intron	NM_033439	NP_254274			interleukin 33 precursor						positive regulation of chemokine secretion|positive regulation of inflammatory response|positive regulation of macrophage activation|positive regulation of transcription from RNA polymerase II promoter	extracellular space	cytokine activity				0		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6647707	6647708	+	5'Flank	DEL	AC	-	-	rs35724588		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6647707_6647708delAC	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13143340	13143340	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13143340delT	uc010mia.1	-						MPDZ_uc010mhx.2_Intron|MPDZ_uc011lmm.1_Intron|MPDZ_uc003zkz.3_Intron|MPDZ_uc010mhy.2_Intron|MPDZ_uc010mhz.2_Intron|MPDZ_uc011lmn.1_Intron|MPDZ_uc003zlb.3_Intron	NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13281040	13281040	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13281040delA	uc003zlb.3	-							NM_003829	NP_003820			multiple PDZ domain protein						interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	15001532	15001532	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15001532delA	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19372238	19372238	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19372238delT	uc003znq.2	+	28					DENND4C_uc011lnc.1_3'UTR|DENND4C_uc011lnd.1_3'UTR|DENND4C_uc003znr.2_3'UTR|DENND4C_uc003zns.2_3'UTR	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	19383903	19383903	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19383903delA								RPS6 (3668 upstream) : ACER2 (13904 downstream)																																			---	---	---	---
SLC24A2	25769	broad.mit.edu	37	9	19694926	19694927	+	Intron	INS	-	T	T	rs146901828	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19694926_19694927insT	uc003zoa.1	-						SLC24A2_uc003zob.1_Intron	NM_020344	NP_065077			solute carrier family 24						visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)														---	---	---	---
DMRTA1	63951	broad.mit.edu	37	9	22451039	22451039	+	Intron	DEL	T	-	-	rs41270141	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22451039delT	uc003zpp.1	+							NM_022160	NP_071443			DMRT-like family A1						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|skin(1)	2		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	22462943	22462944	+	IGR	DEL	GT	-	-	rs35779009		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22462943_22462944delGT								DMRTA1 (10471 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23912663	23912663	+	IGR	DEL	G	-	-	rs62570305		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23912663delG								ELAVL2 (86600 upstream) : None (None downstream)																																			---	---	---	---
IFT74	80173	broad.mit.edu	37	9	26980558	26980558	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26980558delT	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693			coiled-coil domain containing 2 isoform a							cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)														---	---	---	---
MOBKL2B	79817	broad.mit.edu	37	9	27369194	27369196	+	Intron	DEL	CTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27369194_27369196delCTT	uc003zqn.2	-							NM_024761	NP_079037			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	30368654	30368655	+	IGR	INS	-	GT	GT	rs144014574	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30368654_30368655insGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30899312	30899314	+	IGR	DEL	TTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30899312_30899314delTTG								None (None upstream) : None (None downstream)																																			---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33836592	33836592	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33836592delA	uc003ztm.2	+							NM_017811	NP_060281			ubiquitin-conjugating enzyme UBC3B						protein K48-linked ubiquitination|protein monoubiquitination		ATP binding|ubiquitin-protein ligase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)														---	---	---	---
IL11RA	3590	broad.mit.edu	37	9	34655014	34655015	+	Intron	DEL	GC	-	-	rs59679449		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34655014_34655015delGC	uc003zvi.2	+						IL11RA_uc011loq.1_Intron|IL11RA_uc003zvj.2_Intron|IL11RA_uc003zvk.2_Intron|IL11RA_uc010mke.2_Intron|IL11RA_uc003zvl.2_Intron	NM_004512	NP_004503			interleukin 11 receptor, alpha isoform 1							integral to plasma membrane	cytokine receptor activity			skin(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)													---	---	---	---
GNE	10020	broad.mit.edu	37	9	36249530	36249530	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36249530delT	uc010mlh.2	-						CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_5'Flank|GNE_uc011lpl.1_Intron|GNE_uc010mli.2_Intron|GNE_uc010mlj.2_Intron	NM_005476	NP_005467			UDP-N-acetylglucosamine-2-epimerase/N-						cell adhesion|lipopolysaccharide biosynthetic process|N-acetylneuraminate metabolic process|UDP-N-acetylglucosamine metabolic process		ATP binding|N-acylmannosamine kinase activity|UDP-N-acetylglucosamine 2-epimerase activity				0			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	38359414	38359415	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38359414_38359415delTT								SHB (290204 upstream) : ALDH1B1 (33287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44770297	44770300	+	IGR	DEL	AAGC	-	-	rs142859330		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44770297_44770300delAAGC								None (None upstream) : FAM27C (219936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44877601	44877602	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44877601_44877602delAC								None (None upstream) : FAM27C (112634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45128833	45128833	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45128833delC								FAM27C (137342 upstream) : FAM27A (598196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45362789	45362791	+	IGR	DEL	TTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45362789_45362791delTTC								FAM27C (371298 upstream) : FAM27A (364238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45390207	45390210	+	IGR	DEL	CCTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45390207_45390210delCCTC								FAM27C (398716 upstream) : FAM27A (336819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66799202	66799203	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66799202_66799203delTT								LOC442421 (296175 upstream) : AQP7P1 (455064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66821222	66821223	+	IGR	DEL	CT	-	-	rs112498295		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66821222_66821223delCT								LOC442421 (318195 upstream) : AQP7P1 (433044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66832944	66832944	+	IGR	DEL	A	-	-	rs76409247		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66832944delA								LOC442421 (329917 upstream) : AQP7P1 (421323 downstream)																																			---	---	---	---
ANKRD20A3	441425	broad.mit.edu	37	9	67951854	67951854	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67951854delA	uc004aeu.2	+						ANKRD20A3_uc010mnn.2_Intron	NM_001012419	NP_001012419			ankyrin repeat domain 20 family, member A3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	68402732	68402733	+	IGR	INS	-	TGAAT	TGAAT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68402732_68402733insTGAAT								FAM27B (608543 upstream) : MIR1299 (599506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68426898	68426898	+	IGR	DEL	T	-	-	rs67299135		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68426898delT								FAM27B (632709 upstream) : MIR1299 (575341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68430746	68430746	+	IGR	DEL	T	-	-	rs113456947		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68430746delT								FAM27B (636557 upstream) : MIR1299 (571493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69056404	69056406	+	IGR	DEL	AAT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69056404_69056406delAAT								MIR1299 (54083 upstream) : PGM5P2 (23839 downstream)																																			---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71422317	71422317	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71422317delT	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71851219	71851219	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71851219delC	uc004ahe.2	+						TJP2_uc011lrs.1_Intron|TJP2_uc011lrt.1_Intron|TJP2_uc004ahd.2_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Intron	NM_004817	NP_004808			tight junction protein 2 (zona occludens 2)						cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	72611070	72611070	+	IGR	DEL	A	-	-	rs11325727		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72611070delA								C9orf135 (89923 upstream) : MAMDC2 (47427 downstream)																																			---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74364882	74364882	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74364882delT	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	77541135	77541135	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77541135delA								TRPM6 (38125 upstream) : C9orf40 (20365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78118337	78118337	+	IGR	DEL	A	-	-	rs34121105		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78118337delA								OSTF1 (356224 upstream) : PCSK5 (387223 downstream)																																			---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78536483	78536484	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78536483_78536484delTG	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	79187449	79187449	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79187449delG								GCNT1 (65119 upstream) : PRUNE2 (38844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79620107	79620107	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79620107delA								PRUNE2 (99104 upstream) : FOXB2 (14464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80711526	80711527	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80711526_80711527delTG								GNAQ (65334 upstream) : CEP78 (139464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81204966	81204966	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81204966delT								PSAT1 (259959 upstream) : TLE4 (981912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84007059	84007059	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84007059delA								None (None upstream) : TLE1 (191541 downstream)																																			---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84231712	84231712	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84231712delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86503511	86503511	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86503511delA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86583801	86583801	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86583801delA	uc004ang.3	-	17					HNRNPK_uc011lsw.1_3'UTR|HNRNPK_uc004and.3_3'UTR|HNRNPK_uc004ank.3_3'UTR|HNRNPK_uc004anf.3_3'UTR|HNRNPK_uc004anh.3_3'UTR|HNRNPK_uc011lsx.1_3'UTR|HNRNPK_uc004ani.3_3'UTR|HNRNPK_uc004anj.3_3'UTR|HNRNPK_uc004ann.3_3'UTR|HNRNPK_uc004anl.3_3'UTR|HNRNPK_uc004anm.3_3'UTR	NM_031262	NP_112552			heterogeneous nuclear ribonucleoprotein K						interspecies interaction between organisms|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of receptor-mediated endocytosis|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of low-density lipoprotein particle clearance|signal transduction	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nuclear chromatin|nucleoplasm	protein binding|RNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|single-stranded DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	87082382	87082383	+	IGR	DEL	TA	-	-	rs111685301		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87082382_87082383delTA								SLC28A3 (98969 upstream) : NTRK2 (201083 downstream)																																			---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88954433	88954434	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88954433_88954434delAA	uc004aoq.2	-						ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron|ZCCHC6_uc004aov.2_Intron	NM_024617	NP_078893			zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	90507985	90507986	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90507985_90507986insT								C9orf79 (4173 upstream) : FAM75C1 (21422 downstream)																																			---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92073590	92073591	+	Intron	DEL	AC	-	-	rs60334817		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92073590_92073591delAC	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369			semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92087093	92087093	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92087093delA	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369			semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94488677	94488677	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94488677delA	uc004arj.1	-						ROR2_uc004ari.1_Intron	NM_004560	NP_004551			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																		---	---	---	---
IARS	3376	broad.mit.edu	37	9	94985154	94985155	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94985154_94985155delAA	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203			isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
NOL8	55035	broad.mit.edu	37	9	95085870	95085871	+	Intron	DEL	AA	-	-	rs75489638		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95085870_95085871delAA	uc004arv.2	-						CENPP_uc004arz.2_5'Flank|CENPP_uc010mqx.2_5'Flank|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron|NOL8_uc004arx.2_Intron|CENPP_uc004ary.1_5'Flank	NM_017948	NP_060418			nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95396584	95396584	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95396584delA	uc004asl.1	-						IPPK_uc004ask.1_Intron	NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																OREG0019315	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95430185	95430185	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95430185delA	uc004asl.1	-							NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	95449219	95449219	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95449219delG								IPPK (16672 upstream) : BICD2 (24426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	95928721	95928722	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95928721_95928722delTT								NINJ1 (32151 upstream) : WNK2 (18490 downstream)																																			---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96065208	96065208	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96065208delT	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron	NM_006648	NP_006639			WNK lysine deficient protein kinase 2						intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12																		---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97668578	97668580	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97668578_97668580delAAA	uc004ava.2	+						C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212			aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	98774880	98774880	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98774880delT	uc010msa.1	+	4	1867	c.991delT	c.(991-993)TTTfs	p.F331fs	uc011lun.1_Intron					RecName: Full=Uncharacterized protein C9orf102;																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	98810046	98810046	+	IGR	DEL	A	-	-	rs148122302		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98810046delA								NCRNA00092 (26009 upstream) : HSD17B3 (187543 downstream)																																			---	---	---	---
HABP4	22927	broad.mit.edu	37	9	99220909	99220909	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99220909delT	uc010msg.2	+						HABP4_uc010msh.2_Intron	NM_014282	NP_055097			hyaluronan binding protein 4						platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|extracellular region|nucleus	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214)																---	---	---	---
NCBP1	4686	broad.mit.edu	37	9	100432048	100432048	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100432048delA	uc004axq.2	+							NM_002486	NP_002477			nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
NANS	54187	broad.mit.edu	37	9	100811304	100811305	+	Intron	DEL	AA	-	-	rs112265885		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100811304_100811305delAA	uc004ayb.2	+							NM_018946	NP_061819			N-acetylneuraminic acid phosphate synthase						lipopolysaccharide biosynthetic process	cytoplasm	N-acetylneuraminate synthase activity|N-acylneuraminate cytidylyltransferase activity|N-acylneuraminate-9-phosphate synthase activity			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
TBC1D2	55357	broad.mit.edu	37	9	101009308	101009309	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101009308_101009309delAA	uc011lvb.1	-						TBC1D2_uc004ayq.2_Intron|TBC1D2_uc004ayr.2_Intron|TBC1D2_uc004ayo.3_Intron	NM_018421	NP_060891			TBC1 domain family, member 2							cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)														---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101416171	101416172	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101416171_101416172insT	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
NR4A3	8013	broad.mit.edu	37	9	102626462	102626462	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102626462delA	uc004baf.1	+	8					NR4A3_uc004bag.1_3'UTR|NR4A3_uc004bai.2_3'UTR	NM_006981	NP_008912			nuclear receptor subfamily 4, group A, member 3						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding		EWSR1/NR4A3(140)|TAF15/NR4A3(33)	bone(173)	173		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)						T	EWSR1	extraskeletal myxoid chondrosarcoma								---	---	---	---
STX17	55014	broad.mit.edu	37	9	102680786	102680787	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102680786_102680787delTT	uc004bal.3	+						STX17_uc004bak.2_Intron|STX17_uc010msx.2_Intron|STX17_uc011lvd.1_Intron	NM_017919	NP_060389			syntaxin 17						intracellular protein transport|vesicle-mediated transport	endoplasmic reticulum|integral to membrane|nucleolus	SNAP receptor activity			large_intestine(1)	1		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	105859764	105859764	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105859764delA								CYLC2 (78994 upstream) : SMC2 (996777 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107691416	107691416	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107691416delA	uc004bcl.2	-						ABCA1_uc004bcm.2_5'Flank|uc010mtj.1_Intron	NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	108708722	108708723	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108708722_108708723delTT								TMEM38B (171278 upstream) : ZNF462 (916655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110502341	110502341	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110502341delA								KLF4 (250294 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110570549	110570549	+	IGR	DEL	G	-	-	rs117924504	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110570549delG								KLF4 (318502 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111281761	111281762	+	IGR	DEL	TT	-	-	rs35504476		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111281761_111281762delTT								None (None upstream) : ACTL7B (335109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111395079	111395079	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111395079delG								None (None upstream) : ACTL7B (221792 downstream)																																			---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112581971	112581972	+	Intron	INS	-	TG	TG	rs144647153	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112581971_112581972insTG	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
TXNDC8	255220	broad.mit.edu	37	9	113100104	113100105	+	5'UTR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113100104_113100105insC	uc004bes.2	-	1					TXNDC8_uc011lwl.1_5'UTR	NM_001003936	NP_001003936			thioredoxin domain containing 8						cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	Golgi apparatus	electron carrier activity|protein disulfide oxidoreductase activity				0																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113548015	113548015	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113548015delA	uc004bey.2	+						MUSK_uc004bez.1_Intron	NM_005592	NP_005583			skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114520479	114520479	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114520479delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron|C9orf84_uc004bfq.2_Intron|C9orf84_uc010mug.2_Intron	NM_173521	NP_775792			hypothetical protein LOC158401 isoform 1											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114649784	114649788	+	IGR	DEL	GCATG	-	-	rs112166630		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114649784_114649788delGCATG								C9orf84 (92561 upstream) : UGCG (9418 downstream)																																			---	---	---	---
C9orf43	257169	broad.mit.edu	37	9	116177428	116177428	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116177428delT	uc004bho.3	+						C9orf43_uc004bhp.2_Intron	NM_152786	NP_689999			hypothetical protein LOC257169												0																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116210707	116210707	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116210707delT	uc004bhq.2	+							NM_144488	NP_652759			regulator of G-protein signalling 3 isoform 6						inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117008145	117008145	+	Splice_Site	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117008145delG	uc011lxl.1	+	24	2935	c.2935_splice	c.e24-1	p.G979_splice	COL27A1_uc004bii.2_Splice_Site	NM_032888	NP_116277			collagen, type XXVII, alpha 1 precursor						cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118410226	118410226	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118410226delT								DEC1 (245303 upstream) : C9orf27 (240320 downstream)																																			---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118945389	118945389	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118945389delT	uc004bjn.2	+							NM_002581	NP_002572			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																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119501749	119501766	+	Intron	DEL	CTCTGGAATTTGCCCTCC	-	-	rs139010727	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119501749_119501766delCTCTGGAATTTGCCCTCC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	121512437	121512439	+	IGR	DEL	AAA	-	-	rs35528775		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121512437_121512439delAAA								None (None upstream) : DBC1 (416469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	123007117	123007117	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123007117delA								DBC1 (875378 upstream) : MIR147 (140 downstream)																																			---	---	---	---
C5	727	broad.mit.edu	37	9	123751833	123751834	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123751833_123751834delTT	uc004bkv.2	-							NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123896477	123896477	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123896477delT	uc004bkx.1	+						CEP110_uc004bky.1_Intron|CEP110_uc004bkz.1_Intron|CEP110_uc004bla.1_Intron	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123924690	123924690	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123924690delT	uc004bkx.1	+						CEP110_uc004blb.1_Intron|CEP110_uc010mvp.1_Intron	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	124155796	124155796	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124155796delA								STOM (23251 upstream) : GGTA1 (51473 downstream)																																			---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126165852	126165852	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126165852delG	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc010mwh.1_Intron|MIR601_hsa-mir-601|MI0003614_5'Flank	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126959696	126959697	+	IGR	INS	-	A	A	rs145156912	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126959696_126959697insA								LHX2 (164254 upstream) : NEK6 (60189 downstream)																																			---	---	---	---
PSMB7	5695	broad.mit.edu	37	9	127176290	127176290	+	Intron	DEL	A	-	-	rs79494574		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127176290delA	uc004boj.2	-						PSMB7_uc010mwm.2_Intron	NM_002799	NP_002790			proteasome beta 7 subunit proprotein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0																		---	---	---	---
GPR144	347088	broad.mit.edu	37	9	127231187	127231187	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127231187delC	uc010mwn.2	+						GPR144_uc004bom.1_Intron|GPR144_uc010mwo.1_Intron	NM_001161808	NP_001155280			G protein-coupled receptor 144						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127360927	127360932	+	Intron	DEL	AAAAAA	-	-	rs137950041		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127360927_127360932delAAAAAA	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591			nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127929982	127929983	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127929982_127929983insA	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
GAPVD1	26130	broad.mit.edu	37	9	128092597	128092601	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128092597_128092601delTTTTT	uc010mwx.2	+						GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron|GAPVD1_uc004bpr.2_Intron|GAPVD1_uc004bps.2_Intron|GAPVD1_uc010mwy.1_Intron	NM_015635	NP_056450			GTPase activating protein and VPS9 domains 1						endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	129326495	129326495	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129326495delG								FAM125B (52796 upstream) : LMX1B (50253 downstream)																																			---	---	---	---
CIZ1	25792	broad.mit.edu	37	9	130930808	130930809	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130930808_130930809delAA	uc004btt.2	-						CIZ1_uc004btr.2_Intron|CIZ1_uc004bts.2_Intron|CIZ1_uc011maq.1_Intron|CIZ1_uc004btu.2_Intron|CIZ1_uc011mar.1_Intron|CIZ1_uc011mas.1_Intron|CIZ1_uc004btw.2_Intron|CIZ1_uc004btv.2_Intron	NM_001131016	NP_001124488			CDKN1A interacting zinc finger protein 1 isoform							nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
CERCAM	51148	broad.mit.edu	37	9	131186544	131186544	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131186544delC	uc004buz.3	+	4	952	c.554delC	c.(553-555)ACCfs	p.T185fs	CERCAM_uc004buy.1_Frame_Shift_Del_p.T107fs|CERCAM_uc010mxz.2_Frame_Shift_Del_p.T107fs|CERCAM_uc010mya.1_Frame_Shift_Del_p.T26fs	NM_016174	NP_057258	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule 1	185					cellular component movement|leukocyte cell-cell adhesion|lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen|plasma membrane				pancreas(1)	1																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131361423	131361423	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131361423delT	uc004bvl.3	+						SPTAN1_uc011mbg.1_3'UTR|SPTAN1_uc011mbh.1_Intron|SPTAN1_uc004bvm.3_Intron|SPTAN1_uc004bvn.3_Intron	NM_003127	NP_003118			spectrin, alpha, non-erythrocytic 1						actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10																		---	---	---	---
SET	6418	broad.mit.edu	37	9	131451836	131451837	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131451836_131451837insC	uc004bvt.3	+						SET_uc004bvu.3_5'UTR|SET_uc010myg.2_RNA|SET_uc011mbj.1_5'Flank	NM_001122821	NP_001116293			SET translocation (myeloid leukemia-associated)						DNA replication|mRNA metabolic process|negative regulation of histone acetylation|negative regulation of neuron apoptosis|negative regulation of transcription, DNA-dependent|nucleocytoplasmic transport|nucleosome assembly|nucleosome disassembly	cytosol|endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm|protein complex	histone binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0		Myeloproliferative disorder(178;0.204)		GBM - Glioblastoma multiforme(294;3.1e-09)				T	NUP214	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	9	131999532	131999532	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131999532delG								IER5L (58992 upstream) : C9orf106 (83763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132194343	132194343	+	IGR	DEL	G	-	-	rs67048043		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132194343delG								C9orf106 (109461 upstream) : C9orf50 (180163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	134676700	134676701	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134676700_134676701delTG								RAPGEF1 (61483 upstream) : MED27 (58798 downstream)																																			---	---	---	---
REXO4	57109	broad.mit.edu	37	9	136272788	136272788	+	Intron	DEL	T	-	-	rs35694504		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136272788delT	uc004cdm.2	-						REXO4_uc011mde.1_Intron|REXO4_uc011mdf.1_Intron|REXO4_uc004cdn.2_Intron|REXO4_uc004cdo.2_Intron	NM_020385	NP_065118			XPMC2 prevents mitotic catastrophe 2 homolog							nucleolus	exonuclease activity|nucleic acid binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)												OREG0019587	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136657133	136657134	+	Intron	INS	-	CA	CA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136657133_136657134insCA	uc004ces.2	-						VAV2_uc004cer.2_Intron|VAV2_uc004cet.1_5'Flank	NM_001134398	NP_001127870			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)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136795503	136795504	+	Intron	INS	-	CTGCCTCCTGGCCTCCACC	CTGCCTCCTGGCCTCCACC	rs140586685	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136795503_136795504insCTGCCTCCTGGCCTCCACC	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			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)														---	---	---	---
NCRNA00094	266655	broad.mit.edu	37	9	136890368	136890368	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136890368delT	uc004ceu.2	+							NR_015427				Homo sapiens cDNA FLJ35348 fis, clone PROST2016918.												0																		---	---	---	---
BRD3	8019	broad.mit.edu	37	9	136915413	136915413	+	Intron	DEL	C	-	-	rs148250297	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136915413delC	uc004cew.2	-						BRD3_uc004cex.2_Intron	NM_007371	NP_031397			bromodomain containing protein 3							nucleus	protein binding		BRD3/C15orf55(3)	stomach(4)|midline_organs(3)|kidney(1)	8				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)				T	NUT|C15orf55	lethal midline carcinoma of young people								---	---	---	---
Unknown	0	broad.mit.edu	37	9	137379857	137379864	+	IGR	DEL	CCTTTCTC	-	-	rs68173061	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137379857_137379864delCCTTTCTC								RXRA (47426 upstream) : COL5A1 (153788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	137752456	137752456	+	Intron	DEL	A	-	-	rs34441602		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137752456delA	uc004cff.2	-											Homo sapiens cDNA clone IMAGE:5468304, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	138117500	138117501	+	IGR	INS	-	CA	CA	rs142327134	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138117500_138117501insCA								OLFM1 (104469 upstream) : KIAA0649 (254147 downstream)																																			---	---	---	---
C9orf86	55684	broad.mit.edu	37	9	139734212	139734212	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139734212delC	uc004cji.1	+	13	2093	c.1825delC	c.(1825-1827)CCCfs	p.P609fs	C9orf86_uc004cjj.1_Frame_Shift_Del_p.P610fs|C9orf86_uc004cjk.1_RNA|C9orf86_uc010nbr.1_Intron|C9orf86_uc004cjl.1_RNA|C9orf86_uc010nbs.1_Frame_Shift_Del_p.P494fs|C9orf86_uc004cjn.1_Frame_Shift_Del_p.P403fs	NM_024718	NP_078994	Q3YEC7	PARF_HUMAN	Rab-like GTP-binding protein 1 isoform 1	609					small GTPase mediated signal transduction	cytoplasm|nucleus	GTP binding|protein binding				0	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.61e-05)|Epithelial(140;0.000183)														---	---	---	---
MAN1B1	11253	broad.mit.edu	37	9	139982205	139982205	+	Intron	DEL	C	-	-	rs78083648	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139982205delC	uc004cld.2	+						MAN1B1_uc004clc.2_Intron|MAN1B1_uc011meo.1_Intron|MAN1B1_uc011mep.1_Intron|MAN1B1_uc010ncc.2_Intron|LOC100289341_uc004clb.3_5'Flank	NM_016219	NP_057303			alpha 1,2-mannosidase						oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|endoplasmic reticulum quality control compartment|integral to membrane	alpha-mannosidase activity|calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140229535	140229536	+	Intron	DEL	AA	-	-	rs79120496		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140229535_140229536delAA	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
NELF	26012	broad.mit.edu	37	9	140350660	140350660	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140350660delG	uc004cna.2	-						C9orf167_uc011mew.1_Intron|NELF_uc011mex.1_5'Flank|NELF_uc010nci.2_Intron|NELF_uc011mey.1_Intron|NELF_uc011mez.1_Intron|NELF_uc004cmz.2_Intron|NELF_uc004cnc.2_Intron|NELF_uc004cnb.2_Intron	NM_001130969	NP_001124441			nasal embryonic LHRH factor isoform a							nucleus|plasma membrane					0	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000222)|Epithelial(140;0.000888)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140681665	140681665	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140681665delA	uc011mfc.1	+						EHMT1_uc004cob.1_Intron	NM_024757	NP_079033			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)														---	---	---	---
FAM157B	100132403	broad.mit.edu	37	9	141105199	141105199	+	5'Flank	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:141105199delC	uc011mfe.1	+							NM_001145249	NP_001138721			family with sequence similarity 157, member B												0																		---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1056344	1056344	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1056344delT	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1335150	1335151	+	Intron	INS	-	GA	GA	rs142713848	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1335150_1335151insGA	uc009xhq.2	-							NM_018702	NP_061172			adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	2011041	2011041	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2011041delA								ADARB2 (231323 upstream) : None (None downstream)																																			---	---	---	---
AKR1E2	83592	broad.mit.edu	37	10	4889684	4889684	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4889684delA	uc001ihi.2	+	10	1040	c.925delA	c.(925-927)AAAfs	p.K309fs	AKR1E2_uc001ihl.1_Intron|AKR1E2_uc009xhw.2_Frame_Shift_Del_p.K211fs|AKR1E2_uc001ihj.2_RNA|AKR1E2_uc001ihk.2_Frame_Shift_Del_p.K252fs	NM_001040177	NP_001035267	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	309						cytoplasm	1,5-anhydro-D-fructose reductase activity				0																		---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5762987	5762987	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5762987delT	uc001iij.2	+							NM_017782	NP_060252			hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6307852	6307853	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6307852_6307853delTT								PFKFB3 (30347 upstream) : PRKCQ (161252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7555735	7555735	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7555735delT								SFMBT2 (102285 upstream) : ITIH5 (45901 downstream)																																			---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7749273	7749275	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7749273_7749275delTTT	uc001ijs.2	+							NM_002216	NP_002207			inter-alpha globulin inhibitor H2 polypeptide						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11047219	11047226	+	5'Flank	DEL	GAGAGAGA	-	-	rs68120130		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11047219_11047226delGAGAGAGA	uc001iki.3	+						CELF2_uc010qbi.1_5'Flank|CELF2_uc010qbj.1_5'Flank	NM_001025077	NP_001020248			CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
C10orf47	254427	broad.mit.edu	37	10	11908096	11908097	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11908096_11908097delAA	uc001ikx.2	+						uc001iky.1_Intron	NM_153256	NP_694988			hypothetical protein LOC254427											central_nervous_system(1)	1																		---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12671038	12671038	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12671038delG	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
UCMA	221044	broad.mit.edu	37	10	13269715	13269718	+	Intron	DEL	AAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13269715_13269718delAAAA	uc001imd.2	-							NM_145314	NP_660357			upper zone of growth plate and cartilage matrix							proteinaceous extracellular matrix					0																		---	---	---	---
CDNF	441549	broad.mit.edu	37	10	14870843	14870843	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14870843delA	uc001inb.1	-						CDNF_uc010qbv.1_Intron|CDNF_uc001inc.1_Intron	NM_001029954	NP_001025125			arginine-rich, mutated in early stage							extracellular region	growth factor activity				0																		---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16831047	16831047	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16831047delA	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron|RSU1_uc001ion.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17008453	17008453	+	Intron	DEL	T	-	-	rs71838437		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17008453delT	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
VIM	7431	broad.mit.edu	37	10	17277960	17277960	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17277960delT	uc001iou.2	+						VIM_uc001iov.1_Intron|VIM_uc001iow.1_Intron|VIM_uc001iox.1_Intron|VIM_uc001ioy.1_Intron|VIM_uc001ioz.1_Intron|VIM_uc001ipb.1_Intron|VIM_uc009xjv.1_Intron|VIM_uc001ipc.1_Intron	NM_003380	NP_003371			vimentin						cellular component disassembly involved in apoptosis|cellular component movement|interspecies interaction between organisms|muscle filament sliding	cytosol|intermediate filament	protein C-terminus binding|structural constituent of cytoskeleton			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20453386	20453386	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20453386delT	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	20662125	20662125	+	IGR	DEL	C	-	-	rs77218392		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20662125delC								PLXDC2 (93010 upstream) : NEBL (406780 downstream)																																			---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21276119	21276119	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21276119delT	uc001iqk.2	-							NM_213569	NP_998734			nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	21505701	21505702	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21505701_21505702delAA								NEBL (42585 upstream) : C10orf114 (277720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21677529	21677529	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21677529delA								NEBL (214413 upstream) : C10orf114 (105893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21700978	21700978	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21700978delA								NEBL (237862 upstream) : C10orf114 (82444 downstream)																																			---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24890792	24890792	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24890792delT	uc001isb.2	-						ARHGAP21_uc010qdb.1_Intron|ARHGAP21_uc009xkl.1_Intron|ARHGAP21_uc010qdc.1_Intron	NM_020824	NP_065875			Rho GTPase activating protein 21						signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27356351	27356352	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27356351_27356352delTT	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730			ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28547188	28547189	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28547188_28547189delAA	uc001iua.1	-						MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	29458621	29458621	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29458621delT								BAMBI (486753 upstream) : LYZL1 (119369 downstream)																																			---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30362576	30362577	+	Intron	INS	-	TCCT	TCCT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30362576_30362577insTCCT	uc001iuz.2	-											RecName: Full=Uncharacterized protein KIAA1462;											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30684719	30684720	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30684719_30684720insT								MTPAP (21342 upstream) : MAP3K8 (38146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31349197	31349197	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31349197delA								ZNF438 (28331 upstream) : LOC220930 (256261 downstream)																																			---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31750177	31750177	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31750177delT	uc001ivs.3	+						ZEB1_uc001ivr.3_Intron|ZEB1_uc010qee.1_Intron|ZEB1_uc010qef.1_Intron|ZEB1_uc009xlh.1_Intron|ZEB1_uc009xli.1_Intron|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_Intron|ZEB1_uc001ivt.3_Intron|ZEB1_uc001ivu.3_Intron|ZEB1_uc001ivv.3_Intron|ZEB1_uc010qeh.1_Intron|ZEB1_uc009xll.2_Intron|ZEB1_uc009xlm.1_Intron|ZEB1_uc009xln.1_Intron|ZEB1_uc009xlo.1_Intron|ZEB1_uc009xlp.2_Intron	NM_030751	NP_110378			zinc finger E-box binding homeobox 1 isoform b						cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
KIF5B	3799	broad.mit.edu	37	10	32329483	32329484	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32329483_32329484delAA	uc001iwe.3	-							NM_004521	NP_004512			kinesin family member 5B						stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	34250282	34250283	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34250282_34250283delTT								NRP1 (626276 upstream) : PARD3 (149815 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34550772	34550779	+	Intron	DEL	ACACACAC	-	-	rs72445310	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34550772_34550779delACACACAC	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	36671043	36671044	+	IGR	DEL	TT	-	-	rs140585256		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36671043_36671044delTT								FZD8 (740681 upstream) : ANKRD30A (743741 downstream)																																			---	---	---	---
ZNF248	57209	broad.mit.edu	37	10	38109196	38109197	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38109196_38109197delCT	uc009xmc.2	-						ZNF248_uc001izb.2_Intron					SubName: Full=ZNF248 protein; SubName: Full=Zinc finger protein 248; SubName: Full=Zinc finger protein 248, isoform CRA_b;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38210363	38210363	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38210363delT								ZNF248 (63351 upstream) : ZNF25 (28432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39124538	39124542	+	IGR	DEL	GGAAT	-	-	rs66758419		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39124538_39124542delGGAAT								LOC399744 (383458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42451185	42451186	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42451185_42451186insG								None (None upstream) : LOC441666 (376129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42614291	42614292	+	IGR	DEL	GC	-	-	rs113632191		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42614291_42614292delGC								None (None upstream) : LOC441666 (213023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42643837	42643837	+	IGR	DEL	A	-	-	rs145388281	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42643837delA								None (None upstream) : LOC441666 (183478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42662461	42662461	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42662461delA								None (None upstream) : LOC441666 (164854 downstream)																																			---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43303301	43303302	+	Intron	DEL	CA	-	-	rs151119002		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43303301_43303302delCA	uc001jaj.2	+							NM_014753	NP_055568			BMS1-like, ribosome assembly protein						ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
HNRNPF	3185	broad.mit.edu	37	10	43903094	43903094	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43903094delA	uc001jas.2	-						HNRNPF_uc001jat.2_Intron|HNRNPF_uc001jav.2_Intron|HNRNPF_uc001jau.2_Intron	NM_001098206	NP_001091676			heterogeneous nuclear ribonucleoprotein F						regulation of RNA splicing	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44579107	44579108	+	IGR	INS	-	GT	GT	rs151213869	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44579107_44579108insGT								HNRNPA3P1 (293242 upstream) : CXCL12 (286499 downstream)																																			---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	46049282	46049283	+	Intron	DEL	CA	-	-	rs35051312		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46049282_46049283delCA	uc001jcj.1	-						MARCH8_uc001jck.1_Intron	NM_001002265	NP_001002265			cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	46985613	46985614	+	IGR	DEL	TT	-	-	rs77607175		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46985613_46985614delTT								SYT15 (15012 upstream) : GPRIN2 (7932 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47021225	47021225	+	Intron	DEL	C	-	-	rs9330488	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47021225delC	uc001jed.3	-											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																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47062881	47062882	+	Intron	INS	-	T	T	rs142898535		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47062881_47062882insT	uc001jed.3	-											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																		---	---	---	---
FAM21B	55747	broad.mit.edu	37	10	47909378	47909378	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47909378delA	uc009xni.2	+						FAM21B_uc001jep.3_Intron	NM_018232	NP_060702			hypothetical protein LOC55747						retrograde transport, endosome to Golgi	early endosome membrane|WASH complex				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	48980053	48980053	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48980053delA	uc001jgc.1	+											full-length cDNA clone CS0DI009YC01 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49632499	49632499	+	Intron	DEL	T	-	-	rs78072348		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49632499delT	uc009xnz.2	+						MAPK8_uc001jgl.2_Intron|MAPK8_uc001jgm.2_Intron|MAPK8_uc001jgo.2_Intron|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Intron|MAPK8_uc010qgk.1_Intron|MAPK8_uc001jgp.2_Intron|MAPK8_uc001jgq.2_Intron	NM_139047	NP_620635			mitogen-activated protein kinase 8 isoform JNK1						activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|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|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	51821149	51821150	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51821149_51821150insC	uc001jiz.1	-											Homo sapiens cDNA FLJ31813 fis, clone NT2RI2009517.																														---	---	---	---
A1CF	29974	broad.mit.edu	37	10	52566433	52566433	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52566433delT	uc001jjj.2	-	13					A1CF_uc010qhn.1_3'UTR|A1CF_uc001jji.2_3'UTR|A1CF_uc001jjh.2_3'UTR|A1CF_uc010qho.1_3'UTR|A1CF_uc009xov.2_3'UTR	NM_138932	NP_620310			apobec-1 complementation factor isoform 2						cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	54335556	54335557	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54335556_54335557delAA								DKK1 (258140 upstream) : MBL2 (189584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55033324	55033324	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55033324delA								MBL2 (501864 upstream) : PCDH15 (529211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55308365	55308366	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55308365_55308366delAG								MBL2 (776905 upstream) : PCDH15 (254169 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56238568	56238569	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56238568_56238569insA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56359666	56359666	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56359666delA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
ANK3	288	broad.mit.edu	37	10	62201855	62201855	+	Intron	DEL	T	-	-	rs71954214		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62201855delT	uc010qih.1	-						ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_001149	NP_001140			ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64022583	64022584	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64022583_64022584delAA	uc001jlw.2	-						ZNF365_uc001jly.3_Intron|RTKN2_uc001jlx.2_Intron	NM_145307	NP_660350			rhotekin 2						signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)																	---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68135348	68135349	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68135348_68135349delAA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
HERC4	26091	broad.mit.edu	37	10	69743720	69743720	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69743720delA	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_Intron	NM_022079	NP_071362			hect domain and RLD 4 isoform a						cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70672842	70672842	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70672842delA	uc001jou.2	+						DDX50_uc001jot.2_Intron|DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70708584	70708585	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70708584_70708585insA								DDX50 (1982 upstream) : DDX21 (7307 downstream)																																			---	---	---	---
PPA1	5464	broad.mit.edu	37	10	71963161	71963161	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71963161delT	uc001jqv.1	-							NM_021129	NP_066952			pyrophosphatase 1						diphosphate metabolic process|tRNA aminoacylation for protein translation	cytosol	inorganic diphosphatase activity|magnesium ion binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72216821	72216821	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72216821delT								NODAL (15356 upstream) : KIAA1274 (21743 downstream)																																			---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72617506	72617506	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72617506delT	uc001jrm.2	+							NM_003901	NP_003892			sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
CBARA1	10367	broad.mit.edu	37	10	74267946	74267946	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74267946delA	uc001jtb.1	-	7	758	c.625delT	c.(625-627)TCAfs	p.S209fs	CBARA1_uc010qjw.1_5'UTR|CBARA1_uc010qjx.1_Intron|CBARA1_uc009xqo.1_RNA	NM_006077	NP_006068	Q9BPX6	MICU1_HUMAN	calcium binding atopy-related autoantigen 1	207					calcium ion import|defense response|elevation of mitochondrial calcium ion concentration	integral to membrane|mitochondrial inner membrane	calcium ion binding|protein binding			ovary(1)	1																		---	---	---	---
USP54	159195	broad.mit.edu	37	10	75286617	75286617	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75286617delA	uc001juo.2	-						USP54_uc001juk.2_Intron|USP54_uc001jul.2_Intron|USP54_uc001jum.2_Intron|USP54_uc001jun.2_Intron|USP54_uc001jup.2_Intron	NM_152586	NP_689799			ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
USP54	159195	broad.mit.edu	37	10	75299152	75299152	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75299152delT	uc001juo.2	-						USP54_uc001jum.2_Intron|USP54_uc001jun.2_Intron|USP54_uc001jup.2_Intron|USP54_uc010qkl.1_Intron|USP54_uc001juq.1_Intron	NM_152586	NP_689799			ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
VDAC2	7417	broad.mit.edu	37	10	76981855	76981855	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76981855delA	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366			voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)													---	---	---	---
MIR606	693191	broad.mit.edu	37	10	77312184	77312184	+	5'Flank	DEL	C	-	-	rs1367290		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312184delC	hsa-mir-606|MI0003619	+																							0																		---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	78021243	78021243	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78021243delA	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81032041	81032041	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81032041delA	uc001kaf.2	+						ZMIZ1_uc001kag.2_Intron	NM_020338	NP_065071			retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
C10orf57	80195	broad.mit.edu	37	10	81841885	81841885	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81841885delT	uc001kbl.2	+						LOC219347_uc001kbi.3_5'Flank|LOC219347_uc009xsk.2_5'Flank|LOC219347_uc009xsl.2_5'Flank|LOC219347_uc009xsm.2_5'Flank|LOC219347_uc001kbj.3_5'Flank|C10orf57_uc009xsn.2_Intron|C10orf57_uc010qlv.1_Intron|C10orf57_uc010qlw.1_Intron|C10orf57_uc001kbn.3_Intron|C10orf57_uc009xsp.2_Intron|C10orf57_uc001kbo.3_Intron	NM_025125	NP_079401			hypothetical protein LOC80195							integral to membrane					0	Prostate(51;0.0095)|all_epithelial(25;0.175)		Epithelial(14;0.0793)|Colorectal(32;0.109)|all cancers(16;0.154)															---	---	---	---
ANXA11	311	broad.mit.edu	37	10	81916277	81916277	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81916277delT	uc001kbq.1	-						ANXA11_uc010qlx.1_Intron|ANXA11_uc001kbr.1_Intron|ANXA11_uc001kbs.1_Intron|ANXA11_uc001kbt.1_Intron|ANXA11_uc010qly.1_Intron|ANXA11_uc009xsq.1_Intron|ANXA11_uc001kbu.1_Intron	NM_145869	NP_665876			annexin A11						cell cycle|cytokinesis, completion of separation|phagocytosis|response to calcium ion	azurophil granule|melanosome|midbody|nuclear envelope|nucleoplasm|phagocytic vesicle|specific granule|spindle	calcium-dependent phospholipid binding|calcium-dependent protein binding|S100 alpha binding			ovary(1)	1	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82060467	82060468	+	IGR	INS	-	A	A	rs76473443		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82060467_82060468insA								MAT1A (11033 upstream) : DYDC1 (35396 downstream)																																			---	---	---	---
SH2D4B	387694	broad.mit.edu	37	10	82403551	82403551	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82403551delT	uc001kck.1	+						SH2D4B_uc001kcl.1_Intron|SH2D4B_uc001kcm.1_Intron|SH2D4B_uc001kcn.1_Intron	NM_207372	NP_997255			SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	83258233	83258233	+	IGR	DEL	T	-	-	rs67086534		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83258233delT								SH2D4B (851917 upstream) : NRG3 (376837 downstream)																																			---	---	---	---
GHITM	27069	broad.mit.edu	37	10	85910380	85910380	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85910380delT	uc001kcs.1	+						GHITM_uc010qma.1_Intron|GHITM_uc010qmb.1_Intron	NM_014394	NP_055209			growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
C10orf99	387695	broad.mit.edu	37	10	85944312	85944313	+	Intron	INS	-	T	T	rs113216230		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85944312_85944313insT	uc001kcu.2	+							NM_207373	NP_997256			hypothetical protein LOC387695 precursor							extracellular region				pancreas(1)	1																		---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86215040	86215042	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86215040_86215042delTTT	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86787405	86787405	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86787405delT								FAM190B (509129 upstream) : GRID1 (571907 downstream)																																			---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88596063	88596064	+	Intron	INS	-	CTTTA	CTTTA	rs143426955	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88596063_88596064insCTTTA	uc001kdy.2	+							NM_004329	NP_004320			bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8								Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				---	---	---	---
FAM35A	54537	broad.mit.edu	37	10	88930220	88930220	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88930220delT	uc001kei.3	+						FAM35A_uc001kej.3_Intron	NM_019054	NP_061927			hypothetical protein LOC54537											ovary(2)|skin(2)	4																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90682146	90682146	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90682146delA	uc001kfk.2	+	10	1630	c.1207delA	c.(1207-1209)AAAfs	p.K403fs	STAMBPL1_uc010qmx.1_Frame_Shift_Del_p.K403fs|STAMBPL1_uc009xto.2_RNA|STAMBPL1_uc001kfl.2_Frame_Shift_Del_p.K403fs|STAMBPL1_uc001kfn.2_Frame_Shift_Del_p.K237fs	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	403							metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
IFIT1	3434	broad.mit.edu	37	10	91155578	91155578	+	Intron	DEL	A	-	-	rs77969642		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91155578delA	uc001kgi.2	+						LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron|IFIT1_uc009xtt.2_Intron|IFIT1_uc001kgj.2_5'Flank	NM_001548	NP_001539			interferon-induced protein with						cellular response to exogenous dsRNA|intracellular transport of viral proteins in host cell|negative regulation of defense response to virus by host|negative regulation of helicase activity|negative regulation of protein binding|negative regulation of viral genome replication|positive regulation of viral genome replication|response to virus|type I interferon-mediated signaling pathway	cytoplasm	protein binding				0																		---	---	---	---
MARCH5	54708	broad.mit.edu	37	10	94066970	94066971	+	Intron	DEL	GC	-	-	rs61157486		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94066970_94066971delGC	uc001khx.1	+						MARCH5_uc010qno.1_Intron	NM_017824	NP_060294			membrane-associated ring finger (C3HC4) 5						cell aging|protein autoubiquitination|protein localization in mitochondrion|protein polyubiquitination|regulation of mitochondrial fission	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	GTPase binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94702782	94702782	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94702782delT	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			SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
PDE6C	5146	broad.mit.edu	37	10	95415723	95415724	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95415723_95415724delAC	uc001kiu.3	+							NM_006204	NP_006195			phosphodiesterase 6C						visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)|skin(1)	4		Colorectal(252;0.123)																---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97317235	97317235	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97317235delA	uc001kkw.2	-						SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
C10orf131	100127889	broad.mit.edu	37	10	97686606	97686607	+	Intron	DEL	TG	-	-	rs72143165		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97686606_97686607delTG	uc010qoo.1	+						uc001klg.1_Intron|uc001klj.1_Intron	NM_001130446	NP_001123918			hypothetical protein LOC100127889												0																		---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98739920	98739921	+	5'Flank	DEL	AA	-	-	rs5787211		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98739920_98739921delAA	uc001kmv.2	+						C10orf12_uc009xvg.1_Intron	NM_015652	NP_056467			hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	100104312	100104314	+	IGR	DEL	TCT	-	-	rs7081279	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100104312_100104314delTCT								LOXL4 (76305 upstream) : PYROXD2 (39009 downstream)																																			---	---	---	---
HPS1	3257	broad.mit.edu	37	10	100204031	100204031	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100204031delA	uc010qpf.1	-						HPS1_uc001kpi.1_Intron|HPS1_uc001kpk.1_Intron|HPS1_uc009xwb.2_Intron|HPS1_uc010qph.1_Intron|HPS1_uc001kpl.2_Intron|HPS1_uc001kpm.1_Intron	NM_000195	NP_000186			Hermansky-Pudlak syndrome 1 protein isoform a						lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity			skin(1)	1		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)										Hermansky-Pudlak_syndrome		OREG0031976	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)	---	---	---	---
Unknown	0	broad.mit.edu	37	10	102179071	102179071	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102179071delA								C10orf75 (30957 upstream) : WNT8B (43741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102405818	102405821	+	IGR	DEL	GAGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102405818_102405821delGAGA								HIF1AN (92138 upstream) : PAX2 (99647 downstream)																																			---	---	---	---
TLX1NB	100038246	broad.mit.edu	37	10	102888859	102888860	+	Intron	INS	-	T	T	rs146757692	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102888859_102888860insT	uc001ksv.2	-						TLX1_uc001ksw.2_5'Flank	NM_001085398	NP_001078867			TLX1 divergent												0																		---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104682888	104682888	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104682888delT	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron|CNNM2_uc001kwl.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105179557	105179557	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105179557delT	uc001kwy.1	+							NM_014976	NP_055791			programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105194784	105194784	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105194784delA	uc001kwy.1	+							NM_014976	NP_055791			programmed cell death 11						mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
NEURL	9148	broad.mit.edu	37	10	105351810	105351810	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105351810delT	uc001kxh.2	+	6					SH3PXD2A_uc010qqr.1_Intron	NM_004210	NP_004201			neuralized-like						nervous system development	perinuclear region of cytoplasm	zinc ion binding				0				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	109806803	109806803	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109806803delA								SORCS1 (882511 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110196898	110196898	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110196898delG								None (None upstream) : None (None downstream)																																			---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111651337	111651337	+	Intron	DEL	T	-	-	rs112429910		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111651337delT	uc001kyp.1	-						XPNPEP1_uc009xxt.1_Intron|XPNPEP1_uc001kyq.1_Intron|XPNPEP1_uc010qrb.1_Intron	NM_020383	NP_065116			X-prolyl aminopeptidase (aminopeptidase P) 1,						bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	111908269	111908269	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111908269delT								ADD3 (12949 upstream) : MXI1 (59094 downstream)																																			---	---	---	---
PDCD4	27250	broad.mit.edu	37	10	112657766	112657766	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112657766delT	uc001kzh.2	+						PDCD4_uc001kzg.2_Intron|PDCD4_uc010qre.1_Intron	NM_014456	NP_055271			programmed cell death 4 isoform 1						apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	116977035	116977035	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116977035delG	uc001lcg.2	+							NM_207303	NP_997186			attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118707457	118707457	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118707457delA	uc009xyw.2	-						KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Intron|KIAA1598_uc010qsq.1_Intron|KIAA1598_uc001lcy.3_Intron	NM_001127211	NP_001120683			shootin1 isoform a						axon guidance	axon					0				all cancers(201;0.00494)														---	---	---	---
KCNK18	338567	broad.mit.edu	37	10	118956864	118956865	+	5'Flank	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118956864_118956865insG	uc010qsr.1	+							NM_181840	NP_862823			potassium channel, subfamily K, member 18							integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)														---	---	---	---
SLC18A2	6571	broad.mit.edu	37	10	119028673	119028674	+	Intron	INS	-	ACAC	ACAC	rs140277762	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119028673_119028674insACAC	uc001ldd.1	+						SLC18A2_uc009xyy.1_Intron	NM_003054	NP_003045			solute carrier family 18 (vesicular monoamine),						neurotransmitter secretion	clathrin sculpted monoamine transport vesicle membrane|integral to plasma membrane|membrane fraction	monoamine transmembrane transporter activity				0		Colorectal(252;0.19)		all cancers(201;0.029)	Alseroxylon(DB00386)|Reserpine(DB00206)|Tetrabenazine(DB04844)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	119555236	119555239	+	IGR	DEL	ATCA	-	-	rs150339147		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119555236_119555239delATCA								EMX2 (246180 upstream) : RAB11FIP2 (209190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120776342	120776342	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120776342delT								C10orf46 (261584 upstream) : NANOS1 (12886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120947522	120947523	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120947522_120947523delTT								PRDX3 (9177 upstream) : GRK5 (19674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	121312536	121312536	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121312536delA								RGS10 (10314 upstream) : TIAL1 (20442 downstream)																																			---	---	---	---
PLEKHA1	59338	broad.mit.edu	37	10	124184396	124184396	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124184396delT	uc001lge.1	+						PLEKHA1_uc001lgf.1_Intron|PLEKHA1_uc001lgg.1_Intron|PLEKHA1_uc001lgh.2_Intron	NM_001001974	NP_001001974			pleckstrin homology domain containing, family A						B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
C10orf88	80007	broad.mit.edu	37	10	124711352	124711352	+	Intron	DEL	A	-	-	rs75488600		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124711352delA	uc001lgw.2	-						C10orf88_uc001lgx.2_Intron	NM_024942	NP_079218			hypothetical protein LOC80007												0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126599282	126599283	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126599282_126599283delTT								FAM175B (74044 upstream) : ZRANB1 (29689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126856404	126856405	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126856404_126856405delAA								CTBP2 (6780 upstream) : LOC100169752 (406535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127257399	127257399	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127257399delA								CTBP2 (407775 upstream) : LOC100169752 (5541 downstream)																																			---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128273926	128273926	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128273926delG	uc010qum.1	-						C10orf90_uc009yao.2_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128864540	128864542	+	Intron	DEL	CTC	-	-	rs35188301		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128864540_128864542delCTC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128982577	128982578	+	Intron	INS	-	C	C	rs140997294	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128982577_128982578insC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|FAM196A_uc001ljv.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129769413	129769416	+	Intron	DEL	CTGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129769413_129769416delCTGA	uc001lkb.2	+						PTPRE_uc009yat.2_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129859191	129859191	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129859191delT	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc010qup.1_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkd.2_Intron|PTPRE_uc010quq.1_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	130361032	130361037	+	IGR	DEL	GAGGAG	-	-	rs147711950		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130361032_130361037delGAGGAG								MKI67 (436564 upstream) : MGMT (904417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130742462	130742463	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130742462_130742463delAC								MKI67 (817994 upstream) : MGMT (522991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133140516	133140516	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133140516delT								TCERG1L (30532 upstream) : PPP2R2D (607444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133261307	133261307	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133261307delA								TCERG1L (151323 upstream) : PPP2R2D (486653 downstream)																																			---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134027323	134027323	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134027323delC	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc001llb.2_Intron|STK32C_uc001llc.1_Intron	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	134341100	134341101	+	IGR	DEL	AC	-	-	rs148220789		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134341100_134341101delAC								C10orf91 (79276 upstream) : INPP5A (10252 downstream)																																			---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135113670	135113670	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135113670delA	uc001lmg.1	-						TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135202325	135202359	+	Intron	DEL	GTCATCCCGGGGCTCTCTTTCTCCATGCAGGTCTG	-	-	rs144417516	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135202325_135202359delGTCATCCCGGGGCTCTCTTTCTCCATGCAGGTCTG	uc001lmv.2	+						PAOX_uc001lmw.2_Intron|PAOX_uc001lmx.2_Intron|PAOX_uc001lmy.2_Intron|PAOX_uc001lmz.2_Intron|PAOX_uc001lna.2_Intron|PAOX_uc001lnb.2_Intron|PAOX_uc001lnc.2_Intron	NM_152911	NP_690875			polyamine oxidase isoform 1						polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135524466	135524467	+	IGR	INS	-	A	A	rs149688375		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135524466_135524467insA								LOC653544 (29273 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	341009	341010	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:341009_341010insG								IFITM3 (20095 upstream) : B4GALNT4 (28785 downstream)																																			---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	372694	372695	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:372694_372695insG	uc001lpb.2	+	3	297_298	c.288_289insG	c.(286-291)CCTGGGfs	p.P96fs		NM_178537	NP_848632	Q76KP1	B4GN4_HUMAN	beta	96_97	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
CDHR5	53841	broad.mit.edu	37	11	618299	618299	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:618299delC	uc001lqj.2	-						IRF7_uc010qwf.1_5'Flank|IRF7_uc001lqf.2_5'Flank|IRF7_uc010qwg.1_5'Flank|IRF7_uc001lqg.2_5'Flank|IRF7_uc001lqh.2_5'Flank|IRF7_uc001lqi.2_5'Flank|IRF7_uc010qwh.1_5'Flank|CDHR5_uc001lqk.2_Intron|CDHR5_uc009ycc.2_Intron|CDHR5_uc009ycd.2_Intron|CDHR5_uc001lql.2_Intron	NM_021924	NP_068743			mucin and cadherin-like isoform 1						calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
AP2A2	161	broad.mit.edu	37	11	968433	968444	+	Intron	DEL	CCCATCCCCGTC	-	-	rs36207972		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:968433_968444delCCCATCCCCGTC	uc001lss.2	+						AP2A2_uc001lst.1_Intron|AP2A2_uc009yco.1_Intron	NM_012305	NP_036437			adaptor-related protein complex 2, alpha 2						axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|cytosol	lipid binding|protein transporter activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1232294	1232294	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1232294delA	uc009ycr.1	+							NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1283962	1283973	+	Intron	DEL	TCCTGTCCCGCC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1283962_1283973delTCCTGTCCCGCC	uc009ycr.1	+							NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	1361104	1361105	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1361104_1361105delAG								TOLLIP (30265 upstream) : BRSK2 (50024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1793685	1793686	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1793685_1793686delGT								CTSD (8463 upstream) : SYT8 (55023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2036380	2036380	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2036380delA								H19 (17315 upstream) : IGF2 (113968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2374034	2374034	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2374034delT	uc001lwe.2	-											Homo sapiens, clone IMAGE:4940779, mRNA.																														---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2528002	2528003	+	Intron	INS	-	T	T	rs11023096	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2528002_2528003insT	uc001lwn.2	+						KCNQ1_uc009ydo.1_Intron|KCNQ1_uc009ydp.1_Intron|KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209			potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	4747691	4747692	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4747691_4747692delAA								OR51E2 (28615 upstream) : OR51F1 (42518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	4780940	4780941	+	IGR	DEL	TA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4780940_4780941delTA								OR51E2 (61864 upstream) : OR51F1 (9269 downstream)																																			---	---	---	---
HBG2	3048	broad.mit.edu	37	11	5274395	5274395	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5274395delA	uc001mai.1	-							NM_000559	NP_000550			A-gamma globin						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5811075	5811076	+	Intron	DEL	AA	-	-	rs142142181	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5811075_5811076delAA	uc009yet.1	+						TRIM5_uc001mbq.1_Intron|OR52N1_uc010qzo.1_5'Flank	NM_006074	NP_006065			tripartite motif-containing 22						immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9176695	9176697	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9176695_9176697delAAA	uc001mhl.2	-						DENND5A_uc001mhk.2_Intron|DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	9672553	9672553	+	IGR	DEL	T	-	-	rs112039790		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9672553delT								WEE1 (61242 upstream) : SWAP70 (13075 downstream)																																			---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9746451	9746451	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9746451delT	uc001mhw.2	+						SWAP70_uc001mhv.2_Intron|SWAP70_uc001mhx.2_Intron	NM_015055	NP_055870			SWAP-70 protein							cytoplasm|lamellipodium|nucleus|plasma membrane	calcium ion binding|DNA binding			ovary(2)|central_nervous_system(1)	3				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10034209	10034209	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10034209delT	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
CTR9	9646	broad.mit.edu	37	11	10776406	10776406	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10776406delT	uc001mja.2	+							NM_014633	NP_055448			SH2 domain binding protein 1						histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	10896343	10896343	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10896343delT	uc001mjl.1	+						uc001mjm.1_Intron					Homo sapiens, clone IMAGE:3930408, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11128044	11128045	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11128044_11128045delAA								ZBED5 (248424 upstream) : GALNTL4 (164376 downstream)																																			---	---	---	---
MICAL2	9645	broad.mit.edu	37	11	12247121	12247121	+	Intron	DEL	G	-	-	rs147231254	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12247121delG	uc001mjz.2	+						MICAL2_uc010rch.1_Intron|MICAL2_uc001mka.2_Intron|MICAL2_uc010rci.1_Intron|MICAL2_uc001mkb.2_Intron|MICAL2_uc001mkc.2_Intron|MICAL2_uc001mkd.2_Intron|MICAL2_uc010rcj.1_Intron	NM_014632	NP_055447			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)														---	---	---	---
PARVA	55742	broad.mit.edu	37	11	12503727	12503727	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12503727delA	uc001mki.2	+						PARVA_uc010rck.1_Intron	NM_018222	NP_060692			parvin, alpha						cell adhesion|cell junction assembly|cilium morphogenesis	actin cytoskeleton|cytosol|focal adhesion	actin binding			breast(3)	3				Epithelial(150;0.00624)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12686657	12686657	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12686657delA								PARVA (135247 upstream) : TEAD1 (9312 downstream)																																			---	---	---	---
BTBD10	84280	broad.mit.edu	37	11	13437590	13437590	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13437590delA	uc001mkz.2	-						BTBD10_uc010rcl.1_Intron|BTBD10_uc001mla.2_Intron|BTBD10_uc009ygn.2_Intron|BTBD10_uc010rcm.1_Intron|BTBD10_uc010rcn.1_Intron|BTBD10_uc009ygo.2_Intron	NM_032320	NP_115696			K+ channel tetramerization protein							nucleus					0				Epithelial(150;0.0214)														---	---	---	---
FAR1	84188	broad.mit.edu	37	11	13749288	13749288	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13749288delT	uc001mld.2	+							NM_032228	NP_115604			fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	14424962	14424962	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14424962delT								RRAS2 (44233 upstream) : COPB1 (54087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15872417	15872418	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15872417_15872418delTT								INSC (603665 upstream) : SOX6 (115578 downstream)																																			---	---	---	---
PLEKHA7	144100	broad.mit.edu	37	11	16935866	16935866	+	Intron	DEL	A	-	-	rs12287420	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16935866delA	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228			pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3																		---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17469666	17469666	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17469666delT	uc001mnc.2	-						ABCC8_uc010rcy.1_Intron	NM_000352	NP_000343			ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)													---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	17940210	17940213	+	Intron	DEL	CTCT	-	-	rs1080246		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17940210_17940213delCTCT	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron	NM_012139	NP_036271			deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1																		---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18339159	18339159	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18339159delT	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron|HPS5_uc001mog.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
LDHA	3939	broad.mit.edu	37	11	18419946	18419946	+	Intron	DEL	T	-	-	rs113763578		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18419946delT	uc001mok.3	+						LDHA_uc010rdc.1_Intron|LDHA_uc009yhn.2_Intron|LDHA_uc009yho.2_Intron|LDHA_uc001mol.3_Intron|LDHA_uc010rdd.1_Intron	NM_005566	NP_005557			lactate dehydrogenase A isoform 1						glycolysis|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity|protein binding			central_nervous_system(3)	3					NADH(DB00157)													---	---	---	---
LDHC	3948	broad.mit.edu	37	11	18441642	18441644	+	Intron	DEL	AAC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18441642_18441644delAAC	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144			L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	19003469	19003469	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19003469delT								MRGPRX1 (46920 upstream) : MRGPRX2 (72536 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19731339	19731339	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19731339delA	uc001mpp.2	+							NM_001111018	NP_001104488			neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20065349	20065350	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20065349_20065350delAA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
HTATIP2	10553	broad.mit.edu	37	11	20404503	20404504	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20404503_20404504delTT	uc009yia.1	+						HTATIP2_uc009yib.1_Intron|HTATIP2_uc001mpx.2_Intron|HTATIP2_uc001mpz.2_Intron	NM_006410	NP_006401			HIV-1 Tat interactive protein 2, 30kDa isoform						angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0																		---	---	---	---
SLC6A5	9152	broad.mit.edu	37	11	20676319	20676319	+	Frame_Shift_Del	DEL	G	-	-	rs16906628	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20676319delG	uc001mqd.2	+	16	2572	c.2299delG	c.(2299-2301)GGGfs	p.G767fs	SLC6A5_uc009yic.2_Frame_Shift_Del_p.G532fs	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	767	Cytoplasmic (Potential).				synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)													---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21195296	21195297	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21195296_21195297delTG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22617825	22617826	+	IGR	INS	-	AC	AC	rs138917170	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22617825_22617826insAC								SLC17A6 (216781 upstream) : FANCF (26253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22996515	22996515	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22996515delA								SVIP (145133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23734587	23734587	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23734587delT								SVIP (883205 upstream) : LUZP2 (783969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23772021	23772022	+	IGR	INS	-	GATA	GATA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23772021_23772022insGATA								SVIP (920639 upstream) : LUZP2 (746534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	26088826	26088826	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26088826delT								LUZP2 (984644 upstream) : ANO3 (122003 downstream)																																			---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26674101	26674101	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26674101delA	uc001mqt.3	+						ANO3_uc010rdr.1_Intron|ANO3_uc010rds.1_Intron|ANO3_uc010rdt.1_Intron	NM_031418	NP_113606			transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
CCDC34	91057	broad.mit.edu	37	11	27362455	27362455	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27362455delT	uc001mrh.1	-							NM_030771	NP_110398			coiled-coil domain containing 34 isoform 1												0																		---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28130378	28130378	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28130378delT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron|KIF18A_uc001msc.2_5'Flank|KIF18A_uc001msd.2_5'Flank|METT5D1_uc001msf.1_5'Flank	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	28880866	28880866	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28880866delT								METT5D1 (525812 upstream) : None (None downstream)																																			---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31645312	31645312	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31645312delA	uc001mtb.2	+						ELP4_uc001mta.1_Intron|ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31785302	31785303	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31785302_31785303delTT	uc001mtb.2	+						ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
PAX6	5080	broad.mit.edu	37	11	31812317	31812317	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31812317delG	uc001mtd.3	-	11	2014	c.1124delC	c.(1123-1125)CCAfs	p.P375fs	PAX6_uc001mte.3_Frame_Shift_Del_p.P375fs|PAX6_uc001mtg.3_Frame_Shift_Del_p.P389fs|PAX6_uc001mtf.3_Frame_Shift_Del_p.P375fs|PAX6_uc001mth.3_Frame_Shift_Del_p.P375fs|PAX6_uc009yjr.2_Frame_Shift_Del_p.P375fs	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	375	Pro/Ser/Thr-rich.		P -> Q (in AN; reduced DNA binding ability).		blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)													Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				---	---	---	---
WT1	7490	broad.mit.edu	37	11	32413476	32413476	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32413476delA	uc001mtn.1	-						WT1_uc001mtl.1_Intron|WT1_uc001mtm.1_Intron|WT1_uc001mto.1_Intron|WT1_uc001mtp.1_Intron|WT1_uc001mtq.1_Intron|WT1_uc009yjs.1_Intron	NM_024426	NP_077744			Wilms tumor 1 isoform D						adrenal cortex formation|branching involved in ureteric bud morphogenesis|camera-type eye development|cardiac muscle cell fate commitment|cellular response to cAMP|cellular response to gonadotropin stimulus|germ cell development|glomerular basement membrane development|glomerular visceral epithelial cell differentiation|induction of apoptosis|male genitalia development|male gonad development|mesenchymal to epithelial transition|metanephric epithelium development|metanephric S-shaped body morphogenesis|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of female gonad development|negative regulation of metanephric glomerular mesangial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of translation|positive regulation of male gonad development|positive regulation of transcription, DNA-dependent|posterior mesonephric tubule development|regulation of organ formation|RNA splicing|sex determination|vasculogenesis|visceral serous pericardium development	cytoplasm|nuclear speck|nucleoplasm	C2H2 zinc finger domain binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding		EWSR1/WT1(231)	haematopoietic_and_lymphoid_tissue(318)|soft_tissue(231)|kidney(132)|pleura(2)|lung(2)|upper_aerodigestive_tract(1)|peritoneum(1)	687	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)					D|Mis|N|F|S	EWSR1	Wilms|desmoplastic small round cell tumor	Wilms			Denys-Drash_syndrome|Frasier_syndrome|Familial_Wilms_tumor|Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				---	---	---	---
PRRG4	79056	broad.mit.edu	37	11	32852020	32852020	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32852020delT	uc001mtx.2	+							NM_024081	NP_076986			proline rich Gla (G-carboxyglutamic acid) 4							extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)																	---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32997895	32997895	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32997895delA	uc001mty.2	+	13	5350	c.5083delA	c.(5083-5085)AAAfs	p.K1695fs	QSER1_uc001mtz.1_Frame_Shift_Del_p.K1456fs	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1695										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
CSTF3	1479	broad.mit.edu	37	11	33168842	33168842	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33168842delA	uc001muh.2	-						CSTF3_uc001mui.2_Intron|CSTF3_uc001muj.2_Intron	NM_001326	NP_001317			cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33240839	33240841	+	IGR	DEL	GAT	-	-	rs112889650		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33240839_33240841delGAT								CSTF3 (57802 upstream) : HIPK3 (38327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33699045	33699047	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33699045_33699047delTTT								C11orf41 (3401 upstream) : CD59 (25511 downstream)																																			---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34145710	34145710	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34145710delA	uc001mvk.2	+						NAT10_uc010ren.1_Intron	NM_024662	NP_078938			N-acetyltransferase 10 isoform a							nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	34860888	34860891	+	IGR	DEL	ACAC	-	-	rs67819737		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34860888_34860891delACAC								EHF (177807 upstream) : APIP (35823 downstream)																																			---	---	---	---
CD44	960	broad.mit.edu	37	11	35169639	35169640	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35169639_35169640delAA	uc001mvu.2	+						CD44_uc001mvv.2_Intron|CD44_uc001mvw.2_Intron|CD44_uc001mvx.2_Intron|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Intron|CD44_uc010rer.1_Intron|CD44_uc009ykh.2_Intron	NM_000610	NP_000601			CD44 antigen isoform 1 precursor						cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)													---	---	---	---
SLC1A2	6506	broad.mit.edu	37	11	35355212	35355212	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35355212delT	uc001mwd.2	-						SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron	NM_004171	NP_004162			excitatory amino acid transporter 2						D-aspartate import|L-glutamate import|synaptic transmission	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|central_nervous_system(1)	3	all_lung(20;0.211)|all_epithelial(35;0.234)	all_hematologic(20;0.109)	STAD - Stomach adenocarcinoma(6;0.00731)		L-Glutamic Acid(DB00142)													---	---	---	---
LDLRAD3	143458	broad.mit.edu	37	11	36095552	36095552	+	Intron	DEL	G	-	-	rs867928	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36095552delG	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron|uc001mwl.2_Intron	NM_174902	NP_777562			low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)																---	---	---	---
PRR5L	79899	broad.mit.edu	37	11	36379259	36379259	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36379259delA	uc001mwo.3	+							NM_001160167	NP_001153639			protor-2 isoform a											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	37842606	37842606	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37842606delA								None (None upstream) : None (None downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40651972	40651972	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40651972delT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40700816	40700816	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40700816delT	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	41626582	41626582	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41626582delA								LRRC4C (145259 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	41760291	41760291	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41760291delT								LRRC4C (278968 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42730695	42730695	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42730695delC								None (None upstream) : API5 (602810 downstream)																																			---	---	---	---
API5	8539	broad.mit.edu	37	11	43354244	43354245	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43354244_43354245delAC	uc010rfh.1	+						API5_uc010rfg.1_Intron|API5_uc001mxf.2_Intron|API5_uc010rfi.1_Intron|API5_uc001mxg.2_Intron	NM_001142930	NP_001136402			apoptosis inhibitor 5 isoform a						anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43410525	43410525	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43410525delA	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44307235	44307236	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44307235_44307236delTT	uc001myb.2	-							NM_021926	NP_068745			aristaless-like homeobox 4						hair follicle development						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	44999931	44999934	+	IGR	DEL	GTGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44999931_44999934delGTGA								LOC221122 (355 upstream) : PRDM11 (115630 downstream)																																			---	---	---	---
PRDM11	56981	broad.mit.edu	37	11	45192629	45192631	+	Intron	DEL	TTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45192629_45192631delTTG	uc001myo.2	+							NM_020229	NP_064614			PR domain containing 11											upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	46241687	46241687	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46241687delA								PHF21A (98702 upstream) : CREB3L1 (57541 downstream)																																			---	---	---	---
F2	2147	broad.mit.edu	37	11	46742602	46742603	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46742602_46742603delTT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47062638	47062638	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47062638delC	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47576215	47576215	+	5'Flank	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47576215delG	uc001nfp.2	-						CELF1_uc001nfn.2_5'Flank|CELF1_uc001nfq.1_5'Flank	NM_001025596	NP_001020767			CUG triplet repeat, RNA-binding protein 1						embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47623942	47623942	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47623942delT								C1QTNF4 (7981 upstream) : MTCH2 (14917 downstream)																																			---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47843814	47843815	+	Intron	DEL	TT	-	-	rs71875671		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47843814_47843815delTT	uc001ngm.2	-						NUP160_uc009ylw.2_Intron	NM_015231	NP_056046			nucleoporin 160kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48173013	48173013	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48173013delT	uc001ngp.3	+							NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48249899	48249899	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48249899delA								OR4B1 (10609 upstream) : OR4X2 (16757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48358899	48358900	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48358899_48358900insG								OR4C3 (11419 upstream) : OR4C45 (8002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48361533	48361533	+	IGR	DEL	G	-	-	rs143230488		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48361533delG								OR4C3 (14053 upstream) : OR4C45 (5369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48764742	48764742	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48764742delG								OR4A47 (253470 upstream) : FOLH1 (403446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49295407	49295408	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49295407_49295408insT								FOLH1 (65185 upstream) : LOC440040 (284672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49958142	49958142	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49958142delT								LOC440040 (126175 upstream) : OR4C13 (15833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50228603	50228603	+	IGR	DEL	A	-	-	rs112861391		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50228603delA								OR4C12 (224566 upstream) : LOC441601 (10397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55065031	55065032	+	RNA	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55065031_55065032insT	uc001nhl.1	-	2		c.391_392insA								Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit20-11-30-F.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	55687898	55687898	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55687898delG								OR5W2 (5840 upstream) : OR5I1 (15035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55687900	55687900	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55687900delC								OR5W2 (5842 upstream) : OR5I1 (15033 downstream)																																			---	---	---	---
P2RX3	5024	broad.mit.edu	37	11	57123766	57123766	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57123766delA	uc001nju.2	+							NM_002559	NP_002550			purinergic receptor P2X3						positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0																		---	---	---	---
RTN4RL2	349667	broad.mit.edu	37	11	57236924	57236925	+	Intron	DEL	TT	-	-	rs34554166		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57236924_57236925delTT	uc010rjt.1	+							NM_178570	NP_848665			reticulon 4 receptor-like 2 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
CLP1	10978	broad.mit.edu	37	11	57428126	57428126	+	Intron	DEL	A	-	-	rs74496835		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57428126delA	uc001nkw.2	+						CLP1_uc010rjw.1_Intron|CLP1_uc009yml.2_Intron	NM_006831	NP_006822			ATP/GTP-binding protein isoform 1						mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|siRNA loading onto RISC involved in RNA interference|targeting of mRNA for destruction involved in RNA interference|termination of RNA polymerase II transcription|tRNA splicing, via endonucleolytic cleavage and ligation	nucleoplasm|tRNA-intron endonuclease complex	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity			ovary(1)	1																		---	---	---	---
C11orf31	280636	broad.mit.edu	37	11	57510632	57510632	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57510632delT	uc010rjx.1	+	5					CTNND1_uc001nlf.1_Intron	NM_170746	NP_734467			selenoprotein H						cell redox homeostasis		selenium binding				0																		---	---	---	---
GIF	2694	broad.mit.edu	37	11	59611620	59611620	+	Intron	DEL	T	-	-	rs72085643		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59611620delT	uc001noi.2	-						GIF_uc010rkz.1_Intron	NM_005142	NP_005133			gastric intrinsic factor (vitamin B synthesis)						cobalamin metabolic process|cobalamin transport|cobalt ion transport	apical plasma membrane|endosome|extracellular space|microvillus	cobalamin binding			ovary(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59997717	59997718	+	5'Flank	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59997717_59997718delGA	uc001nov.2	-						uc001now.2_5'Flank|uc001nox.2_5'Flank|uc001noy.2_5'Flank|uc009ymw.2_5'Flank					Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit17-05-01-R.																														---	---	---	---
MS4A1	931	broad.mit.edu	37	11	60231865	60231865	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60231865delT	uc001npp.2	+						MS4A1_uc001npq.2_Intron|MS4A1_uc009yna.2_Intron|MS4A1_uc009ymz.2_Intron|MS4A1_uc010rlc.1_Intron	NM_152866	NP_690605			membrane-spanning 4-domains, subfamily A, member						B cell activation|immune response	integral to plasma membrane				ovary(3)|lung(2)	5					Ibritumomab(DB00078)|Rituximab(DB00073)|Tositumomab(DB00081)													---	---	---	---
PRPF19	27339	broad.mit.edu	37	11	60666410	60666410	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60666410delA	uc001nqf.2	-							NM_014502	NP_055317			PRP19/PSO4 pre-mRNA processing factor 19						DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SYT7	9066	broad.mit.edu	37	11	61306848	61306849	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61306848_61306849insG	uc001nrv.2	-						SYT7_uc009ynr.2_Intron|uc001nrw.1_Intron	NM_004200	NP_004191			synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	61414908	61414908	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61414908delA								RPLP0P2 (7987 upstream) : DAGLA (33002 downstream)																																			---	---	---	---
INTS5	80789	broad.mit.edu	37	11	62417596	62417596	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62417596delT	uc001nud.2	-							NM_030628	NP_085131			integrator complex subunit 5						snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2																		---	---	---	---
ZBTB3	79842	broad.mit.edu	37	11	62519423	62519425	+	3'UTR	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62519423_62519425delAAA	uc001nuz.2	-	2						NM_024784	NP_079060			zinc finger and BTB domain containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62649529	62649529	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62649529delA	uc001nwd.2	+	5	1116	c.892delA	c.(892-894)AAAfs	p.K298fs	SLC3A2_uc001nwb.2_Frame_Shift_Del_p.K329fs|SLC3A2_uc001nwc.2_Frame_Shift_Del_p.K299fs|SLC3A2_uc001nwe.2_Frame_Shift_Del_p.K267fs|SLC3A2_uc001nwf.2_Frame_Shift_Del_p.K236fs|SLC3A2_uc001nwg.2_Frame_Shift_Del_p.K197fs|SLC3A2_uc010rml.1_5'Flank	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c	298	Extracellular (Potential).				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	63997567	63997571	+	Frame_Shift_Del	DEL	AAAAA	-	-	rs10708923		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63997567_63997571delAAAAA	uc001nyr.1	-	1	1190_1194	c.758_762delTTTTT	c.(757-762)TTTTTTfs	p.F253fs	DNAJC4_uc001nys.2_5'Flank|DNAJC4_uc001nyt.2_5'Flank|DNAJC4_uc001nyu.2_5'Flank					Homo sapiens cDNA FLJ34477 fis, clone HLUNG2003833.																														---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64383302	64383305	+	Intron	DEL	GTGT	-	-	rs146055795		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64383302_64383305delGTGT	uc001oap.2	-						NRXN2_uc001oar.2_Intron|NRXN2_uc001oas.2_Intron|NRXN2_uc001oao.2_Intron|NRXN2_uc001oaq.2_Intron	NM_138734	NP_620063			neurexin 2 isoform beta precursor						cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
MEN1	4221	broad.mit.edu	37	11	64573491	64573491	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64573491delA	uc001obj.2	-						MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Intron|MEN1_uc001obl.2_Intron|MEN1_uc001obm.2_Intron|MEN1_uc001obn.2_Intron|MEN1_uc001obo.2_Intron|MEN1_uc001obp.2_Intron|MEN1_uc001obq.2_Intron|MEN1_uc001obr.2_Intron	NM_130800	NP_570712			menin isoform 1						DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent	chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction	double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding			parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1)	238								D|Mis|N|F|S		parathyroid tumors|Pancreatic neuroendocrine tumors	parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid			Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1				---	---	---	---
Unknown	0	broad.mit.edu	37	11	64591522	64591523	+	IGR	INS	-	ATG	ATG	rs144977482	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64591522_64591523insATG								MEN1 (12756 upstream) : CDC42BPG (141 downstream)																																			---	---	---	---
MIR612	693197	broad.mit.edu	37	11	65210189	65210189	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65210189delA	hsa-mir-612|MI0003625	+																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65236836	65236836	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65236836delA								MIR612 (24808 upstream) : MALAT1 (28397 downstream)																																			---	---	---	---
PACS1	55690	broad.mit.edu	37	11	66009267	66009267	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66009267delC	uc001oha.1	+						PACS1_uc010rou.1_Intron	NM_018026	NP_060496			phosphofurin acidic cluster sorting protein 1						interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
RBM14	10432	broad.mit.edu	37	11	66388690	66388690	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66388690delT	uc001oit.2	+						RBM14_uc009yrh.2_Intron|RBM14_uc009yri.2_Intron|RBM4_uc009yrj.2_Intron|RBM4_uc009yrk.2_Intron	NM_006328	NP_006319			RNA binding motif protein 14						DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|histone deacetylation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus	mediator complex|ribonucleoprotein complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|protein binding, bridging|RNA binding|RNA polymerase II transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SYT12	91683	broad.mit.edu	37	11	66798159	66798159	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66798159delA	uc009yrl.2	+						SYT12_uc001oju.2_Intron	NM_177963	NP_808878			synaptotagmin XII							cell junction|integral to membrane|synaptic vesicle membrane				ovary(1)	1																		---	---	---	---
PTPRCAP	5790	broad.mit.edu	37	11	67204426	67204428	+	Intron	DEL	GAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67204426_67204428delGAG	uc001oli.1	-							NM_005608	NP_005599			protein tyrosine phosphatase, receptor type,						defense response	integral to membrane|plasma membrane					0			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	68027399	68027399	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68027399delG								SUV420H1 (46331 upstream) : C11orf24 (1406 downstream)																																			---	---	---	---
C11orf24	53838	broad.mit.edu	37	11	68032094	68032097	+	Intron	DEL	CCAT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68032094_68032097delCCAT	uc001onr.3	-						C11orf24_uc001ons.2_Intron	NM_022338	NP_071733			hypothetical protein LOC53838 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	68612418	68612419	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68612418_68612419delTT								CPT1A (3019 upstream) : MRPL21 (46328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68956590	68956591	+	IGR	INS	-	TCG	TCG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68956590_68956591insTCG								TPCN2 (26683 upstream) : MYEOV (105031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69250325	69250326	+	IGR	DEL	TT	-	-	rs35936805		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69250325_69250326delTT								MYEOV (93876 upstream) : CCND1 (205547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69812172	69812172	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69812172delA								FGF3 (177980 upstream) : ANO1 (112236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	70087077	70087077	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70087077delC								FADD (33569 upstream) : PPFIA1 (29746 downstream)																																			---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70677765	70677765	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70677765delA	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70708095	70708095	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70708095delA	uc001oqc.2	-						uc009yso.1_5'Flank	NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70734932	70734932	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70734932delA	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70865036	70865036	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70865036delA	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	70944194	70944194	+	IGR	DEL	A	-	-	rs142343046		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70944194delA								SHANK2 (8386 upstream) : DHCR7 (201265 downstream)																																			---	---	---	---
RNF121	55298	broad.mit.edu	37	11	71705621	71705622	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71705621_71705622delAA	uc001ora.2	+						RNF121_uc001ord.2_Intron|RNF121_uc001orb.2_Intron|RNF121_uc009yst.2_Intron	NM_018320	NP_060790			ring finger protein 121							integral to membrane	zinc ion binding				0																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71790586	71790587	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71790586_71790587delAA	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc001orq.2_Intron|LRTOMT_uc009ysz.2_5'Flank|LRTOMT_uc010rqt.1_5'Flank|LRTOMT_uc010rqu.1_5'Flank|LRTOMT_uc009yta.2_5'Flank|LRTOMT_uc010rqv.1_5'Flank|LRTOMT_uc010rqw.1_5'Flank|LRTOMT_uc001ors.3_5'Flank|LRTOMT_uc001orr.2_5'Flank|LRTOMT_uc010rqs.1_5'Flank	NM_006185	NP_006176			nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
P2RY6	5031	broad.mit.edu	37	11	72974725	72974725	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72974725delA	uc001otm.2	+						P2RY6_uc001otn.2_5'Flank|P2RY6_uc001oto.2_5'Flank|P2RY6_uc001otp.2_5'Flank	NM_176796	NP_789766			pyrimidinergic receptor P2Y6						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1																		---	---	---	---
PGM2L1	283209	broad.mit.edu	37	11	74095170	74095170	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74095170delC	uc001ovb.1	-							NM_173582	NP_775853			phosphoglucomutase 2-like 1						glucose 1-phosphate metabolic process	cytosol	glucose-1,6-bisphosphate synthase activity|phosphoglucomutase activity			ovary(1)	1	Breast(11;3.32e-06)																	---	---	---	---
POLD3	10714	broad.mit.edu	37	11	74329504	74329504	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74329504delT	uc001ovf.1	+						POLD3_uc009yua.1_Intron	NM_006591	NP_006582			DNA-directed DNA polymerase delta 3						base-excision repair|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|mismatch repair|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	delta DNA polymerase complex|nucleoplasm	DNA-directed DNA polymerase activity|protein binding			kidney(2)|ovary(1)	3	Breast(11;3.21e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	74379809	74379810	+	IGR	INS	-	T	T	rs143479217	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74379809_74379810insT								POLD3 (26044 upstream) : CHRDL2 (27665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74456592	74456592	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74456592delA								CHRDL2 (14406 upstream) : RNF169 (3321 downstream)																																			---	---	---	---
XRRA1	143570	broad.mit.edu	37	11	74583605	74583607	+	Intron	DEL	TCA	-	-	rs144416233		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74583605_74583607delTCA	uc009yub.2	-						XRRA1_uc001ovm.2_Intron|XRRA1_uc001ovn.2_Intron|XRRA1_uc001ovo.2_Intron|XRRA1_uc001ovq.3_Intron|XRRA1_uc001ovp.3_Intron|XRRA1_uc001ovr.2_Intron|XRRA1_uc001ovt.2_Intron	NM_182969	NP_892014			X-ray radiation resistance associated 1						response to X-ray	cytoplasm|nucleus				central_nervous_system(1)	1																		---	---	---	---
SLCO2B1	11309	broad.mit.edu	37	11	74853966	74853966	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74853966delA	uc010rrp.1	+											Homo sapiens mRNA for KIAA0880 protein, partial cds.						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)													---	---	---	---
ARRB1	408	broad.mit.edu	37	11	75012187	75012190	+	Intron	DEL	AAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75012187_75012190delAAAA	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032			arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2																		---	---	---	---
RPS3	6188	broad.mit.edu	37	11	75112534	75112534	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75112534delA	uc001owh.2	+						RPS3_uc001owg.2_Intron|RPS3_uc001owi.2_Intron|RPS3_uc001owk.1_Intron|SNORD15B_uc001owl.1_5'Flank	NM_001005	NP_000996			ribosomal protein S3						activation of caspase activity|endocrine pancreas development|induction of apoptosis|negative regulation of DNA repair|negative regulation of NF-kappaB transcription factor activity|response to DNA damage stimulus|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleus|ruffle membrane	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|iron-sulfur cluster binding|mRNA binding|NF-kappaB binding|protein kinase binding|structural constituent of ribosome				0																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76157923	76157923	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76157923delT	uc001oxl.2	+						C11orf30_uc001oxj.2_Intron|C11orf30_uc001oxk.2_Intron|C11orf30_uc009yuj.1_Intron|C11orf30_uc010rsa.1_Intron|C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_5'Flank|C11orf30_uc010rsc.1_5'Flank|C11orf30_uc001oxn.2_5'Flank|C11orf30_uc010rsd.1_5'Flank	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76227407	76227407	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76227407delA	uc001oxl.2	+						C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77633436	77633436	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77633436delA	uc001oys.2	-	13	1624	c.1596delT	c.(1594-1596)TTTfs	p.F532fs	INTS4_uc001oyt.2_RNA	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	532					snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	77940953	77940953	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77940953delT	uc001ozh.2	-						GAB2_uc001ozg.2_Intron	NM_080491	NP_536739			GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78447533	78447534	+	Intron	DEL	GT	-	-	rs58721349		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78447533_78447534delGT	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78593914	78593914	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78593914delT	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78735642	78735642	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78735642delT	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78946917	78946917	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78946917delT	uc001ozl.3	-						ODZ4_uc009yvc.2_Intron	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	80295406	80295407	+	IGR	DEL	GT	-	-	rs11232233		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80295406_80295407delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	82026214	82026214	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82026214delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82088890	82088890	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82088890delA	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82429158	82429158	+	IGR	DEL	A	-	-	rs514326		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82429158delA								None (None upstream) : FAM181B (13895 downstream)																																			---	---	---	---
CCDC90B	60492	broad.mit.edu	37	11	82984691	82984691	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82984691delT	uc001pae.2	-	7	955	c.593delA	c.(592-594)AAGfs	p.K198fs	CCDC90B_uc001pac.2_Frame_Shift_Del_p.K97fs|CCDC90B_uc001pad.2_Frame_Shift_Del_p.K97fs|CCDC90B_uc001paf.2_Frame_Shift_Del_p.K189fs	NM_021825	NP_068597	Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B precursor	198						integral to membrane|mitochondrion|mitochondrion					0		Acute lymphoblastic leukemia(157;0.103)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84240104	84240104	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84240104delT	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84644165	84644165	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84644165delT	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84837589	84837589	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84837589delT	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84936225	84936225	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84936225delA	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	85310393	85310394	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85310393_85310394delTC	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							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)																---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85670108	85670108	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85670108delA	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc001pbk.2_Intron|PICALM_uc010rtk.1_Intron	NM_007166	NP_009097			phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
Unknown	0	broad.mit.edu	37	11	85940977	85940977	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85940977delG								PICALM (160077 upstream) : EED (14838 downstream)																																			---	---	---	---
ME3	10873	broad.mit.edu	37	11	86293952	86293953	+	Intron	DEL	AA	-	-	rs79072936		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86293952_86293953delAA	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_Intron	NM_001014811	NP_001014811			mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)													---	---	---	---
PRSS23	11098	broad.mit.edu	37	11	86544047	86544047	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86544047delA	uc001pcc.1	+						uc001pcd.2_Intron					Homo sapiens serine protease mRNA, complete cds.						proteolysis	extracellular region|nucleus	serine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	87029415	87029415	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87029415delT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89106468	89106468	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89106468delA	uc001pct.2	-						NOX4_uc009yvr.2_Intron|NOX4_uc001pcu.2_Intron|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_Intron|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Intron	NM_016931	NP_058627			NADPH oxidase 4 isoform a						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	89608307	89608307	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89608307delA								TRIM53 (24165 upstream) : TRIM49L (36274 downstream)																																			---	---	---	---
NAALAD2	10003	broad.mit.edu	37	11	89868965	89868967	+	Intron	DEL	TTT	-	-	rs34639551		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89868965_89868967delTTT	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron|NAALAD2_uc001pdd.2_Intron|NAALAD2_uc001pde.2_Intron	NM_005467	NP_005458			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92163678	92163678	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92163678delT	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92286274	92286274	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92286274delA	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
KIAA1731	85459	broad.mit.edu	37	11	93439896	93439896	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93439896delT	uc009ywb.1	+						KIAA1731_uc001pdu.1_Intron	NM_033395	NP_203753			hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
CWC15	51503	broad.mit.edu	37	11	94696475	94696475	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94696475delA	uc001pfd.3	-	8						NM_016403	NP_057487			CWC15 homolog						nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
KDM4D	55693	broad.mit.edu	37	11	94731303	94731303	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94731303delA	uc001pfe.2	+	3	1599	c.767delA	c.(766-768)GAAfs	p.E256fs		NM_018039	NP_060509	Q6B0I6	KDM4D_HUMAN	jumonji domain containing 2D	256	JmjC.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	94767311	94767314	+	IGR	DEL	AAAA	-	-	rs34885164		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94767311_94767314delAAAA								KDM4DL (6551 upstream) : SFRS2B (32742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95078464	95078464	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95078464delA								SESN3 (112759 upstream) : FAM76B (423642 downstream)																																			---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95800038	95800038	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95800038delA	uc001pfw.1	-							NM_032427	NP_115803			mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95988160	95988160	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95988160delT	uc001pfw.1	-							NM_032427	NP_115803			mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
Unknown	0	broad.mit.edu	37	11	98225286	98225287	+	IGR	INS	-	GT	GT	rs61906436		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98225286_98225287insGT								None (None upstream) : CNTN5 (666584 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99419824	99419824	+	Intron	DEL	T	-	-	rs5793994		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99419824delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100056487	100056488	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100056487_100056488delCT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100849810	100849810	+	Intron	DEL	A	-	-	rs34577066		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100849810delA	uc001pge.2	+						ARHGAP42_uc001pgd.2_Intron	NM_152432	NP_689645			Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	101232437	101232437	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101232437delA								PGR (231893 upstream) : TRPC6 (89859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101232445	101232446	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101232445_101232446insG								PGR (231901 upstream) : TRPC6 (89850 downstream)																																			---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101431384	101431384	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101431384delA	uc001pgk.3	-						TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Intron	NM_004621	NP_004612			transient receptor potential cation channel,						axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102417525	102417525	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102417525delT								MMP7 (16047 upstream) : MMP20 (30042 downstream)																																			---	---	---	---
MMP20	9313	broad.mit.edu	37	11	102450054	102450054	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102450054delT	uc001phc.2	-							NM_004771	NP_004762			matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)														---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102743847	102743847	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102743847delA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
MMP13	4322	broad.mit.edu	37	11	102822929	102822929	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102822929delA	uc001phl.2	-							NM_002427	NP_002418			matrix metalloproteinase 13 preproprotein						collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102985853	102985853	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102985853delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103182595	103182595	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103182595delT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	103397976	103397976	+	IGR	DEL	A	-	-	rs34272352		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103397976delA								DYNC2H1 (47385 upstream) : PDGFD (379939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	103517898	103517899	+	IGR	INS	-	AG	AG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103517898_103517899insAG								DYNC2H1 (167307 upstream) : PDGFD (260016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	103777548	103777549	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103777548_103777549delTT								DYNC2H1 (426957 upstream) : PDGFD (366 downstream)																																			---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103814509	103814509	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103814509delA	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484			platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)														---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105929470	105929471	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105929470_105929471delTT	uc001pja.2	-						KBTBD3_uc001pjb.2_Intron|KBTBD3_uc009yxm.2_Intron	NM_198439	NP_940841			BTB and kelch domain containing 3											ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	106048226	106048226	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106048226delG								AASDHPPT (78807 upstream) : GUCY1A2 (509684 downstream)																																			---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106837672	106837673	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106837672_106837673insA	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846			guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107099502	107099505	+	IGR	DEL	CAAA	-	-	rs143349467		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107099502_107099505delCAAA								GUCY1A2 (210331 upstream) : CWF19L2 (97569 downstream)																																			---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107686334	107686334	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686334delT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985			solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)														---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107726378	107726379	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107726378_107726379delAA	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985			solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)														---	---	---	---
C11orf65	160140	broad.mit.edu	37	11	108332127	108332127	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108332127delA	uc001pkh.2	-						C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron	NM_152587	NP_689800			hypothetical protein LOC160140											ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)														---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108412216	108412216	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108412216delT	uc001pkk.2	-						EXPH5_uc010rwa.1_Intron	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
EXPH5	23086	broad.mit.edu	37	11	108412614	108412614	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108412614delT	uc001pkk.2	-						EXPH5_uc010rwa.1_Intron	NM_015065	NP_055880			exophilin 5 isoform a						intracellular protein transport		Rab GTPase binding			skin(3)|ovary(2)	5		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	108899425	108899426	+	IGR	INS	-	TG	TG	rs140598595	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108899425_108899426insTG								DDX10 (87779 upstream) : C11orf87 (393449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	110784651	110784651	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110784651delT								ARHGAP20 (200739 upstream) : C11orf53 (342056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	110959455	110959455	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110959455delA								ARHGAP20 (375543 upstream) : C11orf53 (167252 downstream)																																			---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112145270	112145270	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112145270delT								PTS (4593 upstream) : NCAM1 (686725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	113114442	113114444	+	IGR	DEL	ATA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113114442_113114444delATA								NCAM1 (-34715 upstream) : NCAM1 (-282449 downstream)																																			---	---	---	---
CLDN25	644672	broad.mit.edu	37	11	113650551	113650551	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113650551delG	uc009yyw.1	+	1	34	c.34delG	c.(34-36)GGGfs	p.G12fs		NM_001101389	NP_001094859	C9JDP6	CLD25_HUMAN	claudin 25	12	Helical; (Potential).					integral to membrane|tight junction	structural molecule activity				0																		---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	113972039	113972042	+	Intron	DEL	TTTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113972039_113972042delTTTG	uc001pop.2	+						ZBTB16_uc001poo.1_Intron|ZBTB16_uc001poq.2_Intron	NM_006006	NP_005997			promyelocytic leukemia zinc finger protein						apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114670707	114670710	+	IGR	DEL	TCTT	-	-	rs72216801		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114670707_114670710delTCTT								FAM55B (93055 upstream) : CADM1 (369243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114748271	114748272	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114748271_114748272delTT								FAM55B (170619 upstream) : CADM1 (291681 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115258619	115258619	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115258619delA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148			immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	115431773	115431773	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115431773delT								CADM1 (56532 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116605921	116605921	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116605921delT								None (None upstream) : BUD13 (12967 downstream)																																			---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116906447	116906447	+	Intron	DEL	T	-	-	rs113834558		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116906447delT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116906807	116906808	+	Intron	DEL	TT	-	-	rs77063239		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116906807_116906808delTT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIDT2	51092	broad.mit.edu	37	11	117052324	117052325	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117052324_117052325insC	uc001pqh.1	+						SIDT2_uc010rxe.1_Intron|SIDT2_uc001pqg.2_Intron|SIDT2_uc001pqi.1_Intron	NM_001040455	NP_001035545			SID1 transmembrane family, member 2 precursor							integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)												OREG0021368	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117448153	117448197	+	Intron	DEL	TTCCTTCCTTCCTTCCTTCCTTTCCTTCCTTCCTTCCTTCCTTCC	-	-	rs111840761		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117448153_117448197delTTCCTTCCTTCCTTCCTTCCTTTCCTTCCTTCCTTCCTTCCTTCC	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117451294	117451295	+	Intron	INS	-	T	T	rs141858405	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117451294_117451295insT	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117517040	117517041	+	Intron	INS	-	CT	CT	rs142694348	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117517040_117517041insCT	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
FXYD6	53826	broad.mit.edu	37	11	117713654	117713656	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117713654_117713656delTTT	uc001pro.1	-						FXYD6_uc001prn.1_5'Flank|FXYD6_uc001prp.1_Intron|FXYD6_uc001prq.1_Intron|FXYD6_uc001prr.1_Intron|FXYD6_uc009yzq.1_Intron	NM_022003	NP_071286			FXYD domain-containing ion transport regulator 6							integral to membrane|plasma membrane	ion channel activity			central_nervous_system(1)|skin(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)														---	---	---	---
FXYD6	53826	broad.mit.edu	37	11	117733661	117733663	+	Intron	DEL	GAT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117733661_117733663delGAT	uc001pro.1	-						FXYD6_uc001prp.1_Intron|FXYD6_uc001prq.1_Intron|FXYD6_uc001prr.1_Intron|FXYD6_uc009yzq.1_Intron	NM_022003	NP_071286			FXYD domain-containing ion transport regulator 6							integral to membrane|plasma membrane	ion channel activity			central_nervous_system(1)|skin(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118055461	118055461	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118055461delT								SCN2B (8124 upstream) : AMICA1 (8981 downstream)																																			---	---	---	---
AMICA1	120425	broad.mit.edu	37	11	118078660	118078660	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118078660delA	uc001psk.2	-						AMICA1_uc001psh.2_Intron|AMICA1_uc009yzw.1_Intron|AMICA1_uc001psi.2_Intron|AMICA1_uc001psj.2_Intron|AMICA1_uc010rxw.1_Intron|AMICA1_uc010rxx.1_Intron|AMICA1_uc001psl.1_Intron	NM_001098526	NP_001091996			adhesion molecule, interacts with CXADR antigen						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
CD3D	915	broad.mit.edu	37	11	118211318	118211318	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118211318delA	uc001pss.1	-						CD3D_uc001pst.1_Intron	NM_000732	NP_000723			CD3 antigen, delta subunit isoform A precursor						positive thymic T cell selection|T cell costimulation|T cell receptor signaling pathway	cytoplasm|integral to membrane	protein heterodimerization activity			ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)														---	---	---	---
DDX6	1656	broad.mit.edu	37	11	118629613	118629614	+	Splice_Site	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118629613_118629614insG	uc001pub.2	-	9	1226	c.865_splice	c.e9-1	p.N289_splice	DDX6_uc001pua.2_5'UTR|DDX6_uc001puc.2_Splice_Site_p.N289_splice	NM_004397	NP_004388			DEAD (Asp-Glu-Ala-Asp) box polypeptide 6						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|RNA-induced silencing complex|stress granule	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|RNA helicase activity			ovary(1)	1	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)				T	IGH@	B-NHL								---	---	---	---
RPS25	6230	broad.mit.edu	37	11	118888388	118888388	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118888388delA	uc001pun.2	-						TRAPPC4_uc010ryn.1_5'Flank|TRAPPC4_uc010ryo.1_5'Flank|TRAPPC4_uc010ryp.1_5'Flank|TRAPPC4_uc001pup.2_5'Flank|TRAPPC4_uc010ryq.1_5'Flank	NM_001028	NP_001019			ribosomal protein S25						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)														---	---	---	---
CBL	867	broad.mit.edu	37	11	119148323	119148323	+	Intron	DEL	T	-	-	rs79470692		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119148323delT	uc001pwe.2	+							NM_005188	NP_005179			Cas-Br-M (murine) ecotropic retroviral						epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	11	119612631	119612632	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119612631_119612632delCA								PVRL1 (13196 upstream) : TRIM29 (369363 downstream)																																			---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120318628	120318628	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120318628delT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	11	120873110	120873112	+	IGR	DEL	GGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120873110_120873112delGGA								GRIK4 (16141 upstream) : TBCEL (21691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121710002	121710002	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121710002delT								SORL1 (205531 upstream) : LOC399959 (249809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121800949	121800949	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121800949delA								SORL1 (296478 upstream) : LOC399959 (158862 downstream)																																			---	---	---	---
VWA5A	4013	broad.mit.edu	37	11	123997467	123997467	+	Intron	DEL	A	-	-	rs75352418		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123997467delA	uc001pzu.2	+						VWA5A_uc001pzt.2_Intron	NM_001130142	NP_001123614			BCSC-1 isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
SLC37A2	219855	broad.mit.edu	37	11	124951304	124951304	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124951304delT	uc001qbn.2	+						SLC37A2_uc010sau.1_Intron|SLC37A2_uc010sav.1_5'Flank|SLC37A2_uc001qbp.2_5'Flank	NM_001145290	NP_001138762			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125112244	125112244	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125112244delC	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345			PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125133169	125133169	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125133169delA	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345			PBX/knotted 1 homeobox 2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125472338	125472338	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125472338delT	uc001qcd.2	+						STT3A_uc009zbm.2_Intron|STT3A_uc001qce.2_Intron|STT3A_uc010sbg.1_Intron	NM_152713	NP_689926			integral membrane protein 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)														---	---	---	---
PATE1	160065	broad.mit.edu	37	11	125616675	125616675	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125616675delA	uc001qct.2	+						PATE1_uc009zbr.2_Intron	NM_138294	NP_612151			expressed in prostate and testis precursor							extracellular region					0																		---	---	---	---
FAM118B	79607	broad.mit.edu	37	11	126090301	126090302	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126090301_126090302insT	uc001qdf.2	+						FAM118B_uc009zca.2_Intron|FAM118B_uc001qdg.2_Intron	NM_024556	NP_078832			hypothetical protein LOC79607												0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)														---	---	---	---
SRPR	6734	broad.mit.edu	37	11	126137791	126137791	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126137791delT	uc001qdh.2	-						SRPR_uc010sbm.1_Intron|FOXRED1_uc001qdi.2_5'Flank|FOXRED1_uc010sbn.1_5'Flank|FOXRED1_uc010sbo.1_5'Flank|FOXRED1_uc010sbp.1_5'Flank|FOXRED1_uc010sbq.1_5'Flank|FOXRED1_uc001qdj.2_5'Flank|FOXRED1_uc010sbr.1_5'Flank	NM_003139	NP_003130			signal recognition particle receptor						SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding				0	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)														---	---	---	---
FOXRED1	55572	broad.mit.edu	37	11	126141134	126141135	+	Intron	INS	-	AAGG	AAGG	rs141438450	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126141134_126141135insAAGG	uc001qdi.2	+						SRPR_uc001qdh.2_5'Flank|SRPR_uc010sbm.1_5'Flank|FOXRED1_uc010sbn.1_Intron|FOXRED1_uc010sbo.1_Intron|FOXRED1_uc010sbp.1_Intron|FOXRED1_uc010sbq.1_Intron|FOXRED1_uc001qdj.2_Intron|FOXRED1_uc010sbr.1_Intron|FOXRED1_uc001qdk.2_5'UTR	NM_017547	NP_060017			FAD-dependent oxidoreductase domain containing							integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127569257	127569258	+	IGR	DEL	TT	-	-	rs34757100		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127569257_127569258delTT								KIRREL3 (695902 upstream) : ETS1 (759398 downstream)																																			---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128855833	128855833	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128855833delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron|ARHGAP32_uc009zco.2_Intron|ARHGAP32_uc001qez.2_Intron|ARHGAP32_uc001qfb.2_3'UTR	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129499340	129499340	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129499340delG								BARX2 (177167 upstream) : TMEM45B (186401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	130080949	130080949	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130080949delT								ST14 (693 upstream) : ZBTB44 (15627 downstream)																																			---	---	---	---
ZBTB44	29068	broad.mit.edu	37	11	130108688	130108689	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130108688_130108689insT	uc001qga.2	-						ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qfz.2_Intron	NM_014155	NP_054874			zinc finger and BTB domain containing 44						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)														---	---	---	---
NTM	50863	broad.mit.edu	37	11	131846045	131846046	+	Intron	INS	-	CTTCCTTC	CTTCCTTC	rs58735891		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131846045_131846046insCTTCCTTC	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131897926	131897926	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131897926delT	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132414116	132414116	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132414116delA	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132500422	132500425	+	Intron	DEL	TGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132500422_132500425delTGTG	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	133428551	133428552	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133428551_133428552delTT								OPCML (26148 upstream) : SPATA19 (281965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	95190	95191	+	5'Flank	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95190_95191insA	uc010sdi.1	-						uc010sdj.1_5'Flank					SubName: Full=DEAD/H box polypeptide 11 like 11;																														---	---	---	---
CCDC77	84318	broad.mit.edu	37	12	531358	531359	+	Intron	INS	-	A	A	rs144287663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:531358_531359insA	uc001qig.2	+						CCDC77_uc009zdk.2_Intron|CCDC77_uc010sdp.1_Intron|CCDC77_uc010sdq.1_Intron	NM_032358	NP_115734			coiled-coil domain containing 77 isoform a							centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)															---	---	---	---
WNK1	65125	broad.mit.edu	37	12	1018421	1018422	+	3'UTR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1018421_1018422insT	uc001qio.3	+	28					WNK1_uc001qip.3_3'UTR|WNK1_uc001qir.3_3'UTR	NM_018979	NP_061852			WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1334615	1334616	+	Intron	INS	-	AAA	AAA	rs139203394	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1334615_1334616insAAA	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc009zdp.2_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
TSPAN9	10867	broad.mit.edu	37	12	3328004	3328004	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3328004delA	uc001qlp.2	+							NM_006675	NP_006666			tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4122180	4122182	+	IGR	DEL	AAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4122180_4122182delAAG								PARP11 (139572 upstream) : CCND2 (260720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6407251	6407252	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6407251_6407252insC								CD9 (59824 upstream) : PLEKHG6 (12350 downstream)																																			---	---	---	---
SCNN1A	6337	broad.mit.edu	37	12	6478461	6478483	+	Intron	DEL	CACCTCCCTCCTGCCACCCTACG	-	-	rs71450142	by1000genomes;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6478461_6478483delCACCTCCCTCCTGCCACCCTACG	uc001qnx.2	-						SCNN1A_uc001qnw.2_Intron|SCNN1A_uc010sfb.1_Intron	NM_001038	NP_001029			sodium channel, nonvoltage-gated 1 alpha isoform						excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
LTBR	4055	broad.mit.edu	37	12	6494334	6494334	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6494334delG	uc001qny.1	+						LTBR_uc010sfc.1_Intron|LTBR_uc001qnz.1_Intron	NM_002342	NP_002333			lymphotoxin beta receptor precursor						apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity			lung(2)	2																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6704291	6704291	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6704291delT	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
CLEC4C	170482	broad.mit.edu	37	12	7889828	7889828	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7889828delA	uc001qtg.1	-						CLEC4C_uc001qth.1_Intron|CLEC4C_uc001qti.1_Intron	NM_130441	NP_569708			C-type lectin domain family 4, member C isoform						innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)														---	---	---	---
CLEC4C	170482	broad.mit.edu	37	12	7889903	7889903	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7889903delT	uc001qtg.1	-						CLEC4C_uc001qth.1_Intron|CLEC4C_uc001qti.1_Intron	NM_130441	NP_569708			C-type lectin domain family 4, member C isoform						innate immune response	integral to membrane	sugar binding			ovary(2)|skin(1)	3				Kidney(36;0.0915)														---	---	---	---
C3AR1	719	broad.mit.edu	37	12	8212893	8212894	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8212893_8212894insA	uc001qtv.1	-							NM_004054	NP_004045			complement component 3a receptor 1						blood circulation|chemotaxis|elevation of cytosolic calcium ion concentration|inflammatory response	integral to plasma membrane	C3a anaphylatoxin receptor activity|complement component C3a receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)	1				Kidney(36;0.0893)														---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8833922	8833922	+	5'Flank	DEL	A	-	-	rs112409279		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8833922delA	uc001quu.2	+						RIMKLB_uc009zgf.1_5'Flank	NM_020734	NP_065785			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9230027	9230028	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9230027_9230028delGA	uc001qvk.1	-						A2M_uc001qvj.1_Intron|A2M_uc009zgk.1_Intron	NM_000014	NP_000005			alpha-2-macroglobulin precursor						blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	9391909	9391909	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9391909delT	uc001qvm.1	+											Homo sapiens cDNA FLJ44260 fis, clone TLIVE2000979.																														---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10783476	10783476	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10783476delA	uc001qys.2	-							NM_018423	NP_060893			serine/threonine/tyrosine kinase 1							integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8															HNSCC(73;0.22)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	11695791	11695791	+	IGR	DEL	A	-	-	rs35125929		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11695791delA								PRB2 (147293 upstream) : ETV6 (106997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	12804300	12804300	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12804300delA								CREBL2 (6259 upstream) : GPR19 (9695 downstream)																																			---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	14018581	14018581	+	Intron	DEL	A	-	-	rs74837716		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14018581delA	uc001rbt.2	-							NM_000834	NP_000825			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)													---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14656992	14656992	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14656992delT	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
PYROXD1	79912	broad.mit.edu	37	12	21614916	21614917	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21614916_21614917insT	uc001rew.2	+						PYROXD1_uc009ziq.2_Intron|PYROXD1_uc009zir.2_Intron	NM_024854	NP_079130			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			ovary(1)	1																		---	---	---	---
CMAS	55907	broad.mit.edu	37	12	22198293	22198293	+	5'Flank	DEL	C	-	-	rs144692617	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22198293delC	uc001rfm.2	+						CMAS_uc001rfn.2_5'Flank	NM_018686	NP_061156			cytidine monophospho-N-acetylneuraminic acid						lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
LYRM5	144363	broad.mit.edu	37	12	25350567	25350568	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25350567_25350568insT	uc001rgo.2	+						CASC1_uc001rgk.2_5'Flank|CASC1_uc001rgm.3_5'Flank|CASC1_uc001rgl.2_5'Flank|CASC1_uc001rgj.2_5'Flank|CASC1_uc010sje.1_5'Flank|CASC1_uc010sjf.1_5'Flank|CASC1_uc010sjg.1_5'Flank|CASC1_uc010sjh.1_5'Flank|LYRM5_uc001rgn.2_Intron	NM_001001660	NP_001001660			LYR motif containing 5												0	all_cancers(2;4.75e-35)|all_epithelial(2;1.91e-37)|all_lung(3;1.07e-23)|Lung NSC(3;5.49e-23)|Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.0016)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;2.21e-21)|Epithelial(3;8.04e-19)|all cancers(3;2.26e-16)|STAD - Stomach adenocarcinoma(2;0.00138)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	29052509	29052510	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29052509_29052510delTG								CCDC91 (349411 upstream) : FAR2 (249722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30609351	30609354	+	IGR	DEL	TCTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30609351_30609354delTCTC								TMTC1 (671659 upstream) : IPO8 (172569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	31510387	31510387	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31510387delT								FAM60A (31228 upstream) : DENND5B (24770 downstream)																																			---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31562360	31562362	+	Intron	DEL	AAA	-	-	rs111670680		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31562360_31562362delAAA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	31962664	31962664	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31962664delT								H3F3C (17489 upstream) : C12orf35 (149689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34363933	34363934	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34363933_34363934insC								ALG10 (182699 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38706563	38706564	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38706563_38706564delAA								None (None upstream) : ALG10B (3993 downstream)																																			---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41690561	41690561	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41690561delA	uc010skn.1	+							NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42972185	42972185	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42972185delT	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571			prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43877713	43877713	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43877713delT	uc010skx.1	-							NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	43962682	43962682	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43962682delA								ADAMTS20 (16958 upstream) : PUS7L (159732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46024655	46024656	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46024655_46024656delAA								ANO6 (190468 upstream) : LOC400027 (95154 downstream)																																			---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46582919	46582919	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46582919delA	uc001rpa.2	-						SLC38A1_uc001rpb.2_Intron|SLC38A1_uc001rpc.2_Intron|SLC38A1_uc001rpd.2_Intron|SLC38A1_uc001rpe.2_Intron	NM_030674	NP_109599			amino acid transporter system A1						cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
ENDOU	8909	broad.mit.edu	37	12	48110555	48110555	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48110555delT	uc001rpu.1	-						ENDOU_uc010sll.1_Intron|ENDOU_uc001rpt.1_Intron|ENDOU_uc010slm.1_Intron|uc001rpv.2_5'Flank	NM_006025	NP_006016			placental protein 11 precursor						female pregnancy|immune response|proteolysis	cytoplasm|extracellular space|plasma membrane	endoribonuclease activity|growth factor activity|manganese ion binding|polysaccharide binding|RNA binding|scavenger receptor activity|serine-type peptidase activity			ovary(2)|pancreas(1)	3																OREG0021752	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
COL2A1	1280	broad.mit.edu	37	12	48380331	48380332	+	Intron	INS	-	G	G	rs144941834	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48380331_48380332insG	uc001rqu.2	-						COL2A1_uc009zkw.2_Intron|COL2A1_uc001rqv.2_Intron	NM_001844	NP_001835			collagen, type II, alpha 1 isoform 1 precursor						axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	48406830	48406830	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48406830delG								COL2A1 (8545 upstream) : SENP1 (29928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49286116	49286117	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49286116_49286117delTT								RND1 (26463 upstream) : CCDC65 (11776 downstream)																																			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49433407	49433407	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49433407delA	uc001rta.3	-							NM_003482	NP_003473			myeloid/lymphoid or mixed-lineage leukemia 2						chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49434936	49434936	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49434936delG	uc001rta.3	-	31	6617	c.6617delC	c.(6616-6618)CCTfs	p.P2206fs		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2206	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
TROAP	10024	broad.mit.edu	37	12	49722647	49722647	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49722647delA	uc001rtx.3	+						TROAP_uc009zlh.2_Intron|TROAP_uc001rty.2_Intron	NM_005480	NP_005471			tastin isoform 1						cell adhesion	cytoplasm				ovary(1)	1																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50596172	50596173	+	Intron	DEL	AA	-	-	rs113986199		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50596172_50596173delAA	uc001rwj.3	-						LIMA1_uc001rwg.3_5'Flank|LIMA1_uc001rwh.3_Intron|LIMA1_uc001rwi.3_Intron|LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441			LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ATF1	466	broad.mit.edu	37	12	51173906	51173906	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51173906delT	uc001rww.3	+						ATF1_uc010smu.1_Intron	NM_005171	NP_005162			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								T	EWSR1|FUS	malignant melanoma of soft parts |angiomatoid fibrous histiocytoma 								---	---	---	---
GALNT6	11226	broad.mit.edu	37	12	51768744	51768744	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51768744delT	uc001ryk.2	-						GALNT6_uc009zma.1_Intron|GALNT6_uc001ryl.1_Intron	NM_007210	NP_009141			polypeptide N-acetylgalactosaminyltransferase 6						protein O-linked glycosylation	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52050608	52050608	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52050608delA	uc001ryw.2	+							NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
RARG	5916	broad.mit.edu	37	12	53613059	53613059	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53613059delT	uc001sce.2	-						RARG_uc001scd.2_Intron|RARG_uc010sob.1_Intron|RARG_uc001scf.2_Intron|RARG_uc001scg.2_Intron|RARG_uc010soc.1_Intron|RARG_uc010sod.1_Intron	NM_000966	NP_000957			retinoic acid receptor, gamma isoform 1						canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid	integral to membrane|transcription factor complex	retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			breast(2)|ovary(1)|lung(1)	4					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)													---	---	---	---
ATF7	11016	broad.mit.edu	37	12	53933841	53933842	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53933841_53933842insA	uc001sdy.2	-						ATF7_uc010sok.1_Intron|ATF7_uc001sdz.2_Intron|ATF7_uc010sol.1_Intron	NM_001130059	NP_001123531			activating transcription factor 7 isoform 1						interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	55692082	55692082	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55692082delT								OR6C6 (3066 upstream) : OR6C1 (22302 downstream)																																			---	---	---	---
RDH16	8608	broad.mit.edu	37	12	57385362	57385362	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57385362delA	uc010sqx.1	-						GPR182_uc001smk.2_5'Flank					Synthetic construct DNA, clone: pF1KSDA0352, Homo sapiens ZBTB39 gene for zinc finger and BTB domain-containing protein 39, complete cds, without stop codon, in Flexi system.						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	binding|electron carrier activity|retinol dehydrogenase activity				0																		---	---	---	---
TMEM194A	23306	broad.mit.edu	37	12	57466469	57466469	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57466469delT	uc001smy.2	-						TMEM194A_uc001smx.2_Intron|TMEM194A_uc010sra.1_Intron	NM_001130963	NP_001124435			transmembrane protein 194A isoform a							integral to membrane					0																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57646799	57646801	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57646799_57646801delAAA	uc010srn.1	-						STAC3_uc001snp.2_5'Flank|STAC3_uc009zpl.2_5'Flank|STAC3_uc001snq.2_5'Flank|STAC3_uc010srm.1_5'Flank					Homo sapiens mRNA for KIAA1002 protein, partial cds.							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57779477	57779477	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57779477delA	uc001snt.2	-						R3HDM2_uc001sns.2_Intron|R3HDM2_uc009zpo.1_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57862547	57862547	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57862547delT	uc001snx.2	+						GLI1_uc009zpq.2_Intron	NM_005269	NP_005260			GLI family zinc finger 1 isoform 1						epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)															---	---	---	---
DTX3	196403	broad.mit.edu	37	12	58001615	58001615	+	Intron	DEL	A	-	-	rs79231341		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58001615delA	uc001sow.1	+						DTX3_uc001sox.1_Intron|DTX3_uc001soy.1_Intron|GEFT_uc009zpy.2_5'Flank|GEFT_uc001soz.1_5'Flank	NM_178502	NP_848597			deltex homolog 3						Notch signaling pathway	cytoplasm	zinc ion binding			breast(1)|central_nervous_system(1)	2	Melanoma(17;0.122)																	---	---	---	---
MON2	23041	broad.mit.edu	37	12	62959937	62959938	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62959937_62959938insT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron|MON2_uc001srg.2_Intron	NM_015026	NP_055841			MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63614326	63614326	+	IGR	DEL	A	-	-	rs61936401	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63614326delA								AVPR1A (67736 upstream) : DPY19L2 (338367 downstream)																																			---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64828154	64828154	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64828154delT	uc001ssb.2	+							NM_007235	NP_009166			tRNA exportin						intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66539677	66539677	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66539677delA	uc001stc.2	-	5	484	c.408delT	c.(406-408)TTTfs	p.F136fs	LLPH_uc010ssx.1_RNA|TMBIM4_uc001std.2_Frame_Shift_Del_p.F105fs|TMBIM4_uc009zqr.2_Frame_Shift_Del_p.F183fs|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_Frame_Shift_Del_p.F136fs|TMBIM4_uc009zqs.2_Frame_Shift_Del_p.F136fs	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	136	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	66660470	66660471	+	IGR	INS	-	GTGTGTGTGTGT	GTGTGTGTGTGT	rs112447842		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66660470_66660471insGTGTGTGTGTGT								IRAK3 (12078 upstream) : HELB (35885 downstream)																																			---	---	---	---
HELB	92797	broad.mit.edu	37	12	66731962	66731962	+	RNA	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66731962delA	uc010ssz.1	+	13		c.3448delA			HELB_uc009zqt.1_RNA					Homo sapiens helicase B mRNA, complete cds.						DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)														---	---	---	---
MDM2	4193	broad.mit.edu	37	12	69218526	69218526	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69218526delT	uc001sui.2	+						MDM2_uc009zri.2_Intron|MDM2_uc009zqx.2_Intron|MDM2_uc009zqw.2_Intron|MDM2_uc001suk.2_Intron|MDM2_uc009zqy.1_Intron|MDM2_uc001sun.3_Intron|MDM2_uc009zqz.2_Intron|MDM2_uc009zra.2_Intron|MDM2_uc001sum.1_Intron|MDM2_uc009zrd.2_Intron|MDM2_uc009zrc.2_Intron|MDM2_uc009zre.2_Intron|MDM2_uc009zrf.2_Intron|MDM2_uc001suo.2_Intron|MDM2_uc009zrg.2_Intron|MDM2_uc009zrh.2_Intron	NM_002392	NP_002383			mouse double minute 2 homolog isoform MDM2						cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission	cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex	enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|central_nervous_system(1)	3	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)					A		sarcoma|glioma|colorectal|other								---	---	---	---
MDM2	4193	broad.mit.edu	37	12	69234988	69234989	+	3'UTR	DEL	AA	-	-	rs34886328		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69234988_69234989delAA	uc001sui.2	+	11					MDM2_uc009zri.2_3'UTR|MDM2_uc009zqx.2_3'UTR|MDM2_uc009zqw.2_3'UTR|MDM2_uc001suk.2_3'UTR|MDM2_uc001sun.3_3'UTR|MDM2_uc009zqz.2_3'UTR|MDM2_uc009zra.2_3'UTR|MDM2_uc009zrd.2_3'UTR|MDM2_uc009zrc.2_3'UTR|MDM2_uc009zre.2_3'UTR|MDM2_uc009zrf.2_3'UTR|MDM2_uc001suo.2_3'UTR|MDM2_uc009zrg.2_3'UTR|MDM2_uc009zrh.2_3'UTR	NM_002392	NP_002383			mouse double minute 2 homolog isoform MDM2						cellular response to hypoxia|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|establishment of protein localization|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein complex assembly|protein destabilization|protein localization to nucleus|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to antibiotic|synaptic transmission	cytosol|endocytic vesicle membrane|insoluble fraction|nucleolus|nucleoplasm|plasma membrane|protein complex	enzyme binding|identical protein binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|central_nervous_system(1)	3	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)					A		sarcoma|glioma|colorectal|other								---	---	---	---
YEATS4	8089	broad.mit.edu	37	12	69784045	69784045	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69784045delA	uc001sux.2	+	7	854	c.633delA	c.(631-633)TTAfs	p.L211fs		NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41	211	Interaction with MLLT10.|Potential.|Interaction with TACC1.				histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	75981849	75981850	+	IGR	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75981849_75981850insC								KRR1 (76431 upstream) : PHLDA1 (437378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76378548	76378549	+	IGR	INS	-	GA	GA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76378548_76378549insGA								KRR1 (473130 upstream) : PHLDA1 (40679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79148066	79148066	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79148066delG								NAV3 (541278 upstream) : SYT1 (109707 downstream)																																			---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	81063246	81063246	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81063246delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82958654	82958655	+	IGR	DEL	GA	-	-	rs10567468		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82958654_82958655delGA								C12orf26 (85713 upstream) : TMTC2 (122279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85023080	85023080	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85023080delT								None (None upstream) : SLC6A15 (230189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85345226	85345226	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85345226delT								SLC6A15 (38620 upstream) : TSPAN19 (62869 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88448067	88448067	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88448067delT	uc001tar.2	-						CEP290_uc001taq.2_Intron|uc001tas.2_5'Flank	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
TMTC3	160418	broad.mit.edu	37	12	88586254	88586254	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88586254delT	uc001tau.2	+							NM_181783	NP_861448			transmembrane and tetratricopeptide repeat							integral to membrane	binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88690372	88690372	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88690372delA								TMTC3 (96709 upstream) : KITLG (196197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90288119	90288120	+	IGR	INS	-	T	T	rs145479919	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90288119_90288120insT								LOC338758 (182391 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91203023	91203023	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91203023delA								None (None upstream) : C12orf12 (142970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91871462	91871463	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91871462_91871463delAA								DCN (294656 upstream) : BTG1 (507403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91907248	91907248	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91907248delC								DCN (330442 upstream) : BTG1 (471618 downstream)																																			---	---	---	---
UBE2N	7334	broad.mit.edu	37	12	93824709	93824710	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93824709_93824710delAA	uc001tcp.2	-							NM_003348	NP_003339			ubiquitin-conjugating enzyme E2N						DNA double-strand break processing|double-strand break repair via homologous recombination|histone ubiquitination|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of DNA repair|positive regulation of histone modification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity|postreplication repair|protein K63-linked ubiquitination|proteolysis|regulation of histone ubiquitination|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-MMS2 complex|UBC13-UEV1A complex|ubiquitin ligase complex	ATP binding|ubiquitin binding|ubiquitin-protein ligase activity				0													Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
MRPL42	28977	broad.mit.edu	37	12	93876198	93876198	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93876198delT	uc001tcr.2	+						MRPL42_uc001tcq.2_Intron|MRPL42_uc001tcs.2_Intron|MRPL42_uc001tct.2_Intron	NM_172177	NP_751917			mitochondrial ribosomal protein L42 isoform a						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome			ovary(2)	2																		---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95546645	95546645	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95546645delT	uc001tdp.3	-						FGD6_uc009zsx.2_Intron	NM_018351	NP_060821			FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96030954	96030955	+	IGR	INS	-	CGTAACGTAG	CGTAACGTAG	rs72473615		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96030954_96030955insCGTAACGTAG								USP44 (85691 upstream) : NTN4 (20629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	96030975	96030989	+	IGR	DEL	CGTAACGTAACGTAA	-	-	rs72241555		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96030975_96030989delCGTAACGTAACGTAA								USP44 (85712 upstream) : NTN4 (20595 downstream)																																			---	---	---	---
RMST	196475	broad.mit.edu	37	12	97883236	97883237	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97883236_97883237delAA	uc001tey.1	+						MIR1251_hsa-mir-1251|MI0006386_5'Flank	NR_024037				Homo sapiens C23up NCRMS mRNA, partial sequence; alternatively spliced.												0																		---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99847462	99847462	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99847462delG	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	100069882	100069882	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100069882delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ACTR6	64431	broad.mit.edu	37	12	100600452	100600453	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100600452_100600453delTC	uc001thb.1	+						ACTR6_uc010svh.1_Intron|ACTR6_uc001thc.1_Intron|ACTR6_uc001thd.1_Intron|ACTR6_uc009ztu.1_Intron|ACTR6_uc001the.1_Intron|ACTR6_uc001thf.1_Intron|uc001thg.1_Intron	NM_022496	NP_071941			ARP6 actin-related protein 6 homolog							cytoplasm|cytoskeleton				ovary(1)	1																		---	---	---	---
ACTR6	64431	broad.mit.edu	37	12	100617457	100617458	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100617457_100617458insA	uc001thb.1	+						ACTR6_uc001thc.1_Intron|ACTR6_uc001thd.1_Intron|ACTR6_uc009ztu.1_Intron|ACTR6_uc001the.1_Intron|ACTR6_uc001thf.1_Intron|uc001thg.1_5'Flank	NM_022496	NP_071941			ARP6 actin-related protein 6 homolog							cytoplasm|cytoskeleton				ovary(1)	1																		---	---	---	---
DEPDC4	120863	broad.mit.edu	37	12	100646135	100646135	+	3'UTR	DEL	A	-	-	rs66721214		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100646135delA	uc001thi.2	-	5					DEPDC4_uc001thh.1_Intron	NM_152317	NP_689530			DEP domain containing 4						intracellular signal transduction						0																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101689631	101689632	+	Intron	DEL	GT	-	-	rs36059562		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101689631_101689632delGT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101700374	101700374	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101700374delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101739836	101739836	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101739836delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102071262	102071262	+	Intron	DEL	A	-	-	rs74710518		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102071262delA	uc001tii.2	+						MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron|MYBPC1_uc001til.2_Intron|MYBPC1_uc001tim.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
DRAM1	55332	broad.mit.edu	37	12	102283259	102283260	+	Intron	INS	-	GAAG	GAAG	rs146359103	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102283259_102283260insGAAG	uc001tix.2	+						DRAM1_uc010svv.1_Intron	NM_018370	NP_060840			DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	103984654	103984654	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103984654delT	uc001tjw.2	+							NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104134268	104134268	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104134268delA	uc001tjw.2	+						STAB2_uc009zug.2_Intron	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
TDG	6996	broad.mit.edu	37	12	104369443	104369443	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104369443delT	uc001tkg.2	+						TDG_uc010swh.1_Intron|TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron	NM_003211	NP_003202			thymine-DNA glycosylase						depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)									BER_DNA_glycosylases					---	---	---	---
NFYB	4801	broad.mit.edu	37	12	104526183	104526184	+	Intron	DEL	AA	-	-	rs78874288		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104526183_104526184delAA	uc001tkl.1	-						NFYB_uc001tkk.1_Intron|NFYB_uc009zum.1_Intron	NM_006166	NP_006157			nuclear transcription factor Y, beta							CCAAT-binding factor complex	repressing transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	105039427	105039427	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105039427delC	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883			carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0																		---	---	---	---
SLC41A2	84102	broad.mit.edu	37	12	105198776	105198777	+	3'UTR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105198776_105198777insA	uc001tla.2	-	10						NM_032148	NP_115524			solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107783624	107783629	+	Intron	DEL	TGTGTG	-	-	rs67656571		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107783624_107783629delTGTGTG	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107905285	107905285	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107905285delC	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
PRDM4	11108	broad.mit.edu	37	12	108132985	108132985	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108132985delA	uc001tmp.2	-						PRDM4_uc010sww.1_Intron|PRDM4_uc001tmq.2_Intron	NM_012406	NP_036538			PR domain containing 4						cell proliferation|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111537986	111537987	+	Intron	DEL	TG	-	-	rs113761718		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111537986_111537987delTG	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112190083	112190085	+	Intron	DEL	TTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112190083_112190085delTTG	uc001tsq.2	+						ACAD10_uc009zvx.2_Intron|ACAD10_uc001tss.1_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
DTX1	1840	broad.mit.edu	37	12	113499016	113499016	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113499016delA	uc001tuk.1	+							NM_004416	NP_004407			deltex homolog 1						negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter	cytoplasm|nucleus	Notch binding|SH3 domain binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
TPCN1	53373	broad.mit.edu	37	12	113681175	113681175	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113681175delA	uc001tuw.2	+						TPCN1_uc001tux.2_Intron|TPCN1_uc010syt.1_5'Flank	NM_017901	NP_060371			two pore segment channel 1 isoform 2							endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated ion channel activity			skin(2)|ovary(1)	3																		---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115115334	115115335	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115115334_115115335insA	uc001tvt.1	-						TBX3_uc001tvu.1_Intron	NM_016569	NP_057653			T-box 3 protein isoform 2						anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	115524410	115524410	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115524410delT								TBX3 (402441 upstream) : MED13L (871973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115614456	115614459	+	IGR	DEL	GTGA	-	-	rs143967284	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115614456_115614459delGTGA								TBX3 (492487 upstream) : MED13L (781924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115784293	115784294	+	IGR	INS	-	GAGG	GAGG	rs28508591		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115784293_115784294insGAGG								TBX3 (662324 upstream) : MED13L (612089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116095665	116095666	+	IGR	INS	-	CTC	CTC	rs141337461	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116095665_116095666insCTC								TBX3 (973696 upstream) : MED13L (300717 downstream)																																			---	---	---	---
HRK	8739	broad.mit.edu	37	12	117317868	117317868	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117317868delC	uc001twe.2	-							NM_003806	NP_003797			harakiri						apoptosis|induction of apoptosis|negative regulation of survival gene product expression|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria		protein binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0282)														---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118068165	118068166	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118068165_118068166delTG	uc001two.2	-							NM_173598	NP_775869			kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	118413838	118413839	+	IGR	INS	-	AA	AA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118413838_118413839insAA								KSR2 (7810 upstream) : RFC5 (40669 downstream)																																			---	---	---	---
CIT	11113	broad.mit.edu	37	12	120150675	120150675	+	Intron	DEL	A	-	-	rs113783917		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120150675delA	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105			citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	120379354	120379354	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120379354delA								CIT (64262 upstream) : CCDC64 (48294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	120557964	120557964	+	IGR	DEL	A	-	-	rs74526748		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120557964delA								RAB35 (3365 upstream) : GCN1L1 (7052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	121377776	121377776	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121377776delA								SPPL3 (35625 upstream) : C12orf27 (29865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	121625628	121625628	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121625628delC								P2RX7 (1772 upstream) : P2RX4 (22036 downstream)																																			---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	122018158	122018158	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122018158delG	uc001uat.2	-						KDM2B_uc001uas.2_5'UTR|KDM2B_uc001uau.2_Intron|KDM2B_uc001uav.3_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
TMEM120B	144404	broad.mit.edu	37	12	122190657	122190657	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122190657delA	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294			transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)														---	---	---	---
WDR66	144406	broad.mit.edu	37	12	122437595	122437595	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122437595delT	uc009zxk.2	+							NM_144668	NP_653269			WD repeat domain 66								calcium ion binding			ovary(1)|skin(1)	2	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122634439	122634439	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122634439delT								MLXIP (5474 upstream) : LRRC43 (17827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	122637046	122637046	+	IGR	DEL	T	-	-	rs5801480		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122637046delT								MLXIP (8081 upstream) : LRRC43 (15220 downstream)																																			---	---	---	---
RILPL2	196383	broad.mit.edu	37	12	123900176	123900176	+	3'UTR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123900176delC	uc001uey.1	-	4						NM_145058	NP_659495			Rab interacting lysosomal protein-like 2							cytosol|plasma membrane	identical protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124263452	124263453	+	Intron	DEL	TT	-	-	rs34114020		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124263452_124263453delTT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	124671002	124671002	+	IGR	DEL	A	-	-	rs7132226	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124671002delA								ZNF664 (171035 upstream) : FAM101A (102708 downstream)																																			---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	125003643	125003644	+	Intron	INS	-	ACAT	ACAT	rs140955385	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125003643_125003644insACAT	uc010tay.1	-						NCOR2_uc010taz.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_5'Flank	NM_006312	NP_006303			nuclear receptor co-repressor 2 isoform 1						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125161425	125161426	+	IGR	INS	-	GT	GT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125161425_125161426insGT								NCOR2 (109415 upstream) : SCARB1 (100749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126205827	126205828	+	IGR	INS	-	AT	AT	rs141726251	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126205827_126205828insAT								TMEM132B (62238 upstream) : LOC100128554 (721199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126440234	126440234	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126440234delT								TMEM132B (296645 upstream) : LOC100128554 (486793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127258250	127258257	+	5'Flank	DEL	TCATTCAT	-	-	rs72120741		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127258250_127258257delTCATTCAT	uc001uhk.3	-											Homo sapiens cDNA clone IMAGE:6160413.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	128090894	128090894	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128090894delT								None (None upstream) : TMEM132C (808397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128844791	128844794	+	IGR	DEL	ACAC	-	-	rs113134398		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128844791_128844794delACAC								None (None upstream) : TMEM132C (54497 downstream)																																			---	---	---	---
SLC15A4	121260	broad.mit.edu	37	12	129279007	129279007	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129279007delA	uc001uhu.2	-						SLC15A4_uc001uhv.2_Intron	NM_145648	NP_663623			solute carrier family 15, member 4						oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129841792	129841792	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129841792delA	uc009zyl.1	-							NM_133448	NP_597705			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19545821	19545821	+	IGR	DEL	T	-	-	rs112563923		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19545821delT								LOC284232 (99712 upstream) : LOC348021 (36578 downstream)																																			---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19645199	19645199	+	Intron	DEL	T	-	-	rs112500592		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19645199delT	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
DKFZp686A1627	266695	broad.mit.edu	37	13	19690869	19690870	+	Intron	INS	-	CTC	CTC	rs141065369	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19690869_19690870insCTC	uc001umb.1	-							NR_002801				Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	19801216	19801216	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19801216delT								TUBA3C (45280 upstream) : LOC100101938 (35725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20160618	20160618	+	IGR	DEL	A	-	-	rs35378607		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20160618delA								TPTE2 (24904 upstream) : MPHOSPH8 (47262 downstream)																																			---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20236086	20236089	+	Intron	DEL	TTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20236086_20236089delTTTT	uc001umh.2	+						MPHOSPH8_uc001umg.2_Intron	NM_017520	NP_059990			M-phase phosphoprotein 8						cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)														---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20321481	20321481	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20321481delT	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20675173	20675173	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20675173delA								ZMYM2 (14235 upstream) : GJA3 (37222 downstream)																																			---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21146366	21146366	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21146366delT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron	NM_175605	NP_783195			intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21359809	21359809	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21359809delA	uc001unq.3	-							NM_022459	NP_071904			exportin 4						protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21462947	21462949	+	Intron	DEL	TTT	-	-	rs56117403	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21462947_21462949delTTT	uc001unq.3	-						XPO4_uc010tcr.1_Intron	NM_022459	NP_071904			exportin 4						protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	22029773	22029774	+	Intron	DEL	GT	-	-	rs66511848		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22029773_22029774delGT	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22200148	22200148	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22200148delA								EFHA1 (21841 upstream) : FGF9 (45067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23255899	23255900	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23255899_23255900insA								FGF9 (977259 upstream) : SGCG (499160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23622352	23622352	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23622352delT								None (None upstream) : SGCG (132708 downstream)																																			---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23893839	23893839	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23893839delC	uc001uom.2	+						SGCG_uc009zzv.2_Intron|SGCG_uc009zzw.2_Intron	NM_000231	NP_000222			gamma sarcoglycan						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)														---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24167428	24167428	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24167428delA	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron|TNFRSF19_uc001uou.2_Intron	NM_018647	NP_061117			tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26006803	26006803	+	Intron	DEL	T	-	-	rs71186884		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26006803delT	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27257455	27257455	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27257455delA	uc001uqv.2	+						WASF3_uc001uqw.2_Intron	NM_006646	NP_006637			WAS protein family, member 3						actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27531468	27531479	+	IGR	DEL	GGACAGTCTTCA	-	-	rs67745169		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27531468_27531479delGGACAGTCTTCA								GPR12 (196546 upstream) : USP12 (110959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	28368608	28368608	+	IGR	DEL	T	-	-	rs74040898		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28368608delT								GSX1 (519 upstream) : PDX1 (125560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	28569744	28569744	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28569744delA								PRHOXNB (6970 upstream) : FLT3 (7668 downstream)																																			---	---	---	---
POMP	51371	broad.mit.edu	37	13	29230947	29230947	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29230947delT	uc001usf.2	+							NM_015932	NP_057016			proteasome maturation protein						proteasome assembly	cytosol|endoplasmic reticulum|membrane|microsome|nucleus|proteasome complex					0		Lung SC(185;0.0367)		all cancers(112;0.141)|OV - Ovarian serous cystadenocarcinoma(117;0.216)														---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29645309	29645309	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29645309delT	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
UBL3	5412	broad.mit.edu	37	13	30349761	30349761	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30349761delT	uc001usp.2	-							NM_007106	NP_009037			ubiquitin-like 3 precursor							intracellular|plasma membrane					0		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	30578102	30578103	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30578102_30578103delTG								UBL3 (153282 upstream) : KATNAL1 (198665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31740361	31740362	+	IGR	INS	-	GTGT	GTGT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31740361_31740362insGTGT								HSPH1 (3859 upstream) : B3GALTL (33750 downstream)																																			---	---	---	---
FRY	10129	broad.mit.edu	37	13	32753577	32753577	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32753577delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33335235	33335235	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33335235delA	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33913042	33913043	+	Intron	DEL	AG	-	-	rs140914217	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33913042_33913043delAG	uc001uux.2	-						STARD13_uc010abh.1_Intron	NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	34009031	34009034	+	Intron	DEL	GAAG	-	-	rs71792228		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34009031_34009034delGAAG	uc001uux.2	-							NM_052851	NP_443083			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34598466	34598467	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34598466_34598467delAC								RFC3 (57772 upstream) : NBEA (917989 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35923434	35923434	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35923434delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39592899	39592899	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39592899delA	uc001uwy.2	-						C13orf23_uc001uwz.2_Intron	NM_025138	NP_079414			hypothetical protein LOC80209 isoform 1											ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
COG6	57511	broad.mit.edu	37	13	40345248	40345248	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40345248delC	uc010acb.2	+							NM_001145079	NP_001138551			component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41101837	41101837	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41101837delA	uc010acc.1	-							NM_002015	NP_002006			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)														---	---	---	---
SUGT1L1	283507	broad.mit.edu	37	13	41396419	41396419	+	Intron	DEL	A	-	-	rs113285533		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41396419delA	uc001uxp.1	-							NR_003365				Homo sapiens cDNA FLJ35913 fis, clone TESTI2010239.												0																		---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41826691	41826691	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41826691delA	uc001uxx.2	-						MTRF1_uc001uxy.2_Intron|MTRF1_uc001uxz.2_Intron|MTRF1_uc010tff.1_Intron|MTRF1_uc001uyc.1_Intron	NM_004294	NP_004285			mitochondrial translational release factor 1						regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)														---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41941505	41941505	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41941505delT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron	NM_024561	NP_078837			NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42249231	42249231	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42249231delA	uc001uyj.2	-							NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42293886	42293886	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42293886delA	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43389046	43389046	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43389046delT								C13orf30 (23363 upstream) : EPSTI1 (73076 downstream)																																			---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43845803	43845804	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43845803_43845804delAC	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44037322	44037323	+	Intron	INS	-	AC	AC	rs147410210	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44037322_44037323insAC	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	44874690	44874690	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44874690delT								LOC121838 (270092 upstream) : SERP2 (73288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	44979306	44979306	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44979306delG	uc001uzl.2	-											Homo sapiens hypothetical gene supported by BC025370, mRNA (cDNA clone IMAGE:3945331).																														---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46716269	46716269	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46716269delA	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
Unknown	0	broad.mit.edu	37	13	47063518	47063518	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47063518delA								C13orf18 (51193 upstream) : LRCH1 (63778 downstream)																																			---	---	---	---
ESD	2098	broad.mit.edu	37	13	47368715	47368715	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47368715delT	uc001vbn.2	-						ESD_uc001vbo.2_Intron	NM_001984	NP_001975			esterase D/formylglutathione hydrolase							cytoplasmic membrane-bounded vesicle	carboxylesterase activity|S-formylglutathione hydrolase activity			ovary(1)	1		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	47616440	47616440	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47616440delT								HTR2A (145390 upstream) : SUCLA2 (900352 downstream)																																			---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49761480	49761481	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49761480_49761481delTT	uc001vcm.2	+						FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron|FNDC3A_uc001vcp.1_Intron|FNDC3A_uc001vcq.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	50384893	50384893	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50384893delT								KPNA3 (17836 upstream) : LOC220429 (79652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	50416753	50416754	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50416753_50416754delTT								KPNA3 (49696 upstream) : LOC220429 (47791 downstream)																																			---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50943445	50943445	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50943445delT	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron|uc001ven.1_Intron|uc001veo.1_Intron|uc001vep.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51226862	51226862	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51226862delT								DLEU1 (124192 upstream) : DLEU7 (59897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	51441577	51441580	+	IGR	DEL	CTTC	-	-	rs71742306		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51441577_51441580delCTTC								DLEU7 (23692 upstream) : RNASEH2B (42312 downstream)																																			---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52529924	52529924	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52529924delA	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron|ATP7B_uc001vfv.2_Intron|ATP7B_uc010tgs.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52541371	52541371	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52541371delT	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron|ATP7B_uc010tgw.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
VPS36	51028	broad.mit.edu	37	13	52999941	52999942	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52999941_52999942insA	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159			vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53525860	53525860	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53525860delT								PCDH8 (103086 upstream) : OLFM4 (77112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55274381	55274381	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55274381delG								MIR1297 (388198 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57659456	57659456	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57659456delT								None (None upstream) : PRR20C (55596 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60671913	60671914	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60671913_60671914delAA	uc001vht.2	-						DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	60780131	60780131	+	IGR	DEL	T	-	-	rs58705094		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60780131delT								DIAPH3 (42012 upstream) : TDRD3 (190460 downstream)																																			---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61058809	61058810	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61058809_61058810delTT	uc001via.2	+						TDRD3_uc010aef.2_Intron|TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61107775	61107776	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61107775_61107776delAA	uc001via.2	+						TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	62676105	62676105	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62676105delT								PCDH20 (674026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62914163	62914163	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62914163delT								PCDH20 (912084 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63267468	63267468	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63267468delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63634727	63634727	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63634727delC								None (None upstream) : OR7E156P (676841 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67619696	67619696	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67619696delA	uc001vik.2	-						PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	70860517	70860517	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:70860517delA								ATXN8OS (146632 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71448136	71448136	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71448136delA								ATXN8OS (734251 upstream) : DACH1 (563962 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72309694	72309695	+	Intron	DEL	AC	-	-	rs147197114	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72309694_72309695delAC	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72333064	72333067	+	Intron	DEL	TTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72333064_72333067delTTTT	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	73272960	73272960	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73272960delT								DACH1 (831630 upstream) : C13orf37 (9535 downstream)																																			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73337441	73337441	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73337441delA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73545341	73545344	+	Intron	DEL	TGTA	-	-	rs72273510		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73545341_73545344delTGTA	uc001vjc.2	+						PIBF1_uc001vjb.2_Intron|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337			progesterone-induced blocking factor 1							centrosome				ovary(1)|breast(1)	2		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	73610141	73610141	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73610141delT								PIBF1 (19552 upstream) : KLF5 (18973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73863677	73863677	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73863677delT								KLF5 (212002 upstream) : KLF12 (396473 downstream)																																			---	---	---	---
KLF12	11278	broad.mit.edu	37	13	74306388	74306388	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74306388delT	uc001vjf.2	-						KLF12_uc010aeq.2_Intron	NM_007249	NP_009180			Kruppel-like factor 12						negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	74717340	74717341	+	IGR	INS	-	CT	CT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74717340_74717341insCT								KLF12 (8946 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74993489	74993492	+	5'Flank	DEL	TCCC	-	-	rs72439247		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74993489_74993492delTCCC	uc001vjj.1	-											Homo sapiens cDNA FLJ35839 fis, clone TESTI2006659.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	75067645	75067645	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75067645delA								KLF12 (359251 upstream) : LOC647288 (744245 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75863376	75863376	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75863376delA	uc001vjl.1	-						TBC1D4_uc010tht.1_Intron|TBC1D4_uc010thu.1_Intron|TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	76001229	76001231	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76001229_76001231delTTT	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76060728	76060728	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76060728delA								TBC1D4 (4478 upstream) : COMMD6 (38622 downstream)																																			---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76102190	76102191	+	Intron	DEL	AA	-	-	rs67236741		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76102190_76102191delAA	uc001vjo.1	-						COMMD6_uc001vjn.1_Intron|COMMD6_uc010aet.1_Intron|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091			COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)														---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76108113	76108113	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76108113delT	uc001vjo.1	-						COMMD6_uc001vjn.1_Intron|COMMD6_uc010aet.1_Intron|COMMD6_uc001vjp.1_Intron	NM_203495	NP_987091			COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76426098	76426098	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76426098delA	uc001vjv.2	+						LMO7_uc010thv.1_Intron|LMO7_uc010thw.1_Intron	NM_015842	NP_056667			LIM domain only 7 isoform 2							cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	77001516	77001516	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77001516delG								LMO7 (567512 upstream) : KCTD12 (452788 downstream)																																			---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77793595	77793596	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77793595_77793596delTT	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77834802	77834802	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802delA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	78998897	78998900	+	Intron	DEL	ACAG	-	-	rs2876727		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78998897_78998900delACAG	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79112240	79112240	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79112240delT	uc001vks.2	+						uc001vku.1_Intron					Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79423870	79423870	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79423870delA								RNF219 (189170 upstream) : RBM26 (470230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81079096	81079096	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81079096delT								SPRY2 (164010 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81264732	81264732	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81264732delA								SPRY2 (349646 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81950715	81950716	+	IGR	INS	-	AC	AC	rs150048952	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81950715_81950716insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83404829	83404829	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83404829delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	84078369	84078369	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84078369delT								None (None upstream) : SLITRK1 (372975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85891849	85891849	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85891849delA								None (None upstream) : SLITRK6 (475073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86011621	86011621	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86011621delT								None (None upstream) : SLITRK6 (355301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89426550	89426550	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89426550delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91672644	91672644	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91672644delA								LOC144776 (93793 upstream) : MIR17HG (327430 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92144204	92144205	+	Intron	DEL	AC	-	-	rs140298451	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92144204_92144205delAC	uc010tif.1	+							NM_004466	NP_004457			glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	93723819	93723819	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93723819delA								GPC5 (204334 upstream) : GPC6 (155259 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94900929	94900930	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94900929_94900930delGA	uc001vlt.2	+						GPC6_uc010tig.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPR180	160897	broad.mit.edu	37	13	95271823	95271823	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95271823delT	uc001vly.2	+						GPR180_uc001vlz.2_Intron|GPR180_uc010afi.2_Intron	NM_180989	NP_851320			G protein-coupled receptor 180 precursor							integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95696129	95696129	+	Intron	DEL	A	-	-	rs4148539		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95696129delA	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95859281	95859281	+	Intron	DEL	A	-	-	rs112178408		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95859281delA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96090665	96090665	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96090665delT	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268			claudin 10 isoform a						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)															---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96148972	96148972	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96148972delG	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268			claudin 10 isoform a						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)															---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96598578	96598579	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96598578_96598579insG	uc001vmt.2	-							NM_020121	NP_064506			UDP-glucose ceramide glucosyltransferase-like 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	97564511	97564511	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97564511delA								HS6ST3 (72700 upstream) : OXGR1 (73462 downstream)																																			---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	97885105	97885106	+	Intron	INS	-	TG	TG	rs148350145	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97885105_97885106insTG	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	98018543	98018543	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98018543delT	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron|MBNL2_uc010tij.1_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	98552833	98552833	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98552833delA								RAP2A (432582 upstream) : IPO5 (53096 downstream)																																			---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98666535	98666535	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98666535delA	uc001vne.2	+							NM_002271	NP_002262			importin 5						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98792395	98792395	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98792395delT	uc001vnh.2	+							NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99607581	99607581	+	Intron	DEL	T	-	-	rs9513518	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99607581delT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron	NM_015296	NP_056111			dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100289144	100289144	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100289144delT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102990436	102990436	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102990436delT	uc001vpf.2	-						uc001vph.1_Intron|uc001vpg.1_Intron	NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	103023256	103023256	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103023256delT	uc001vpf.2	-						uc001vph.1_Intron	NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	105060831	105060832	+	IGR	DEL	AA	-	-	rs34880663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105060831_105060832delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106772478	106772478	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106772478delT								DAOA (629096 upstream) : EFNB2 (369620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107059899	107059899	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107059899delA								DAOA (916517 upstream) : EFNB2 (82199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110317800	110317801	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110317800_110317801insG								MYO16 (457445 upstream) : IRS2 (88385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110695735	110695736	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110695735_110695736delCA								IRS2 (256821 upstream) : COL4A1 (105575 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110908230	110908231	+	Intron	INS	-	A	A	rs147787666		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110908230_110908231insA	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	111703603	111703603	+	IGR	DEL	G	-	-	rs55702387		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111703603delG								ANKRD10 (136187 upstream) : ARHGEF7 (64021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112120280	112120283	+	IGR	DEL	TGTG	-	-	rs149617346		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112120280_112120283delTGTG								C13orf16 (123687 upstream) : SOX1 (601630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112506545	112506545	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112506545delA								C13orf16 (509952 upstream) : SOX1 (215368 downstream)																																			---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113528139	113528157	+	Intron	DEL	CCTGGGATACAGTCGGGGG	-	-	rs67506160		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113528139_113528157delCCTGGGATACAGTCGGGGG	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc010ago.2_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	114026111	114026112	+	IGR	INS	-	C	C	rs144165406	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114026111_114026112insC								GRTP1 (7648 upstream) : ADPRHL1 (50148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	114063188	114063189	+	IGR	INS	-	G	G	rs11409959		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114063188_114063189insG								GRTP1 (44725 upstream) : ADPRHL1 (13071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	114570217	114570218	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114570217_114570218insG								GAS6 (3171 upstream) : FLJ44054 (16392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19025830	19025830	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19025830delA								None (None upstream) : OR11H12 (351764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19123482	19123482	+	IGR	DEL	A	-	-	rs75032948		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19123482delA								None (None upstream) : OR11H12 (254112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19426939	19426940	+	IGR	INS	-	AC	AC	rs150451851	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19426939_19426940insAC								OR11H12 (48367 upstream) : POTEG (126425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20086237	20086237	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20086237delT								P704P (65965 upstream) : OR4Q3 (129350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20992727	20992727	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20992727delT								RNASE10 (13413 upstream) : RNASE9 (31526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21610228	21610229	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21610228_21610229insA								ZNF219 (37365 upstream) : OR5AU1 (12868 downstream)																																			---	---	---	---
RPGRIP1	57096	broad.mit.edu	37	14	21816470	21816470	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21816470delT	uc001wag.2	+						RPGRIP1_uc001wah.2_Intron|RPGRIP1_uc001wai.2_Intron|RPGRIP1_uc001wak.2_Intron|RPGRIP1_uc010aim.2_Intron|RPGRIP1_uc001wal.2_Intron|RPGRIP1_uc001wam.2_Intron	NM_020366	NP_065099			retinitis pigmentosa GTPase regulator						response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22356275	22356276	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22356275_22356276insT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc001wby.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22409532	22409540	+	Intron	DEL	TCTCTCTCT	-	-	rs3045130		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22409532_22409540delTCTCTCTCT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010ajb.1_Intron|uc001wck.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23083079	23083079	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23083079delT								ABHD4 (1822 upstream) : OXA1L (152652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23436495	23436495	+	IGR	DEL	T	-	-	rs74242673	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23436495delT								HAUS4 (10160 upstream) : JUB (3917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23696019	23696023	+	IGR	DEL	TTCTT	-	-	rs114237040		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23696019_23696023delTTCTT								SLC7A8 (43170 upstream) : HOMEZ (46821 downstream)																																			---	---	---	---
C14orf167	55449	broad.mit.edu	37	14	24419553	24419553	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24419553delA	uc001wkz.2	-						C14orf167_uc001wky.2_Intron|C14orf167_uc001wkx.2_Intron|C14orf167_uc010akx.1_Intron	NR_023923				Homo sapiens PRO1488 mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	25037062	25037062	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25037062delA								CMA1 (59591 upstream) : CTSG (5663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26404276	26404277	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26404276_26404277insT								STXBP6 (885105 upstream) : NOVA1 (510813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28323426	28323426	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28323426delA								None (None upstream) : FOXG1 (912861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29992992	29992994	+	IGR	DEL	AAC	-	-	rs149629582		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29992992_29992994delAAC								C14orf23 (728993 upstream) : PRKD1 (52695 downstream)																																			---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31188518	31188518	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31188518delT	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010ame.1_Intron	NM_016106	NP_057190			vesicle transport-related protein isoform a						post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
AP4S1	11154	broad.mit.edu	37	14	31546946	31546946	+	Intron	DEL	T	-	-	rs72386557		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31546946delT	uc001wqy.3	+						AP4S1_uc001wqw.3_Intron|AP4S1_uc001wqx.3_Intron|AP4S1_uc010amh.2_Intron|AP4S1_uc001wqz.3_Intron	NM_001128126	NP_001121598			adaptor-related protein complex 4, sigma 1							coated pit|Golgi apparatus	protein transporter activity				0	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.221)	GBM - Glioblastoma multiforme(265;0.00553)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31591470	31591471	+	Intron	DEL	GT	-	-	rs112242799		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31591470_31591471delGT	uc001wrc.1	-						HECTD1_uc001wra.1_Intron|HECTD1_uc001wrb.1_Intron|HECTD1_uc001wrd.1_Intron	NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	32019217	32019217	+	IGR	DEL	T	-	-	rs112510915		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32019217delT								HEATR5A (92537 upstream) : NUBPL (11374 downstream)																																			---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	34145188	34145190	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34145188_34145190delAAA	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	34669510	34669513	+	IGR	DEL	GATG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34669510_34669513delGATG								EGLN3 (249223 upstream) : C14orf147 (232632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	34768672	34768672	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34768672delA								EGLN3 (348385 upstream) : C14orf147 (133473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	36346845	36346847	+	IGR	DEL	TTC	-	-	rs143482923	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36346845_36346847delTTC								BRMS1L (5677 upstream) : MBIP (420917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	36346847	36346847	+	IGR	DEL	C	-	-	rs11361536		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36346847delC								BRMS1L (5679 upstream) : MBIP (420917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	36704509	36704510	+	IGR	INS	-	T	T	rs111545805		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36704509_36704510insT								BRMS1L (363341 upstream) : MBIP (63254 downstream)																																			---	---	---	---
TRAPPC6B	122553	broad.mit.edu	37	14	39627730	39627730	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39627730delT	uc001wut.1	-						TRAPPC6B_uc001wuu.1_Intron|TRAPPC6B_uc001wuv.1_Intron|TRAPPC6B_uc010tqd.1_Intron	NM_001079537	NP_001073005			trafficking protein particle complex 6B isoform						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)														---	---	---	---
CTAGE5	4253	broad.mit.edu	37	14	39818198	39818198	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39818198delT	uc001wvg.3	+						CTAGE5_uc001wuz.3_Intron|CTAGE5_uc001wuy.3_Intron|CTAGE5_uc001wvb.3_Intron|CTAGE5_uc001wvc.3_Intron|CTAGE5_uc001wva.3_Intron|CTAGE5_uc001wvh.3_Intron|CTAGE5_uc001wvf.3_Intron|CTAGE5_uc001wvi.3_Intron|CTAGE5_uc010amz.2_Intron|CTAGE5_uc001wvj.3_Intron	NM_005930	NP_005921			CTAGE family, member 5 isoform 1								enzyme activator activity|protein binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	41425249	41425250	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41425249_41425250insA	uc001wvl.1	+											human full-length cDNA clone CS0DC023YN15 of Neuroblastoma of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	44861897	44861897	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44861897delA								None (None upstream) : FSCB (111458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46574150	46574153	+	IGR	DEL	GAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46574150_46574153delGAAG								C14orf106 (851545 upstream) : RPL10L (546069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46740327	46740328	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46740327_46740328insA								None (None upstream) : RPL10L (379894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48321456	48321456	+	IGR	DEL	A	-	-	rs68177641		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48321456delA								MDGA2 (177468 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48571654	48571654	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48571654delA								MDGA2 (427666 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49763132	49763133	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49763132_49763133insT								None (None upstream) : SDCCAG1 (269894 downstream)																																			---	---	---	---
C14orf138	79609	broad.mit.edu	37	14	50576439	50576439	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50576439delA	uc001wxo.1	-						C14orf138_uc001wxn.1_Intron|C14orf138_uc001wxp.1_Intron|C14orf138_uc001wxq.1_Intron	NM_024558	NP_078834			hypothetical protein LOC79609 isoform a								methyltransferase activity				0	all_epithelial(31;0.000822)|Breast(41;0.0065)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50929313	50929313	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50929313delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52089830	52089830	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52089830delA	uc001wzb.2	+							NM_001042481	NP_001035946			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52188411	52188418	+	Intron	DEL	AGGAAGGA	-	-	rs112816584		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52188411_52188418delAGGAAGGA	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron|FRMD6_uc001wze.2_Intron|FRMD6_uc001wzf.2_Intron|FRMD6_uc001wzg.2_Intron	NM_152330	NP_689543			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
PSMC6	5706	broad.mit.edu	37	14	53180740	53180740	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53180740delA	uc010tqx.1	+						PSMC6_uc010tqw.1_Intron	NM_002806	NP_002797			proteasome 26S ATPase subunit 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding, bridging			lung(1)	1	Breast(41;0.176)																	---	---	---	---
STYX	6815	broad.mit.edu	37	14	53235546	53235546	+	Intron	DEL	T	-	-	rs72129074		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53235546delT	uc010tqy.1	+						STYX_uc001xaa.2_Intron	NM_001130701	NP_001124173			serine/threonine/tyrosine interacting protein						protein dephosphorylation|spermatogenesis	cytoplasm	protein tyrosine/serine/threonine phosphatase activity				0	Breast(41;0.176)																	---	---	---	---
LGALS3	3958	broad.mit.edu	37	14	55603031	55603031	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55603031delA	uc001xbr.2	+							NM_002306	NP_002297			galectin 3						cell differentiation|innate immune response|mRNA processing|RNA splicing	mitochondrial inner membrane|plasma membrane|spliceosomal complex	IgE binding|sugar binding				0																		---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56692794	56692794	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56692794delA	uc001xch.2	+							NM_021255	NP_067078			pellino 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	57150085	57150085	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57150085delT								C14orf101 (33855 upstream) : OTX2 (117342 downstream)																																			---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60118639	60118639	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60118639delA	uc001xen.1	-						RTN1_uc001xem.1_Intron	NM_021136	NP_066959			reticulon 1 isoform A						neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60429499	60429500	+	Intron	DEL	AA	-	-	rs78669215		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60429499_60429500delAA	uc001xep.1	+											Homo sapiens cDNA FLJ46156 fis, clone TESTI4001569.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60772215	60772215	+	IGR	DEL	T	-	-	rs11348030		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60772215delT								PPM1A (6412 upstream) : C14orf39 (130460 downstream)																																			---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60920204	60920204	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60920204delT	uc001xez.3	-						C14orf39_uc010apo.2_Intron	NM_174978	NP_777638			hypothetical protein LOC317761											ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)														---	---	---	---
SLC38A6	145389	broad.mit.edu	37	14	61518736	61518736	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61518736delT	uc001xfg.1	+						SLC38A6_uc001xfh.1_Intron|SLC38A6_uc001xfi.2_Intron|SLC38A6_uc001xfj.1_Intron|SLC38A6_uc001xfk.2_Intron|SLC38A6_uc010trz.1_Intron	NM_153811	NP_722518			solute carrier family 38, member 6						amino acid transport|sodium ion transport	integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0981)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62298445	62298445	+	IGR	DEL	T	-	-	rs77981820		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62298445delT								SNAPC1 (35300 upstream) : SYT16 (155358 downstream)																																			---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62480278	62480278	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62480278delT	uc001xfu.1	+						SYT16_uc010tsd.1_Intron	NM_031914	NP_114120			synaptotagmin XIV-like											central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)														---	---	---	---
ESR2	2100	broad.mit.edu	37	14	64746715	64746715	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64746715delA	uc001xha.1	-	3	987	c.519delT	c.(517-519)TTTfs	p.F173fs	ESR2_uc001xgu.2_Frame_Shift_Del_p.F173fs|ESR2_uc001xgv.2_Frame_Shift_Del_p.F173fs|ESR2_uc001xgw.2_RNA|ESR2_uc001xgx.2_Frame_Shift_Del_p.F173fs|ESR2_uc001xgy.1_Frame_Shift_Del_p.F173fs|ESR2_uc001xgz.1_Frame_Shift_Del_p.F173fs|ESR2_uc010aqb.1_Intron|ESR2_uc010aqc.1_Frame_Shift_Del_p.F173fs	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1	173	Nuclear receptor.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)													---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67628093	67628094	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67628093_67628094delTT	uc001xiy.2	+						GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
EIF2S1	1965	broad.mit.edu	37	14	67831425	67831425	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67831425delT	uc001xjg.2	+							NM_004094	NP_004085			eukaryotic translation initiation factor 2,							cytosol|eukaryotic translation initiation factor 2 complex|polysome|stress granule	protein binding|ribosome binding|translation initiation factor activity			ovary(1)	1				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)														---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68231297	68231297	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68231297delA	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkb.2_5'Flank|ZFYVE26_uc001xkc.3_Intron	NM_015346	NP_056161			zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68485844	68485844	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68485844delA	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68585678	68585678	+	Intron	DEL	T	-	-	rs79456007		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68585678delT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68997877	68997878	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68997877_68997878delAA	uc001xkf.1	+						RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	14	69516145	69516146	+	IGR	INS	-	ACA	ACA	rs145321337	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69516145_69516146insACA								ACTN1 (70062 upstream) : DCAF5 (1492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	70187395	70187395	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70187395delT								KIAA0247 (5536 upstream) : SFRS5 (6224 downstream)																																			---	---	---	---
SMOC1	64093	broad.mit.edu	37	14	70413844	70413847	+	Intron	DEL	TCCC	-	-	rs3051816		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70413844_70413847delTCCC	uc001xls.1	+						SMOC1_uc001xlt.1_Intron	NM_022137	NP_071420			secreted modular calcium-binding protein 1						cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	71310300	71310300	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71310300delA								MAP3K9 (34412 upstream) : PCNX (63822 downstream)																																			---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71482778	71482778	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71482778delA	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73255143	73255143	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73255143delG	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206			D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73581862	73581865	+	Intron	DEL	GTGT	-	-	rs148098788		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73581862_73581865delGTGT	uc001xno.2	+						RBM25_uc010ttu.1_Intron|RBM25_uc001xnp.2_Intron	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73714298	73714299	+	Intron	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73714298_73714299delGT	uc010ttx.1	+						PAPLN_uc001xnw.3_Intron|PAPLN_uc010arl.2_Intron|PAPLN_uc010ttw.1_Intron|PAPLN_uc010tty.1_Intron|uc001xnx.2_5'Flank	NM_173462	NP_775733			papilin							proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74067344	74067345	+	IGR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74067344_74067345insG								ACOT4 (4876 upstream) : ACOT6 (16203 downstream)																																			---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74153808	74153808	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74153808delA	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
ZNF410	57862	broad.mit.edu	37	14	74362864	74362866	+	Intron	DEL	TTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74362864_74362866delTTC	uc001xoz.1	+						ZNF410_uc001xoy.1_Intron|ZNF410_uc010ary.1_Intron|ZNF410_uc010tuf.1_Intron|ZNF410_uc010tug.1_Intron|ZNF410_uc010tuh.1_Intron|ZNF410_uc010tui.1_Intron|ZNF410_uc010arz.1_Intron|ZNF410_uc001xpa.1_Intron|ZNF410_uc001xpb.1_Intron|ZNF410_uc001xpc.1_Intron|ZNF410_uc010tuj.1_5'Flank	NM_021188	NP_067011			zinc finger protein 410						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00369)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76172199	76172199	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76172199delT	uc001xrx.2	+						TTLL5_uc001xrw.1_Intron|TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
C14orf179	112752	broad.mit.edu	37	14	76514077	76514078	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76514077_76514078delTT	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron|C14orf179_uc001xse.2_Intron	NM_001102564	NP_001096034			hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76906932	76906933	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76906932_76906933delCT	uc001xsq.1	+						ESRRB_uc001xsr.2_Intron|ESRRB_uc001xso.2_Intron	NM_004452	NP_004443			estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77395194	77395194	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77395194delA								C14orf166B (58549 upstream) : C14orf4 (95694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77525100	77525101	+	Intron	DEL	AA	-	-	rs113373883		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77525100_77525101delAA	uc001xsz.2	-											Homo sapiens cDNA clone IMAGE:5271982.																														---	---	---	---
TMED8	283578	broad.mit.edu	37	14	77837086	77837087	+	Intron	DEL	GT	-	-	rs149584626		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77837086_77837087delGT	uc001xto.1	-						TMED8_uc010ast.1_Intron	NM_213601	NP_998766			transmembrane emp24 protein transport domain						transport	integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77968902	77968902	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77968902delT								ISM2 (3692 upstream) : SPTLC2 (4370 downstream)																																			---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	77985397	77985397	+	Intron	DEL	T	-	-	rs28516852	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77985397delT	uc001xub.2	-							NM_004863	NP_004854			serine palmitoyltransferase, long chain base							integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ALKBH1	8846	broad.mit.edu	37	14	78149924	78149925	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78149924_78149925delTT	uc001xuc.1	-						ALKBH1_uc001xud.1_Intron	NM_006020	NP_006011			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	80413641	80413642	+	IGR	DEL	AG	-	-	rs11621469	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80413641_80413642delAG								NRXN3 (82883 upstream) : DIO2 (250228 downstream)																																			---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81186474	81186474	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81186474delA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81307320	81307320	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81307320delT	uc001xux.2	-						C14orf145_uc001xuz.2_Intron|C14orf145_uc001xuy.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	81712337	81712337	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81712337delT								GTF2A1 (24616 upstream) : STON2 (14663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82065145	82065145	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82065145delT								SEL1L (64940 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84520219	84520220	+	IGR	INS	-	A	A	rs140671010		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84520219_84520220insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85309807	85309807	+	IGR	DEL	A	-	-	rs112637312		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85309807delA								None (None upstream) : FLRT2 (686681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87548342	87548342	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87548342delT								None (None upstream) : GALC (755822 downstream)																																			---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88967013	88967013	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88967013delT	uc001xwv.3	-						PTPN21_uc010twc.1_Intron|PTPN21_uc010atf.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89183042	89183042	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89183042delC	uc001xxg.2	-						EML5_uc001xxh.1_5'Flank	NM_183387	NP_899243			echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90429218	90429218	+	Intron	DEL	A	-	-	rs113407792		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90429218delA	uc001xxy.2	+						TDP1_uc010atm.2_Intron|TDP1_uc001xxz.2_Intron|TDP1_uc010atn.2_Intron|TDP1_uc001xya.2_Intron|TDP1_uc001xyb.2_Intron|TDP1_uc010ato.2_5'Flank|TDP1_uc001xyc.1_5'Flank	NM_018319	NP_060789			tyrosyl-DNA phosphodiesterase 1						cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)									Repair_of_DNA-protein_crosslinks					---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91660889	91660892	+	Intron	DEL	TTTT	-	-	rs78149646		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91660889_91660892delTTTT	uc001xzb.2	+						C14orf159_uc001xyy.2_Intron|C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836			hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91773348	91773348	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91773348delC	uc010aty.2	-							NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	91911021	91911022	+	IGR	INS	-	G	G	rs143172219	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91911021_91911022insG								CCDC88C (26888 upstream) : SMEK1 (12936 downstream)																																			---	---	---	---
CHGA	1113	broad.mit.edu	37	14	93387662	93387663	+	5'Flank	INS	-	CTCT	CTCT	rs145378031	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93387662_93387663insCTCT	uc001ybc.3	+						CHGA_uc010aum.2_5'Flank|CHGA_uc001ybd.3_5'Flank	NM_001275	NP_001266			chromogranin A precursor						regulation of blood pressure	extracellular region|stored secretory granule				skin(2)	2		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)														---	---	---	---
C14orf139	79686	broad.mit.edu	37	14	95878591	95878591	+	5'Flank	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95878591delC	uc001yeh.3	-							NR_026779				RecName: Full=Uncharacterized protein C14orf139;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	96336531	96336531	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96336531delT								TCL1A (155998 upstream) : C14orf132 (169131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97593191	97593192	+	IGR	DEL	GT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97593191_97593192delGT								VRK1 (245241 upstream) : C14orf64 (798755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99517207	99517207	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99517207delT								C14orf177 (333110 upstream) : BCL11B (118420 downstream)																																			---	---	---	---
CCDC85C	317762	broad.mit.edu	37	14	100045548	100045548	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100045548delC	uc010avr.2	-							NM_001144995	NP_001138467			coiled-coil domain containing 85C												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	100657730	100657730	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100657730delT								DEGS2 (31718 upstream) : YY1 (47372 downstream)																																			---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102839251	102839251	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102839251delA	uc001ylw.1	+						TECPR2_uc010txw.1_Intron|TECPR2_uc010awl.2_Intron|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659			tectonin beta-propeller repeat containing 2								protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CDC42BPB	9578	broad.mit.edu	37	14	103474403	103474404	+	Intron	INS	-	T	T	rs150105545	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103474403_103474404insT	uc001ymi.1	-							NM_006035	NP_006026			CDC42-binding protein kinase beta						actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)														---	---	---	---
BAG5	9529	broad.mit.edu	37	14	104025913	104025913	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104025913delA	uc001yni.1	-	2					BAG5_uc001ynh.1_3'UTR|BAG5_uc001ynj.1_3'UTR	NM_004873	NP_004864			BCL2-associated athanogene 5 isoform b						apoptosis|negative regulation of protein refolding|negative regulation of ubiquitin-protein ligase activity|neuron death|protein folding|regulation of inclusion body assembly	inclusion body|perinuclear region of cytoplasm	chaperone binding|ubiquitin protein ligase binding			ovary(2)	2		Melanoma(154;0.155)	Epithelial(46;0.144)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	104363048	104363048	+	IGR	DEL	C	-	-	rs76163217		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104363048delC								PPP1R13B (49121 upstream) : C14orf2 (15578 downstream)																																			---	---	---	---
KIAA0284	283638	broad.mit.edu	37	14	105353063	105353063	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105353063delC	uc010axb.2	+	12	2711	c.2487delC	c.(2485-2487)AGCfs	p.S829fs	INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Frame_Shift_Del_p.S759fs|KIAA0284_uc001yps.2_Frame_Shift_Del_p.S735fs|KIAA0284_uc001ypt.2_5'Flank	NM_001112726	NP_001106197	Q9Y4F5	K0284_HUMAN	hypothetical protein LOC283638 isoform 1	829						cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106529381	106529381	+	RNA	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106529381delC	uc010tyt.1	-	1573		c.32144delG								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106691601	106691602	+	Intron	INS	-	C	C	rs150089392		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106691601_106691602insC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106772599	106772600	+	Intron	INS	-	G	G	rs67623243		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106772599_106772600insG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20003460	20003460	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20003460delC								None (None upstream) : GOLGA6L6 (733634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20074098	20074099	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20074098_20074099delAA								None (None upstream) : GOLGA6L6 (662995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20108363	20108363	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20108363delT								None (None upstream) : GOLGA6L6 (628731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20111580	20111580	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20111580delG								None (None upstream) : GOLGA6L6 (625514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20861682	20861682	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20861682delC								GOLGA8C (80656 upstream) : BCL8 (8374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21194918	21194919	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21194918_21194919delTT	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	22438890	22438890	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22438890delA								OR4N3P (24505 upstream) : MIR1268 (74339 downstream)																																			---	---	---	---
MIR1268	100302233	broad.mit.edu	37	15	22514339	22514339	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22514339delA	hsa-mir-1268|MI0006405	-																							0																		---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25222784	25222784	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222784delA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718			small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25318657	25318657	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25318657delT	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-10_uc001yxt.2_5'Flank|SNORD116-11_uc001yxu.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25972202	25972203	+	Intron	INS	-	AAAA	AAAA	rs33946132		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25972202_25972203insAAAA	uc010ayu.2	-							NM_024490	NP_077816			ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28200305	28200305	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28200305delT	uc001zbh.3	-	17	1951	c.1841delA	c.(1840-1842)AAGfs	p.K614fs	OCA2_uc010ayv.2_Frame_Shift_Del_p.K590fs	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	614	Cytoplasmic (Potential).		K -> N (in OCA2).|K -> E (in OCA2).		eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										Oculocutaneous_Albinism				---	---	---	---
APBA2	321	broad.mit.edu	37	15	29329449	29329449	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29329449delT	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc010uas.1_Intron	NM_005503	NP_005494			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	31192949	31192949	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31192949delT								ARHGAP11B (215140 upstream) : MTMR15 (3106 downstream)																																			---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31293996	31293997	+	3'UTR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31293996_31293997delAA	uc001zfm.2	-	27					TRPM1_uc010azy.2_3'UTR|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	31403443	31403443	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31403443delA								TRPM1 (9519 upstream) : KLF13 (215640 downstream)																																			---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33923503	33923503	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33923503delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34528550	34528550	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34528550delT	uc001zhw.2	-						SLC12A6_uc001zhv.2_Intron|SLC12A6_uc001zhx.2_Intron|SLC12A6_uc001zhy.2_Intron|SLC12A6_uc001zhz.2_Intron|SLC12A6_uc001zia.2_Intron|SLC12A6_uc001zib.2_Intron|SLC12A6_uc001zic.2_Intron|SLC12A6_uc010bau.2_Intron|SLC12A6_uc001zid.2_Intron|SLC12A6_uc001zht.2_Intron|SLC12A6_uc001zhu.2_Intron	NM_133647	NP_598408			solute carrier family 12, member 6 isoform a						angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	34781074	34781081	+	IGR	DEL	AAAAAAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34781074_34781081delAAAAAAAA								GOLGA8A (99073 upstream) : GOLGA8B (36404 downstream)																																			---	---	---	---
RASGRP1	10125	broad.mit.edu	37	15	38792549	38792549	+	Intron	DEL	G	-	-	rs12904148	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38792549delG	uc001zke.3	-						RASGRP1_uc010bbe.2_Intron|RASGRP1_uc010bbf.2_Intron|RASGRP1_uc010bbg.2_Intron|RASGRP1_uc001zkd.3_Intron	NM_005739	NP_005730			RAS guanyl releasing protein 1 isoform a						cell differentiation|platelet activation|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|lipid binding|protein binding			large_intestine(1)|ovary(1)	2		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38952601	38952602	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38952601_38952602insT								RASGRP1 (95594 upstream) : C15orf53 (36197 downstream)																																			---	---	---	---
FSIP1	161835	broad.mit.edu	37	15	40062826	40062826	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40062826delA	uc001zki.2	-							NM_152597	NP_689810			fibrous sheath interacting protein 1											ovary(2)|skin(1)	3		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)														---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40477243	40477243	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40477243delT	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40949220	40949220	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40949220delT	uc010bbs.1	+						CASC5_uc010bbt.1_Intron	NM_170589	NP_733468			cancer susceptibility candidate 5 isoform 1						acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
FAM82A2	55177	broad.mit.edu	37	15	41029962	41029962	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41029962delA	uc001zmo.1	-						FAM82A2_uc001zmp.1_Intron|FAM82A2_uc001zmq.1_Intron	NM_018145	NP_060615			family with sequence similarity 82, member A2						apoptosis|cell differentiation	integral to membrane|microtubule|mitochondrial membrane|nucleus|spindle pole	protein binding				0																		---	---	---	---
INO80	54617	broad.mit.edu	37	15	41282311	41282312	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41282311_41282312delAA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
INO80	54617	broad.mit.edu	37	15	41308143	41308143	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41308143delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
MGA	23269	broad.mit.edu	37	15	41923797	41923797	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41923797delT	uc001zog.1	+							NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
GANC	2595	broad.mit.edu	37	15	42579747	42579747	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42579747delT	uc001zpi.2	+						GANC_uc001zph.2_Intron|GANC_uc001zpj.1_Intron	NM_198141	NP_937784			glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43252975	43252975	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43252975delT	uc001zqq.2	-							NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44088542	44088542	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44088542delT	uc001zsx.1	-						C15orf63_uc001ztb.2_Intron|MIR1282_hsa-mir-1282|MI0006429_5'Flank|SERINC4_uc001ztc.1_Intron|SERINC4_uc001ztd.1_Intron|SERINC4_uc010bds.1_Intron|SERINC4_uc001zte.1_Intron	NM_025165	NP_079441			elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	44569150	44569150	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44569150delA								FRMD5 (81721 upstream) : CASC4 (11779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45079284	45079284	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45079284delA								TRIM69 (19259 upstream) : C15orf43 (169619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46260147	46260148	+	IGR	INS	-	AA	AA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46260147_46260148insAA								SQRDL (276669 upstream) : None (None downstream)																																			---	---	---	---
SECISBP2L	9728	broad.mit.edu	37	15	49337693	49337693	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49337693delG	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron|SECISBP2L_uc010beq.1_Intron	NM_014701	NP_055516			SECIS binding protein 2-like											breast(1)|skin(1)	2																		---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51744403	51744403	+	Intron	DEL	A	-	-	rs77324452		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51744403delA	uc002abf.2	-						DMXL2_uc002abd.2_Intron|DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron|DMXL2_uc002abc.2_5'Flank	NM_015263	NP_056078			Dmx-like 2							cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	52271304	52271304	+	IGR	DEL	A	-	-	rs77297518		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52271304delA								LEO1 (7346 upstream) : MAPK6 (40107 downstream)																																			---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55783155	55783155	+	Intron	DEL	A	-	-	rs74830467		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55783155delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	56059647	56059647	+	IGR	DEL	T	-	-	rs5812816		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56059647delT								PRTG (24470 upstream) : NEDD4 (59484 downstream)																																			---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	56983487	56983487	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56983487delT	uc002adu.2	-						ZNF280D_uc002adv.2_Intron|ZNF280D_uc010bfq.2_Intron|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfr.1_Intron	NM_017661	NP_060131			suppressor of hairy wing homolog 4 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)														---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57530405	57530405	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57530405delT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron|TCF12_uc002aee.2_Intron|TCF12_uc010bft.2_Intron|TCF12_uc010ugo.1_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58354413	58354413	+	Intron	DEL	A	-	-	rs4646558		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58354413delA	uc002aex.2	-						ALDH1A2_uc002aey.2_Intron|ALDH1A2_uc010ugv.1_Intron|ALDH1A2_uc010ugw.1_Intron	NM_003888	NP_003879			aldehyde dehydrogenase 1A2 isoform 1						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
FAM81A	145773	broad.mit.edu	37	15	59806474	59806475	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59806474_59806475delTT	uc002agc.2	+							NM_152450	NP_689663			hypothetical protein LOC145773											ovary(1)	1																		---	---	---	---
GTF2A2	2958	broad.mit.edu	37	15	59942804	59942804	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59942804delA	uc002agg.2	-							NM_004492	NP_004483			general transcription factor IIA, 2, 12kDa						interspecies interaction between organisms|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIA complex	protein heterodimerization activity|protein homodimerization activity|TBP-class protein binding|transcription coactivator activity			central_nervous_system(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62283822	62283822	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62283822delT	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62853865	62853865	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62853865delT								C2CD4B (396383 upstream) : MGC15885 (75506 downstream)																																			---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63928473	63928473	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63928473delT	uc002amp.2	-							NM_003922	NP_003913			hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63964903	63964903	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63964903delA	uc002amp.2	-							NM_003922	NP_003913			hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64702168	64702168	+	Intron	DEL	G	-	-	rs10468032	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64702168delG	uc002anm.2	+							NM_016213	NP_057297			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																		---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65246797	65246799	+	Intron	DEL	CTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65246797_65246799delCTT	uc002aoa.2	+						ANKDD1A_uc002aoc.2_Intron|ANKDD1A_uc010bha.2_Intron	NM_182703	NP_874362			ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65611589	65611589	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65611589delT								PARP16 (32571 upstream) : IGDCC3 (7876 downstream)																																			---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	65960549	65960549	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65960549delT	uc002aph.2	-						DENND4A_uc002api.2_Intron	NM_005848	NP_005839			DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67415838	67415838	+	Intron	DEL	A	-	-	rs34316530		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67415838delA	uc002aqj.2	+						SMAD3_uc010ujr.1_5'Flank	NM_005902	NP_005893			mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)														---	---	---	---
ANP32A	8125	broad.mit.edu	37	15	69093545	69093546	+	Intron	INS	-	GAA	GAA	rs137929136	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69093545_69093546insGAA	uc002arl.2	-							NM_006305	NP_006296			acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
PAQR5	54852	broad.mit.edu	37	15	69685350	69685350	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69685350delA	uc002arz.2	+						PAQR5_uc002asa.2_Intron	NM_017705	NP_060175			progestin and adipoQ receptor family member V						cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2																		---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69737404	69737405	+	Intron	INS	-	A	A	rs138256473		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69737404_69737405insA	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	70401080	70401081	+	IGR	INS	-	TG	TG	rs35151879		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70401080_70401081insTG								TLE3 (10824 upstream) : UACA (545814 downstream)																																			---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72324963	72324963	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72324963delA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron|MYO9A_uc002atn.1_Intron	NM_006901	NP_008832			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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74816831	74816832	+	IGR	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74816831_74816832delGA								UBL7 (63302 upstream) : ARID3B (16716 downstream)																																			---	---	---	---
UBE2Q2	92912	broad.mit.edu	37	15	76191744	76191744	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76191744delT	uc002bbg.2	+						UBE2Q2_uc002bbh.2_Intron|UBE2Q2_uc010umn.1_Intron|UBE2Q2_uc002bbi.2_Intron	NM_173469	NP_775740			ubiquitin-conjugating enzyme E2Q 2 isoform 1						protein K48-linked ubiquitination	cytoplasm	ATP binding|ubiquitin-protein ligase activity			ovary(2)	2																		---	---	---	---
C15orf27	123591	broad.mit.edu	37	15	76380905	76380905	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76380905delG	uc002bbq.2	+						C15orf27_uc010bkp.2_Intron	NM_152335	NP_689548			hypothetical protein LOC123591							integral to membrane					0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76577920	76577920	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76577920delA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76777172	76777172	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76777172delA	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	77105803	77105803	+	Intron	DEL	A	-	-	rs76423188		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77105803delA	uc002bby.2	-						SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron|SCAPER_uc002bca.1_Intron|SCAPER_uc002bcb.1_Intron|SCAPER_uc002bcc.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	77665207	77665208	+	IGR	INS	-	CT	CT	rs144774435	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77665207_77665208insCT								SGK269 (87874 upstream) : HMG20A (48035 downstream)																																			---	---	---	---
WDR61	80349	broad.mit.edu	37	15	78587083	78587083	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78587083delT	uc002bdn.2	-						WDR61_uc002bdo.2_Intron|WDR61_uc010umz.1_Intron|WDR61_uc010una.1_Intron|WDR61_uc010blc.1_3'UTR	NM_025234	NP_079510			WD repeat domain 61								protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78917347	78917348	+	3'UTR	INS	-	G	G	rs143826466	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78917347_78917348insG	uc002bed.1	-	6					CHRNB4_uc002bee.1_Frame_Shift_Ins_p.T215fs|uc002bef.1_5'Flank	NM_000750	NP_000741			cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	80220937	80220938	+	IGR	INS	-	TG	TG	rs150513047	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80220937_80220938insTG								C15orf37 (3741 upstream) : BCL2A1 (32295 downstream)																																			---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81143187	81143187	+	Intron	DEL	C	-	-	rs111709858	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81143187delC	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	81973431	81973431	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81973431delA								TMC3 (307013 upstream) : MEX3B (360697 downstream)																																			---	---	---	---
FSD2	123722	broad.mit.edu	37	15	83428553	83428553	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83428553delT	uc002bjd.2	-						FSD2_uc010uol.1_Intron|FSD2_uc010uom.1_Intron	NM_001007122	NP_001007123			fibronectin type III and SPRY domain containing											central_nervous_system(1)	1																		---	---	---	---
WHAMM	123720	broad.mit.edu	37	15	83495659	83495659	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83495659delA	uc002bje.2	+							NM_001080435	NP_001073904			WAS protein homolog associated with actin, golgi							cytoplasmic vesicle membrane|ER-Golgi intermediate compartment|Golgi apparatus	actin binding				0																		---	---	---	---
HDGFRP3	50810	broad.mit.edu	37	15	83856851	83856851	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83856851delT	uc002bjs.1	-							NM_016073	NP_057157			hepatoma-derived growth factor, related protein						cell proliferation	nucleus	growth factor activity				0																		---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84561733	84561733	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84561733delA	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85121557	85121557	+	RNA	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85121557delA	uc002bko.1	+	3		c.757delA								Homo sapiens cDNA: FLJ22824 fis, clone KAIA3991.																														---	---	---	---
ZNF592	9640	broad.mit.edu	37	15	85314197	85314197	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85314197delG	uc002bld.2	+							NM_014630	NP_055445			zinc finger protein 592						cell death|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(2)	6			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87089453	87089454	+	Intron	DEL	TT	-	-	rs66611676		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87089453_87089454delTT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	88060735	88060735	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88060735delT								AGBL1 (488452 upstream) : NCRNA00052 (59425 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88503723	88503723	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88503723delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron	NM_001012338	NP_001012338			neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)					T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89849001	89849001	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89849001delA	uc010bnp.1	+						FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bnp.1_Intron|FANCI_uc002bnq.1_Intron	NM_001113378	NP_001106849			Fanconi anemia, complementation group I isoform						cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)												Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
LOC254559	254559	broad.mit.edu	37	15	89932350	89932353	+	Intron	DEL	GTGT	-	-	rs10533346		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89932350_89932353delGTGT	uc002bnt.2	+						LOC254559_uc002bnv.2_Intron|LOC254559_uc002bnw.2_Intron					Homo sapiens cDNA FLJ30148 fis, clone BRACE2000267.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	90108350	90108351	+	IGR	DEL	AG	-	-	rs111508704		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90108350_90108351delAG								LOC283761 (41085 upstream) : C15orf42 (10467 downstream)																																			---	---	---	---
ANPEP	290	broad.mit.edu	37	15	90346574	90346574	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90346574delC	uc002bop.3	-							NM_001150	NP_001141			membrane alanine aminopeptidase precursor						angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	90773148	90773152	+	IGR	DEL	AAGGG	-	-	rs10543722		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90773148_90773152delAAGGG								SEMA4B (258 upstream) : CIB1 (326 downstream)																																			---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93475520	93475521	+	Intron	DEL	TT	-	-	rs34925592		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93475520_93475521delTT	uc002bsp.2	+						CHD2_uc002bsm.1_Intron|CHD2_uc002bsn.2_Intron|CHD2_uc002bso.1_Intron|CHD2_uc010urb.1_Intron	NM_001271	NP_001262			chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	95480392	95480392	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95480392delT								MCTP2 (453212 upstream) : LOC145820 (495930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97170610	97170610	+	IGR	DEL	C	-	-	rs79611327		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97170610delC								NR2F2 (287120 upstream) : SPATA8 (156069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99113971	99113971	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99113971delA								FAM169B (56360 upstream) : IGF1R (78790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	101840729	101840729	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101840729delA								SNRPA1 (5269 upstream) : PCSK6 (3405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1075451	1075474	+	IGR	DEL	GGTGTGGAGGGTGCTGAGGTCCCC	-	-	rs72269290	by1000genomes;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1075451_1075474delGGTGTGGAGGGTGCTGAGGTCCCC								SOX8 (38473 upstream) : LOC146336 (38610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1482703	1482705	+	IGR	DEL	GAG	-	-	rs72210635		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1482703_1482705delGAG								C16orf91 (3358 upstream) : CCDC154 (1685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1955831	1955831	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1955831delT								C16orf73 (21536 upstream) : HS3ST6 (5636 downstream)																																			---	---	---	---
TSC2	7249	broad.mit.edu	37	16	2130493	2130493	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2130493delT	uc002con.2	+						TSC2_uc010bsd.2_Intron|TSC2_uc002coo.2_Intron|TSC2_uc010uvv.1_Intron|TSC2_uc010uvw.1_Intron|TSC2_uc002cop.2_Intron|TSC2_uc002coq.2_5'Flank|TSC2_uc002cor.2_5'Flank	NM_000548	NP_000539			tuberous sclerosis 2 isoform 1						cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of cell size|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)						D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2382818	2382818	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2382818delT	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron|ABCA3_uc002cpz.1_5'Flank	NM_001089	NP_001080			ATP-binding cassette, sub-family A member 3						response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	2925704	2925704	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2925704delA								PRSS22 (17533 upstream) : FLYWCH2 (7492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	3057438	3057439	+	IGR	DEL	AA	-	-	rs71394763		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3057438_3057439delAA								PKMYT1 (26964 upstream) : CLDN9 (5018 downstream)																																			---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3367102	3367102	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3367102delT	uc002cut.3	+						ZNF75A_uc002cuv.3_Intron	NM_153028	NP_694573			zinc finger protein 75a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
C16orf90	646174	broad.mit.edu	37	16	3544038	3544038	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3544038delG	uc002cvi.2	-							NM_001080524	NP_001073993			hypothetical protein LOC646174												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	4185219	4185219	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4185219delA								ADCY9 (19033 upstream) : SRL (54158 downstream)																																			---	---	---	---
SRL	6345	broad.mit.edu	37	16	4244901	4244901	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4244901delT	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
SRL	6345	broad.mit.edu	37	16	4247598	4247598	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4247598delT	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
SRL	6345	broad.mit.edu	37	16	4277202	4277209	+	Intron	DEL	GATGGGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4277202_4277209delGATGGGTG	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
MGRN1	23295	broad.mit.edu	37	16	4693983	4693984	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4693983_4693984insT	uc002cwz.2	+						MGRN1_uc002cxa.2_Intron|MGRN1_uc010btx.2_Intron|MGRN1_uc010btw.2_Intron|MGRN1_uc002cxb.2_Intron|MGRN1_uc010uxo.1_Intron|MGRN1_uc010uxp.1_Intron|MGRN1_uc010uxq.1_Intron	NM_001142290	NP_001135762			mahogunin, ring finger 1 isoform 3						endosome to lysosome transport|negative regulation of cAMP-mediated signaling|negative regulation of G-protein coupled receptor protein signaling pathway|protein monoubiquitination	cytosol|early endosome|nucleus|plasma membrane|plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5786821	5786821	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5786821delT								FAM86A (639032 upstream) : A2BP1 (282311 downstream)																																			---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6820598	6820598	+	Intron	DEL	T	-	-	rs35930939		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6820598delT	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	NM_018723	NP_061193			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)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6921489	6921489	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6921489delA	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			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)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7602695	7602696	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7602695_7602696insT	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|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Intron	NM_018723	NP_061193			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	7833434	7833434	+	IGR	DEL	T	-	-	rs111298618		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7833434delT								A2BP1 (70094 upstream) : TMEM114 (786069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9346869	9346870	+	IGR	INS	-	GA	GA	rs112678273		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9346869_9346870insGA								C16orf72 (133324 upstream) : GRIN2A (500397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9406537	9406538	+	IGR	INS	-	CTCGG	CTCGG	rs149556063	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9406537_9406538insCTCGG								C16orf72 (192992 upstream) : GRIN2A (440729 downstream)																																			---	---	---	---
FAM18A	780776	broad.mit.edu	37	16	10865686	10865686	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10865686delT	uc010buo.1	-						FAM18A_uc010uyr.1_Intron|FAM18A_uc010uys.1_Intron|FAM18A_uc010uyt.1_Intron|FAM18A_uc010bun.2_Intron|FAM18A_uc010uyu.1_Intron|FAM18A_uc002dad.3_Intron|FAM18A_uc002daf.1_Intron|FAM18A_uc002dae.1_Intron	NM_001079512	NP_001072980			hypothetical protein LOC780776							integral to membrane					0																		---	---	---	---
FAM18A	780776	broad.mit.edu	37	16	10868933	10868933	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10868933delA	uc010buo.1	-	3	381	c.110delT	c.(109-111)TTCfs	p.F37fs	FAM18A_uc010uyr.1_Intron|FAM18A_uc010uys.1_Intron|FAM18A_uc010uyt.1_RNA|FAM18A_uc010bun.2_RNA|FAM18A_uc010uyu.1_Intron|FAM18A_uc002dad.3_RNA|FAM18A_uc002daf.1_RNA|FAM18A_uc002dae.1_5'UTR	NM_001079512	NP_001072980	A6NH52	FA18A_HUMAN	hypothetical protein LOC780776	37	Helical; (Potential).					integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	11515266	11515266	+	IGR	DEL	T	-	-	rs79184386		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11515266delT								C16orf75 (69649 upstream) : LITAF (126316 downstream)																																			---	---	---	---
RSL1D1	26156	broad.mit.edu	37	16	11940252	11940253	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11940252_11940253delAA	uc002dbp.1	-						RSL1D1_uc010buv.1_Intron|RSL1D1_uc010uyw.1_Intron|RSL1D1_uc010buw.2_Intron	NM_015659	NP_056474			ribosomal L1 domain containing 1						regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12256749	12256749	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12256749delT	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12332062	12332063	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12332062_12332063delAA	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12531179	12531180	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12531179_12531180delCT	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12825719	12825719	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12825719delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810			calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0																		---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13164010	13164013	+	Intron	DEL	TGCA	-	-	rs4780499		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13164010_13164013delTGCA	uc010uyy.1	+							NM_001145204	NP_001138676			shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	13352209	13352209	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13352209delA								SHISA9 (17937 upstream) : ERCC4 (661805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13412181	13412182	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13412181_13412182delTT								SHISA9 (77909 upstream) : ERCC4 (601832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13794677	13794678	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13794677_13794678insT								SHISA9 (460405 upstream) : ERCC4 (219336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13864598	13864599	+	IGR	INS	-	AGG	AGG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13864598_13864599insAGG								SHISA9 (530326 upstream) : ERCC4 (149415 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15105964	15105965	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15105964_15105965delTT	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron|MIR1972_hsa-mir-1972-1|MI0009982_5'Flank	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15117519	15117519	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15117519delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
NDE1	54820	broad.mit.edu	37	16	15754171	15754171	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15754171delA	uc010uzy.1	+						NDE1_uc002dds.2_Intron	NM_001143979	NP_001137451			nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1																		---	---	---	---
NDE1	54820	broad.mit.edu	37	16	15792257	15792257	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15792257delA	uc010uzy.1	+						NDE1_uc002dds.2_Intron	NM_001143979	NP_001137451			nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15873171	15873171	+	Intron	DEL	T	-	-	rs35080541		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15873171delT	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|MYH11_uc002dea.1_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	16	16922725	16922725	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16922725delA								LOC339047 (478288 upstream) : XYLT1 (273458 downstream)																																			---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17429552	17429557	+	Intron	DEL	AAAAAA	-	-	rs147237268		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17429552_17429557delAAAAAA	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17451988	17451989	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17451988_17451989delTT	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17503984	17503984	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17503984delT	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	18027200	18027200	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18027200delA								XYLT1 (462462 upstream) : NOMO2 (483983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18088435	18088435	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18088435delT								XYLT1 (523697 upstream) : NOMO2 (422748 downstream)																																			---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18875512	18875513	+	Intron	INS	-	C	C	rs71141080		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18875512_18875513insC	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18883764	18883764	+	Intron	DEL	A	-	-	rs117332168	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18883764delA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19476434	19476445	+	Intron	DEL	CCTCCCTCCCTC	-	-	rs71812351		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19476434_19476445delCCTCCCTCCCTC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	20175873	20175873	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20175873delT								GPR139 (90773 upstream) : GP2 (145939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	21526198	21526200	+	Intron	DEL	AAA	-	-	rs11326520		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21526198_21526200delAAA	uc002diq.3	+						LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21598985	21598985	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21598985delT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21946462	21946463	+	IGR	INS	-	TC	TC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21946462_21946463insTC								RRN3P1 (114731 upstream) : UQCRC2 (18146 downstream)																																			---	---	---	---
C16orf52	730094	broad.mit.edu	37	16	22085022	22085022	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22085022delT	uc010vbp.1	+						C16orf52_uc002dkb.1_Intron					RecName: Full=Uncharacterized protein C16orf52;												0																		---	---	---	---
POLR3E	55718	broad.mit.edu	37	16	22322823	22322823	+	Intron	DEL	T	-	-	rs145739648		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22322823delT	uc002dkk.2	+						POLR3E_uc002dkj.1_Intron|POLR3E_uc002dkm.2_Intron|POLR3E_uc010vbr.1_Intron|POLR3E_uc002dkl.2_Intron|POLR3E_uc010vbs.1_Intron|POLR3E_uc010vbt.1_Intron	NM_018119	NP_060589			RNA polymerase III polypeptide E						innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA-directed RNA polymerase activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.012)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	23167343	23167343	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23167343delG								USP31 (6752 upstream) : SCNN1G (26697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23399062	23399063	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23399062_23399063delAA								SCNN1B (6443 upstream) : COG7 (753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25040865	25040867	+	5'Flank	DEL	TCT	-	-	rs112587595		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25040865_25040867delTCT	uc010bxu.1	+											SubName: Full=cDNA FLJ40572 fis, clone THYMU2006170;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	25291744	25291744	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25291744delT								ZKSCAN2 (22889 upstream) : HS3ST4 (411603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25300771	25300774	+	IGR	DEL	TTCT	-	-	rs8044599		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25300771_25300774delTTCT								ZKSCAN2 (31916 upstream) : HS3ST4 (402573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25525070	25525071	+	IGR	DEL	AA	-	-	rs74393138		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25525070_25525071delAA								ZKSCAN2 (256215 upstream) : HS3ST4 (178276 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25834058	25834058	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25834058delT	uc002dof.2	+							NM_006040	NP_006031			heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	26654823	26654824	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26654823_26654824delAC								HS3ST4 (505815 upstream) : C16orf82 (423395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26939315	26939318	+	IGR	DEL	GAAA	-	-	rs10574808	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26939315_26939318delGAAA								HS3ST4 (790307 upstream) : C16orf82 (138901 downstream)																																			---	---	---	---
JMJD5	79831	broad.mit.edu	37	16	27217594	27217595	+	Intron	DEL	TT	-	-	rs112161125		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27217594_27217595delTT	uc002doh.2	+						JMJD5_uc010bxv.2_Intron|JMJD5_uc010vcn.1_Intron	NM_024773	NP_079049			jumonji domain containing 5 isoform 2						G2/M transition of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|histone demethylase activity (H3-K36 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	27314627	27314628	+	IGR	DEL	AA	-	-	rs76500406		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27314627_27314628delAA								NSMCE1 (34514 upstream) : IL4R (10623 downstream)																																			---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27624085	27624086	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27624085_27624086insA	uc002dow.2	+							NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27705236	27705236	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27705236delA	uc002dow.2	+						KIAA0556_uc002dox.1_Intron	NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	28980494	28980494	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28980494delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29010427	29010427	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29010427delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29029254	29029254	+	Intron	DEL	G	-	-	rs8043922	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29029254delG	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29088250	29088250	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29088250delT	uc010vct.1	-						RRN3P2_uc010vdm.1_Intron|RRN3P2_uc002dsf.3_Intron|RRN3P2_uc002dsg.3_Intron|RRN3P2_uc010vdn.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29222029	29222029	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29222029delA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29235634	29235635	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29235634_29235635insA	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29438362	29438363	+	IGR	DEL	AT	-	-	rs151067447		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29438362_29438363delAT								RUNDC2C (20013 upstream) : LOC440354 (15863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	30451878	30451878	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30451878delT								DCTPP1 (10505 upstream) : SEPHS2 (3075 downstream)																																			---	---	---	---
ZNF768	79724	broad.mit.edu	37	16	30535536	30535536	+	3'UTR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30535536delC	uc002dyk.3	-	2					ZNF768_uc010vex.1_3'UTR|uc002dyl.1_5'Flank|ZNF768_uc010vew.1_3'UTR	NM_024671	NP_078947			zinc finger protein 768						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF689	115509	broad.mit.edu	37	16	30622813	30622813	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30622813delT	uc002dyx.2	-						ZNF689_uc010bzy.2_5'Flank	NM_138447	NP_612456			zinc finger protein HIT-39						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)															---	---	---	---
STX1B	112755	broad.mit.edu	37	16	31003411	31003412	+	3'UTR	INS	-	AC	AC	rs146032870	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31003411_31003412insAC	uc010cad.2	-	10						NM_052874	NP_443106			syntaxin 1B						intracellular protein transport|neurotransmitter transport|synaptic transmission	integral to plasma membrane	extracellular-glutamate-gated ion channel activity|SNAP receptor activity				0																		---	---	---	---
PRSS36	146547	broad.mit.edu	37	16	31151511	31151512	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31151511_31151512delAA	uc002ebd.2	-						PRSS36_uc010vff.1_Intron|PRSS36_uc010vfg.1_Intron|PRSS36_uc010vfh.1_Intron	NM_173502	NP_775773			protease, serine, 36 precursor						proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	32113339	32113339	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32113339delT								ZNF267 (184713 upstream) : HERC2P4 (49271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32366041	32366041	+	IGR	DEL	A	-	-	rs71390956		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32366041delA								HERC2P4 (202167 upstream) : TP53TG3B (318800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32397196	32397197	+	IGR	INS	-	T	T	rs145601762	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32397196_32397197insT								HERC2P4 (233322 upstream) : TP53TG3B (287644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32570757	32570757	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32570757delA								HERC2P4 (406883 upstream) : TP53TG3B (114084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32574917	32574918	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32574917_32574918delTG								HERC2P4 (411043 upstream) : TP53TG3B (109923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32828004	32828004	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32828004delA								TP53TG3B (139126 upstream) : SLC6A10P (60793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32830678	32830678	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32830678delT								TP53TG3B (141800 upstream) : SLC6A10P (58119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32842387	32842387	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32842387delT								TP53TG3B (153509 upstream) : SLC6A10P (46410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33343169	33343170	+	IGR	DEL	TA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33343169_33343170delTA								SLC6A10P (446706 upstream) : MIR1826 (622338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33420023	33420023	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33420023delT								SLC6A10P (523560 upstream) : MIR1826 (545485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33530019	33530019	+	IGR	DEL	T	-	-	rs111564755		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33530019delT								SLC6A10P (633556 upstream) : MIR1826 (435489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33955778	33955781	+	IGR	DEL	TCTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33955778_33955781delTCTT								None (None upstream) : MIR1826 (9727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33960735	33960735	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33960735delT								None (None upstream) : MIR1826 (4773 downstream)																																			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47292700delA	uc002eet.2	-						ITFG1_uc010vgg.1_Intron|ITFG1_uc010vgh.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47639629	47639629	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47639629delT	uc002eev.3	+						PHKB_uc002eeu.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47675773	47675773	+	Intron	DEL	A	-	-	rs35974190		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47675773delA	uc002eev.3	+						PHKB_uc002eeu.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48885502	48885502	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48885502delG								N4BP1 (241382 upstream) : CBLN1 (426709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49112270	49112270	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49112270delA								N4BP1 (468150 upstream) : CBLN1 (199941 downstream)																																			---	---	---	---
C16orf78	123970	broad.mit.edu	37	16	49428363	49428363	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49428363delA	uc002efr.2	+							NM_144602	NP_653203			hypothetical protein LOC123970											central_nervous_system(1)	1																		---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50211529	50211529	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50211529delT	uc010vgo.1	+						PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_Intron|PAPD5_uc002ega.2_Intron	NM_001040284	NP_001035374			PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
SNX20	124460	broad.mit.edu	37	16	50700881	50700882	+	3'UTR	INS	-	A	A	rs139263389	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50700881_50700882insA	uc010vgp.1	-	4					SNX20_uc002egi.3_3'UTR|uc002egj.2_5'Flank	NM_153337	NP_699168			sorting nexin 20 isoform 2						cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1																		---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50736021	50736021	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50736021delA	uc002egm.1	+						NOD2_uc010cbk.1_Intron|NOD2_uc002egl.1_Intron	NM_022162	NP_071445			nucleotide-binding oligomerization domain						activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	50921747	50921747	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50921747delG								CYLD (85901 upstream) : SALL1 (248139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51308813	51308813	+	IGR	DEL	A	-	-	rs72344945		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51308813delA								SALL1 (123630 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51605961	51605961	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51605961delC								SALL1 (420778 upstream) : TOX3 (865957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53026684	53026684	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53026684delA								TOX3 (444970 upstream) : CHD9 (62261 downstream)																																			---	---	---	---
FTO	79068	broad.mit.edu	37	16	53967839	53967839	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53967839delT	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_5'Flank	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	54028651	54028651	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54028651delT	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	54095439	54095439	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54095439delA	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54212104	54212104	+	IGR	DEL	A	-	-	rs35598105		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54212104delA								FTO (63726 upstream) : IRX3 (105108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54357841	54357841	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54357841delC								IRX3 (37463 upstream) : IRX5 (607270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54613493	54613507	+	IGR	DEL	AGAGGAAGAAGAAGC	-	-	rs62034184	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54613493_54613507delAGAGGAAGAAGAAGC								IRX3 (293115 upstream) : IRX5 (351604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55125217	55125222	+	IGR	DEL	CACTGG	-	-	rs68076891		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55125217_55125222delCACTGG								IRX5 (156824 upstream) : IRX6 (233249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55303476	55303477	+	IGR	INS	-	T	T	rs143995926	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55303476_55303477insT								IRX5 (335083 upstream) : IRX6 (54994 downstream)																																			---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55530772	55530772	+	Intron	DEL	T	-	-	rs243838	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55530772delT	uc002ehz.3	+						MMP2_uc010vhd.1_Intron|MMP2_uc010ccc.2_Intron|MMP2_uc002eia.3_Intron	NM_004530	NP_004521			matrix metalloproteinase 2 isoform a						angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)													---	---	---	---
BBS2	583	broad.mit.edu	37	16	56545008	56545008	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56545008delA	uc002ejd.2	-						BBS2_uc010ccg.2_Intron	NM_031885	NP_114091			Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	16	56679220	56679220	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56679220delC								MT1DP (368 upstream) : MT1B (6591 downstream)																																			---	---	---	---
NUP93	9688	broad.mit.edu	37	16	56765314	56765315	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56765314_56765315delTT	uc002eka.2	+							NM_014669	NP_055484			nucleoporin 93kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
CCDC102A	92922	broad.mit.edu	37	16	57557560	57557560	+	Intron	DEL	T	-	-	rs78972115		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57557560delT	uc002elw.2	-							NM_033212	NP_149989			coiled-coil domain containing 102A											ovary(1)	1																		---	---	---	---
KIFC3	3801	broad.mit.edu	37	16	57876104	57876104	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57876104delA	uc002emr.1	-							NM_001130099	NP_001123571			kinesin family member C3 isoform 3						epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			central_nervous_system(2)|ovary(1)	3		all_neural(199;0.224)																---	---	---	---
KIFC3	3801	broad.mit.edu	37	16	57878012	57878012	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57878012delA	uc002emr.1	-							NM_001130099	NP_001123571			kinesin family member C3 isoform 3						epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			central_nervous_system(2)|ovary(1)	3		all_neural(199;0.224)																---	---	---	---
CNGB1	1258	broad.mit.edu	37	16	57932289	57932289	+	Intron	DEL	T	-	-	rs68119010		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57932289delT	uc002emt.2	-						CNGB1_uc010cdh.2_Intron	NM_001297	NP_001288			cyclic nucleotide gated channel beta 1 isoform						sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58626245	58626245	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58626245delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	58671960	58671960	+	IGR	DEL	T	-	-	rs35674968		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58671960delT								CNOT1 (8210 upstream) : SLC38A7 (28338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59198125	59198125	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59198125delT								GOT2 (429879 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59697591	59697591	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59697591delT								GOT2 (929345 upstream) : None (None downstream)																																			---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61898197	61898200	+	Intron	DEL	GGTT	-	-	rs112735395		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61898197_61898200delGGTT	uc002eog.1	-							NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	62378312	62378313	+	IGR	DEL	AA	-	-	rs112460224		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62378312_62378313delAA								CDH8 (308276 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62518055	62518059	+	IGR	DEL	TCTCT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62518055_62518059delTCTCT								CDH8 (448019 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62658032	62658033	+	IGR	DEL	AT	-	-	rs60295986		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62658032_62658033delAT								CDH8 (587996 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63672879	63672880	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63672879_63672880delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64485469	64485469	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64485469delT								None (None upstream) : CDH11 (495216 downstream)																																			---	---	---	---
LOC283867	283867	broad.mit.edu	37	16	65582046	65582047	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65582046_65582047delGA	uc010cdp.1	-						LOC283867_uc002eol.1_Intron					Homo sapiens cDNA clone IMAGE:5276218.												0				OV - Ovarian serous cystadenocarcinoma(108;0.17)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	65913016	65913016	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65913016delA								LOC283867 (302813 upstream) : CDH5 (487509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66228702	66228703	+	IGR	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66228702_66228703delAC								LOC283867 (618499 upstream) : CDH5 (171822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66248223	66248223	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66248223delA								LOC283867 (638020 upstream) : CDH5 (152302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	66538229	66538229	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66538229delA								BEAN (21485 upstream) : TK2 (5123 downstream)																																			---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66725021	66725021	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66725021delA	uc002epz.2	-						CMTM4_uc002eqa.2_Intron	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
RRAD	6236	broad.mit.edu	37	16	66958603	66958605	+	Intron	DEL	AAC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66958603_66958605delAAC	uc002eqn.2	-						RRAD_uc002eqo.2_Intron	NM_001128850	NP_001122322			Ras-related associated with diabetes						small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)														---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67631245	67631245	+	Intron	DEL	T	-	-	rs113177518		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67631245delT	uc002etl.2	+						CTCF_uc010cek.2_Intron	NM_006565	NP_006556			CCCTC-binding factor						chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)														---	---	---	---
NFATC3	4775	broad.mit.edu	37	16	68128326	68128327	+	Intron	DEL	AA	-	-	rs76091705		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68128326_68128327delAA	uc002evo.1	+						NFATC3_uc010vkl.1_Intron|NFATC3_uc010vkm.1_Intron|NFATC3_uc010vkn.1_Intron|NFATC3_uc010vko.1_Intron|NFATC3_uc010vkp.1_Intron|NFATC3_uc010vkq.1_Intron|NFATC3_uc002evl.2_Intron|NFATC3_uc002evk.2_Intron|NFATC3_uc002evm.1_Intron|NFATC3_uc002evn.1_Intron|NFATC3_uc010vkr.1_Intron|NFATC3_uc010vks.1_Intron|NFATC3_uc010vkt.1_Intron|NFATC3_uc010vku.1_Intron|NFATC3_uc010vkv.1_Intron|NFATC3_uc010vkw.1_Intron|NFATC3_uc010vkx.1_Intron|NFATC3_uc010vky.1_Intron|NFATC3_uc010vkz.1_Intron|NFATC3_uc010vla.1_Intron|NFATC3_uc010vlb.1_Intron|NFATC3_uc010vlc.1_Intron	NM_173165	NP_775188			nuclear factor of activated T-cells,						inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68952818	68952818	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68952818delA	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	69060214	69060214	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69060214delT	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	69089943	69089943	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69089943delA	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70066043	70066044	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70066043_70066044delAA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70072984	70072984	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70072984delT	uc002exy.2	+						PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70156758	70156759	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70156758_70156759delAC	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron	NM_017990	NP_060460			pyruvate dehydrogenase phosphatase regulatory						glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)														---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70196861	70196861	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70196861delT	uc002exy.2	+						uc002eyi.1_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70203635	70203636	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70203635_70203636delTT	uc002exy.2	+						uc002eyi.1_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70205757	70205757	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70205757delT	uc002exy.2	+						uc002eyi.1_Intron|CLEC18C_uc010vlt.1_5'Flank|CLEC18C_uc002eyk.2_5'Flank	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70211512	70211512	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70211512delT	uc002exy.2	+						CLEC18C_uc010vlt.1_Intron|CLEC18C_uc002eyk.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
ST3GAL2	6483	broad.mit.edu	37	16	70418188	70418188	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70418188delA	uc002eyw.2	-						ST3GAL2_uc002eyx.2_Intron	NM_006927	NP_008858			ST3 beta-galactoside alpha-2,3-sialyltransferase						amino sugar metabolic process	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
IL34	146433	broad.mit.edu	37	16	70690422	70690422	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70690422delA	uc002ezh.1	+						IL34_uc002ezi.1_Intron	NM_152456	NP_689669			interleukin 34 precursor						positive regulation of cell proliferation|positive regulation of protein phosphorylation	extracellular space	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71103439	71103439	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71103439delC	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron|HYDIN_uc010vmc.1_Intron|HYDIN_uc010vmd.1_Intron|HYDIN_uc002ezw.3_Intron	NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	71268099	71268099	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71268099delA								HYDIN (3474 upstream) : FTSJD1 (48105 downstream)																																			---	---	---	---
CALB2	794	broad.mit.edu	37	16	71416060	71416065	+	Intron	DEL	AAAATA	-	-	rs67891373	by1000genomes;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71416060_71416065delAAAATA	uc002faa.3	+						CALB2_uc010vme.1_Intron|CALB2_uc002fac.3_Intron	NM_001740	NP_001731			calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71772795	71772795	+	Intron	DEL	G	-	-	rs904764	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71772795delG	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc002faz.2_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	71876360	71876360	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71876360delA								AP1G1 (33384 upstream) : ATXN1L (3539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	72814453	72814454	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72814453_72814454delAA	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																														---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72936678	72936679	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72936678_72936679insG	uc002fck.2	-						ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816			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)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	73500498	73500498	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73500498delA								HTA (372828 upstream) : PSMD7 (830183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73795141	73795141	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73795141delA								HTA (667471 upstream) : PSMD7 (535540 downstream)																																			---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74594034	74594034	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74594034delT	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
ZNRF1	84937	broad.mit.edu	37	16	75064331	75064331	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75064331delA	uc002fdk.2	+						ZNRF1_uc010vmz.1_Intron|ZNRF1_uc002fdl.1_Intron|ZNRF1_uc010cgr.1_Intron	NM_032268	NP_115644			zinc and ring finger protein 1							cell junction|endosome|lysosome|synaptic vesicle membrane	ligase activity|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75715006	75715006	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75715006delA								TERF2IP (23678 upstream) : CNTNAP4 (596170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75903913	75903913	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75903913delT								TERF2IP (212585 upstream) : CNTNAP4 (407263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76003236	76003237	+	IGR	INS	-	TCT	TCT	rs147792701	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76003236_76003237insTCT								TERF2IP (311908 upstream) : CNTNAP4 (307939 downstream)																																			---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76482606	76482607	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76482606_76482607delTT	uc002feu.1	+						CNTNAP4_uc002fev.1_Intron|CNTNAP4_uc010chb.1_Intron|CNTNAP4_uc002fex.1_Intron|CNTNAP4_uc002few.2_Intron	NM_033401	NP_207837			cell recognition protein CASPR4 isoform 1						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77317609	77317610	+	3'UTR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77317609_77317610insT	uc002ffc.3	-	23						NM_199355	NP_955387			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78154880	78154880	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78154880delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	80270195	80270196	+	IGR	INS	-	A	A	rs148983717	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80270195_80270196insA								MAF (635573 upstream) : DYNLRB2 (304658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80629742	80629742	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80629742delA								DYNLRB2 (45203 upstream) : CDYL2 (7936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	81337881	81337882	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81337881_81337882insT								BCMO1 (13134 upstream) : GAN (10689 downstream)																																			---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81847369	81847370	+	Intron	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81847369_81847370delTC	uc002fgt.2	+						PLCG2_uc010chg.1_Intron	NM_002661	NP_002652			phospholipase C, gamma 2						intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84542995	84543011	+	IGR	DEL	CCAGGACCCAGGGTGAC	-	-	rs71151222		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84542995_84543011delCCAGGACCCAGGGTGAC								KIAA1609 (4707 upstream) : COTL1 (56195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	84943581	84943582	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84943581_84943582delTC								CRISPLD2 (465 upstream) : ZDHHC7 (64485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86230136	86230136	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86230136delA								IRF8 (273927 upstream) : LOC732275 (135320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87325504	87325504	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87325504delA	uc002fjt.1	-											Homo sapiens cDNA FLJ43761 fis, clone TESTI2048109.																														---	---	---	---
FBXO31	79791	broad.mit.edu	37	16	87383515	87383517	+	Intron	DEL	AAA	-	-	rs139457187		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87383515_87383517delAAA	uc002fjw.2	-						FBXO31_uc010vot.1_Intron|FBXO31_uc002fjv.2_Intron	NM_024735	NP_079011			F-box protein 31						cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	87617788	87617788	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87617788delG								ZCCHC14 (92328 upstream) : JPH3 (17653 downstream)																																			---	---	---	---
BANP	54971	broad.mit.edu	37	16	88088730	88088730	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88088730delT	uc002fkr.2	+						BANP_uc002fkp.2_Intron|BANP_uc002fkq.2_Intron|BANP_uc010vow.1_Intron|BANP_uc002fks.3_Intron	NM_079837	NP_524576			BTG3 associated nuclear protein isoform b						cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88322456	88322457	+	IGR	DEL	GA	-	-	rs113923759		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88322456_88322457delGA								BANP (211533 upstream) : ZNF469 (171422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88468124	88468131	+	IGR	DEL	TGGATGGG	-	-	rs141467546		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88468124_88468131delTGGATGGG								BANP (357201 upstream) : ZNF469 (25748 downstream)																																			---	---	---	---
SNAI3	333929	broad.mit.edu	37	16	88752673	88752674	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88752673_88752674delCT	uc002flj.2	-						MGC23284_uc002fli.3_Intron	NM_178310	NP_840101			snail homolog 3						oxidation-reduction process		copper ion binding|DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.048)														---	---	---	---
SNAI3	333929	broad.mit.edu	37	16	88754338	88754338	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88754338delA	uc002flj.2	-							NM_178310	NP_840101			snail homolog 3						oxidation-reduction process		copper ion binding|DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.048)														---	---	---	---
ACSF3	197322	broad.mit.edu	37	16	89192220	89192221	+	Intron	INS	-	TGTCTCTCCATTTACTTAGATCCGTGAACACGGTG	TGTCTCTCCATTTACTTAGATCCGTGAACACGGTG	rs35420796		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89192220_89192221insTGTCTCTCCATTTACTTAGATCCGTGAACACGGTG	uc002fmp.2	+						ACSF3_uc010cig.1_Intron|ACSF3_uc010cih.1_Intron|ACSF3_uc002fmq.1_Intron|ACSF3_uc010cii.1_Intron|ACSF3_uc002fmr.1_Intron	NM_174917	NP_777577			acyl-CoA synthetase family member 3 precursor						fatty acid metabolic process	mitochondrion	acid-thiol ligase activity|ATP binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0281)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89473602	89473602	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89473602delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89543603	89543605	+	Intron	DEL	TTT	-	-	rs67973365		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89543603_89543605delTTT	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
DPEP1	1800	broad.mit.edu	37	16	89679869	89679882	+	Intron	DEL	CTCTCTCCCTCCTG	-	-	rs111857923		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89679869_89679882delCTCTCTCCCTCCTG	uc010cin.2	+							NM_001128141	NP_001121613			dipeptidase 1 precursor						proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)													---	---	---	---
DBNDD1	79007	broad.mit.edu	37	16	90071913	90071913	+	3'UTR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90071913delC	uc002fqf.1	-	4					DBNDD1_uc002fqe.1_3'UTR|DBNDD1_uc002fqg.1_RNA	NM_001042610	NP_001036075			dysbindin (dystrobrevin binding protein 1)							cytoplasm					0		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	630649	630649	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:630649delT								VPS53 (12553 upstream) : FAM57A (5198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	701114	701114	+	RNA	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:701114delT	uc002frx.1	+	1		c.1810delT								Homo sapiens cDNA FLJ36482 fis, clone THYMU2017526.																														---	---	---	---
NXN	64359	broad.mit.edu	37	17	716899	716899	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:716899delT	uc002fsa.2	-						NXN_uc010vqd.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
PITPNA	5306	broad.mit.edu	37	17	1431876	1431876	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1431876delA	uc002fst.3	-						PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron	NM_006224	NP_006215			phosphatidylinositol transfer protein, alpha						axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	2589421	2589421	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2589421delA								PAFAH1B1 (513 upstream) : KIAA0664 (3259 downstream)																																			---	---	---	---
USP6	9098	broad.mit.edu	37	17	5044641	5044642	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5044641_5044642delAA	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496			ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5								T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								---	---	---	---
RPAIN	84268	broad.mit.edu	37	17	5324579	5324579	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5324579delT	uc002gbq.2	+						NUP88_uc002gbo.1_5'Flank|NUP88_uc010vsx.1_5'Flank|NUP88_uc010cle.1_5'Flank|NUP88_uc010vsy.1_5'Flank|RPAIN_uc010vsz.1_Intron|RPAIN_uc002gbp.1_Intron|RPAIN_uc010vta.1_Intron|RPAIN_uc010vtb.1_Intron|RPAIN_uc002gbs.2_Intron|RPAIN_uc002gbt.2_Intron|RPAIN_uc002gbu.2_Intron|RPAIN_uc002gbv.2_Intron|RPAIN_uc002gbr.2_Intron|RPAIN_uc002gbw.2_Intron	NM_001033002	NP_001028174			RPA interacting protein isoform b						DNA recombination|DNA repair|DNA-dependent DNA replication|protein import into nucleus|response to UV	cytoplasm|cytoplasm|nucleolus|PML body|PML body	metal ion binding|protein complex binding				0																		---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7120992	7120992	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7120992delG	uc002get.3	-						DLG4_uc010cly.2_5'Flank|DLG4_uc010vto.1_Intron|DLG4_uc002geu.2_5'Flank|ACADVL_uc010vtp.1_Intron|ACADVL_uc010vtq.1_5'Flank|ACADVL_uc002gev.2_5'Flank|ACADVL_uc002gew.2_5'Flank|ACADVL_uc002gex.2_5'Flank	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7794048	7794048	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7794048delG	uc002gje.2	+	3	523	c.373delG	c.(373-375)GGGfs	p.G125fs	CHD3_uc002gjd.2_Frame_Shift_Del_p.G184fs|CHD3_uc002gjf.2_Frame_Shift_Del_p.G125fs|CHD3_uc002gjg.1_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	125				GEGDGG -> PHFQQK (in Ref. 4; AAC50228).	chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7975971	7975971	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7975971delT	uc002gjy.1	-	15						NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7984601	7984601	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7984601delG	uc002gjy.1	-						uc010cnq.1_RNA	NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8449743	8449743	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8449743delA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10138889	10138890	+	IGR	DEL	TT	-	-	rs72812814	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10138889_10138890delTT								GAS7 (37021 upstream) : MYH13 (65293 downstream)																																			---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10440896	10440896	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10440896delT	uc010coi.2	-						uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582			myosin heavy chain IIa						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10460947	10460947	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10460947delT	uc002gml.1	+											Homo sapiens cDNA FLJ40181 fis, clone TESTI2018178.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12323881	12323881	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12323881delT								MAP2K4 (276831 upstream) : MYOCD (245326 downstream)																																			---	---	---	---
HS3ST3A1	9955	broad.mit.edu	37	17	13494979	13494981	+	Intron	DEL	TTT	-	-	rs112132325		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13494979_13494981delTTT	uc002gob.1	-							NM_006042	NP_006033			heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	19328149	19328150	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19328149_19328150delTT								RNF112 (7562 upstream) : SLC47A1 (109017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19512519	19512519	+	IGR	DEL	A	-	-	rs36062953		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19512519delA								SLC47A1 (30173 upstream) : ALDH3A2 (39545 downstream)																																			---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20209172	20209172	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20209172delT	uc002gwq.2	+						CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21002632	21002632	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21002632delT								USP22 (55559 upstream) : DHRS7B (27626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25304776	25304777	+	IGR	INS	-	AC	AC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25304776_25304777insAC								None (None upstream) : WSB1 (316329 downstream)																																			---	---	---	---
NLK	51701	broad.mit.edu	37	17	26508440	26508440	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26508440delA	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
FOXN1	8456	broad.mit.edu	37	17	26837574	26837575	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26837574_26837575delAC	uc010crm.2	+							NM_003593	NP_003584			forkhead box N1						defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|thymus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27509080	27509081	+	5'Flank	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27509080_27509081delAA	uc002hdt.1	-						MYO18A_uc002hdu.1_5'Flank	NM_078471	NP_510880			myosin 18A isoform a						anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27570404	27570404	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27570404delA								MYO18A (62997 upstream) : CRYBA1 (3471 downstream)																																			---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28047745	28047747	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28047745_28047747delAAA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28280529	28280530	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28280529_28280530delCT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
SUZ12P	440423	broad.mit.edu	37	17	29094587	29094587	+	Intron	DEL	A	-	-	rs11310424		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29094587delA	uc002hfn.1	+						SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0																		---	---	---	---
C17orf42	79736	broad.mit.edu	37	17	29231700	29231704	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29231700_29231704delTTTTT	uc002hfu.2	-						C17orf42_uc002hfv.2_Intron|C17orf42_uc002hfw.2_Intron|C17orf42_uc010wbs.1_Intron	NM_024683	NP_078959			hypothetical protein LOC79736						oxidative phosphorylation|regulation of transcription, DNA-dependent|transcription from mitochondrial promoter	mitochondrial nucleoid|ribonucleoprotein complex	DNA polymerase processivity factor activity|nucleic acid binding|protein binding			ovary(1)	1		all_cancers(10;4.64e-07)|all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	29349140	29349141	+	5'Flank	INS	-	AT	AT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29349140_29349141insAT	uc002hgd.1	+											Homo sapiens full length insert cDNA clone ZD88F12.									p.?(1)																					---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30302737	30302737	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30302737delT	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170			joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30534350	30534350	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30534350delA	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777			ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)																---	---	---	---
ZNF207	7756	broad.mit.edu	37	17	30689709	30689709	+	Intron	DEL	T	-	-	rs72079022		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30689709delT	uc002hhh.3	+						ZNF207_uc002hhj.3_Intron|ZNF207_uc002hhi.3_Intron|ZNF207_uc010csz.2_Intron|ZNF207_uc002hhk.1_Intron|ZNF207_uc002hhl.1_Intron	NM_003457	NP_003448			zinc finger protein 207 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31018278	31018278	+	Intron	DEL	A	-	-	rs67496453		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31018278delA	uc002hho.1	-						MYO1D_uc002hhp.1_Intron	NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31547375	31547375	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31547375delA	uc002hhu.2	-						ACCN1_uc002hht.2_Intron	NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	32514784	32514784	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32514784delT								ACCN1 (30959 upstream) : CCL2 (67512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	32859243	32859244	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32859243_32859244insA								CCL1 (168991 upstream) : C17orf102 (41898 downstream)																																			---	---	---	---
LIG3	3980	broad.mit.edu	37	17	33318205	33318205	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33318205delT	uc002hik.1	+						LIG3_uc002hij.2_Intron|LIG3_uc010cth.1_Intron	NM_013975	NP_039269			ligase III, DNA, ATP-dependent isoform alpha						base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			skin(3)|lung(2)|ovary(2)|large_intestine(1)|pancreas(1)	9		Ovarian(249;0.17)			Bleomycin(DB00290)								Other_BER_factors					---	---	---	---
AP2B1	163	broad.mit.edu	37	17	34036426	34036426	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34036426delA	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273			adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)														---	---	---	---
TAF15	8148	broad.mit.edu	37	17	34163122	34163122	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34163122delT	uc002hkd.2	+						TAF15_uc010ctw.1_Intron|TAF15_uc002hkc.2_Intron	NM_139215	NP_631961			TBP-associated factor 15 isoform 1						positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		TAF15/NR4A3(33)	bone(33)|lung(1)|skin(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)				T	TEC|CHN1|ZNF384	extraskeletal myxoid chondrosarcomas|ALL								---	---	---	---
GGNBP2	79893	broad.mit.edu	37	17	34923410	34923410	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34923410delA	uc002hnb.2	+						GGNBP2_uc002hna.2_Intron	NM_024835	NP_079111			zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)														---	---	---	---
DUSP14	11072	broad.mit.edu	37	17	35865221	35865222	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35865221_35865222insT	uc002hnx.2	+						DUSP14_uc002hny.2_Intron	NM_007026	NP_008957			dual specificity phosphatase 14								MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35922492	35922493	+	Intron	INS	-	TTC	TTC	rs148036506	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35922492_35922493insTTC	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron|SYNRG_uc002hof.2_Intron|SYNRG_uc010cvd.1_Intron	NM_007247	NP_009178			synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	36389849	36389849	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36389849delA	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	37393532	37393533	+	IGR	DEL	TG	-	-	rs36105452		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37393532_37393533delTG								STAC2 (11558 upstream) : LOC90110 (15364 downstream)																																			---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38648628	38648628	+	Intron	DEL	T	-	-	rs67433225		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38648628delT	uc010cxb.2	-							NM_032865	NP_116254			tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	39063535	39063538	+	IGR	DEL	TTCC	-	-	rs71764584		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39063535_39063538delTTCC								KRT20 (22056 upstream) : KRT23 (15414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39063596	39063597	+	IGR	INS	-	CCTT	CCTT	rs75186134	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39063596_39063597insCCTT								KRT20 (22117 upstream) : KRT23 (15355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	39301367	39301382	+	IGR	DEL	CCTTCCTTCCTTCCTT	-	-	rs10567144		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39301367_39301382delCCTTCCTTCCTTCCTT								KRTAP4-12 (20948 upstream) : KRTAP4-5 (3796 downstream)																																			---	---	---	---
JUP	3728	broad.mit.edu	37	17	39852078	39852078	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39852078delA	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40851054	40851054	+	3'UTR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40851054delC	uc002iay.2	+	24					CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623			contactin associated protein 1 precursor						axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
PSME3	10197	broad.mit.edu	37	17	40981830	40981830	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40981830delC	uc002ibp.2	+							NM_005789	NP_005780			proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)														---	---	---	---
RPL27	6155	broad.mit.edu	37	17	41154524	41154524	+	Intron	DEL	A	-	-	rs76067241		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41154524delA	uc002icj.2	+						RPL27_uc002ick.2_Intron	NM_000988	NP_000979			ribosomal protein L27						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	structural constituent of ribosome				0		Breast(137;0.000717)|Ovarian(249;0.0776)		BRCA - Breast invasive adenocarcinoma(366;0.157)														---	---	---	---
ETV4	2118	broad.mit.edu	37	17	41623302	41623303	+	5'UTR	INS	-	GTGT	GTGT	rs10624801		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41623302_41623303insGTGT	uc002idw.2	-	1					ETV4_uc010wih.1_5'Flank|ETV4_uc010czh.2_5'UTR|ETV4_uc010wii.1_5'UTR|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron|ETV4_uc002idy.1_5'Flank	NM_001986	NP_001977			ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)				T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								---	---	---	---
Unknown	0	broad.mit.edu	37	17	41666562	41666562	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41666562delT								ETV4 (42800 upstream) : MEOX1 (51205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	42025267	42025267	+	IGR	DEL	A	-	-	rs112096102		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42025267delA								PPY (5434 upstream) : PYY (4842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	43067072	43067072	+	IGR	DEL	C	-	-	rs57638095	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43067072delC								C1QL1 (21428 upstream) : DCAKD (33634 downstream)																																			---	---	---	---
MAP3K14	9020	broad.mit.edu	37	17	43371213	43371214	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43371213_43371214delAC	uc002iiw.1	-						MAP3K14_uc002iiv.1_5'Flank	NM_003954	NP_003945			mitogen-activated protein kinase kinase kinase						cellular response to mechanical stimulus|I-kappaB kinase/NF-kappaB cascade|immune response|positive regulation of I-kappaB kinase/NF-kappaB cascade|T cell costimulation	cytosol	ATP binding|MAP kinase kinase kinase activity|NF-kappaB-inducing kinase activity|protein binding			central_nervous_system(3)|breast(2)|lung(1)|ovary(1)|stomach(1)	8																		---	---	---	---
MAPT	4137	broad.mit.edu	37	17	44049173	44049173	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44049173delG	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519			microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)																---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45329343	45329344	+	5'Flank	INS	-	AC	AC	rs145695537	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45329343_45329344insAC	uc002ilj.2	+						ITGB3_uc002ili.1_5'Flank|ITGB3_uc010wkr.1_5'Flank	NM_000212	NP_000203			integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)													---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45679204	45679204	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45679204delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_5'Flank	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	45854006	45854006	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45854006delA								TBX21 (30521 upstream) : OSBPL7 (30727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47551950	47551950	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47551950delT								PHB (59708 upstream) : NGFR (20705 downstream)																																			---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47723882	47723883	+	5'UTR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47723882_47723883delAA	uc010dbk.2	-	1					SPOP_uc002ipb.2_Intron|SPOP_uc002ipc.2_Intron|SPOP_uc002ipd.2_Intron|SPOP_uc002ipe.2_Intron|SPOP_uc002ipf.2_Intron|SPOP_uc002ipg.2_Intron|SPOP_uc010wlx.1_Intron	NM_003563	NP_003554			speckle-type POZ protein						mRNA processing	nucleus	protein binding			prostate(2)|ovary(2)|lung(2)	6															Prostate(2;0.17)			---	---	---	---
MYST2	11143	broad.mit.edu	37	17	47904634	47904634	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47904634delT	uc002ipm.2	+						MYST2_uc010wma.1_Intron|MYST2_uc010wmb.1_Intron|MYST2_uc010wmc.1_Intron|MYST2_uc010wmd.1_Intron|MYST2_uc010wme.1_Intron|MYST2_uc010wmf.1_Intron|MYST2_uc010wmg.1_Intron	NM_007067	NP_008998			MYST histone acetyltransferase 2						DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	49615115	49615115	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49615115delT								UTP18 (239825 upstream) : CA10 (92560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51518061	51518062	+	IGR	DEL	GT	-	-	rs145846043		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51518061_51518062delGT								None (None upstream) : KIF2B (382177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52499957	52499957	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52499957delA								KIF2B (597384 upstream) : TOM1L1 (478095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	56222062	56222062	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56222062delA								DYNLL2 (54444 upstream) : OR4D1 (10453 downstream)																																			---	---	---	---
HSF5	124535	broad.mit.edu	37	17	56529444	56529444	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56529444delA	uc002iwi.1	-							NM_001080439	NP_001073908			heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57148100	57148100	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57148100delA	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57350820	57350820	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57350820delT	uc002ixk.1	+							NM_182569	NP_872375			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)																	---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58538736	58538736	+	Intron	DEL	A	-	-	rs11287234		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58538736delA	uc002iys.1	-						APPBP2_uc010ddl.1_Intron	NM_006380	NP_006371			amyloid beta precursor protein-binding protein						intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59003211	59003211	+	Intron	DEL	T	-	-	rs111334653		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59003211delT	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyx.1_Intron|BCAS3_uc002iyy.3_Intron	NM_001099432	NP_001092902			breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)															---	---	---	---
TBX2	6909	broad.mit.edu	37	17	59480289	59480308	+	Intron	DEL	GATAGAGAGAGAGAGAGAGA	-	-	rs72277883		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59480289_59480308delGATAGAGAGAGAGAGAGAGA	uc010wox.1	+						TBX2_uc002ize.2_Intron|TBX2_uc002izg.2_Intron	NM_005994	NP_005985			T-box 2						cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0																		---	---	---	---
BRIP1	83990	broad.mit.edu	37	17	59840865	59840865	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59840865delA	uc002izk.1	-						BRIP1_uc002izl.1_Intron	NM_032043	NP_114432			BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1								F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59946936	59946937	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59946936_59946937delAA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59999199	59999199	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59999199delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	61978837	61978839	+	IGR	DEL	TCT	-	-	rs147941855		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61978837_61978839delTCT								CSH2 (4850 upstream) : CSHL1 (8126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	62407331	62407331	+	IGR	DEL	A	-	-	rs954507	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62407331delA								PECAM1 (6126 upstream) : C17orf60 (54238 downstream)																																			---	---	---	---
POLG2	11232	broad.mit.edu	37	17	62488964	62488964	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62488964delT	uc002jei.2	-						POLG2_uc010deg.1_Intron	NM_007215	NP_009146			DNA polymerase subunit gamma-2, mitochondrial						DNA repair|DNA-dependent DNA replication|glycyl-tRNA aminoacylation	mitochondrial chromosome	ATP binding|DNA-directed DNA polymerase activity|glycine-tRNA ligase activity|identical protein binding|single-stranded DNA binding			central_nervous_system(1)	1	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)															---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63532780	63532780	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63532780delA	uc002jfi.2	-						AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646			axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63747018	63747020	+	Intron	DEL	AAA	-	-	rs75469128		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63747018_63747020delAAA	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron|CCDC46_uc002jfk.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64179497	64179497	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64179497delA	uc002jfl.2	-						CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CACNG5	27091	broad.mit.edu	37	17	64859006	64859007	+	Intron	INS	-	TCTCTC	TCTCTC	rs144007490	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64859006_64859007insTCTCTC	uc010wqi.1	+							NM_145811	NP_665810			voltage-dependent calcium channel gamma-5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)															---	---	---	---
PSMD12	5718	broad.mit.edu	37	17	65336874	65336874	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65336874delA	uc002jfy.2	-	11					PSMD12_uc002jga.2_3'UTR|PSMD12_uc002jfz.2_3'UTR	NM_002816	NP_002807			proteasome 26S non-ATPase subunit 12 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)																	---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66278634	66278635	+	Intron	DEL	AA	-	-	rs113123475		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66278634_66278635delAA	uc002jhc.2	+						SLC16A6_uc002jgz.1_Intron|SLC16A6_uc002jha.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
CDC42EP4	23580	broad.mit.edu	37	17	71279773	71279774	+	3'UTR	INS	-	T	T	rs138785432	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71279773_71279774insT	uc002jjn.2	-	2					CDC42EP4_uc002jjo.2_3'UTR|CDC42EP4_uc002jjp.1_3'UTR	NM_012121	NP_036253			Cdc42 effector protein 4						positive regulation of pseudopodium assembly|regulation of cell shape	actin cytoskeleton|cytoplasm|endomembrane system|membrane|microtubule cytoskeleton	GTP-Rho binding				0			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)															---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71620682	71620682	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71620682delA	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72056484	72056484	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72056484delA								C17orf54 (231808 upstream) : RPL38 (143311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	74115317	74115318	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74115317_74115318insT								EXOC7 (15449 upstream) : FOXJ1 (17099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75075957	75075958	+	IGR	DEL	AC	-	-	rs33993825		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75075957_75075958delAC								MGAT5B (129487 upstream) : C17orf86 (8767 downstream)																																			---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75309504	75309504	+	Intron	DEL	C	-	-	rs62079550		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75309504delC	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	75533933	75533933	+	IGR	DEL	T	-	-	rs79954439		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75533933delT								SEPT9 (37257 upstream) : FLJ45079 (341176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77843485	77843485	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77843485delT								CBX4 (30272 upstream) : TBC1D16 (70336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	78107503	78107504	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78107503_78107504insT								GAA (13825 upstream) : EIF4A3 (1515 downstream)																																			---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79372928	79372929	+	5'Flank	INS	-	GTGT	GTGT	rs79761637	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79372928_79372929insGTGT	uc002kaf.2	+							NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
ARHGDIA	396	broad.mit.edu	37	17	79826687	79826687	+	3'UTR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79826687delG	uc002kbp.2	-	5					ARHGDIA_uc002kjk.1_3'UTR|ARHGDIA_uc002kbq.2_3'UTR|ARHGDIA_uc002kbr.2_Frame_Shift_Del_p.Q200fs|ARHGDIA_uc002kbs.1_Intron|ARHGDIA_uc002kbt.1_Intron	NM_004309	NP_004300			Rho GDP dissociation inhibitor (GDI) alpha						anti-apoptosis|cellular component movement|negative regulation of axonogenesis|negative regulation of cell adhesion|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoskeleton|cytosol	GTPase activator activity|identical protein binding|Rho GDP-dissociation inhibitor activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80107134	80107135	+	Intron	INS	-	G	G	rs143649990	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80107134_80107135insG	uc002kdx.1	-						CCDC57_uc002kdy.2_Intron	NM_198082	NP_932348			coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
THOC1	9984	broad.mit.edu	37	18	269398	269399	+	5'Flank	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:269398_269399delAA	uc002kkj.3	-						THOC1_uc002kkk.3_5'Flank|THOC1_uc002kkl.2_5'Flank	NM_005131	NP_005122			THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	569590	569592	+	IGR	DEL	ATG	-	-	rs148271221		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:569590_569592delATG								COLEC12 (68861 upstream) : CETN1 (10777 downstream)																																			---	---	---	---
CLUL1	27098	broad.mit.edu	37	18	605569	605569	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:605569delA	uc002kkp.2	+						CLUL1_uc010wys.1_Intron	NM_014410	NP_055225			clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2																		---	---	---	---
ENOSF1	55556	broad.mit.edu	37	18	684000	684000	+	Intron	DEL	T	-	-	rs112089902		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:684000delT	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982			enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2722732	2722732	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2722732delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2957592	2957592	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2957592delC	uc002klo.2	-							NM_014646	NP_055461			lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2980799	2980799	+	Intron	DEL	C	-	-	rs112666021		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2980799delC	uc002klo.2	-							NM_014646	NP_055461			lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3147910	3147910	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3147910delA	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4073628	4073628	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4073628delA	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4408420	4408420	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4408420delT	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	4511011	4511011	+	IGR	DEL	A	-	-	rs62086981	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4511011delA								DLGAP1 (55745 upstream) : LOC642597 (632661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4711841	4711841	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4711841delA								DLGAP1 (256575 upstream) : LOC642597 (431831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4834108	4834108	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4834108delT								DLGAP1 (378842 upstream) : LOC642597 (309564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4836344	4836344	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4836344delG								DLGAP1 (381078 upstream) : LOC642597 (307328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4955004	4955004	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4955004delA								DLGAP1 (499738 upstream) : LOC642597 (188668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4956889	4956889	+	IGR	DEL	A	-	-	rs35463684		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4956889delA								DLGAP1 (501623 upstream) : LOC642597 (186783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5070977	5070977	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5070977delA								DLGAP1 (615711 upstream) : LOC642597 (72695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5247374	5247374	+	IGR	DEL	T	-	-	rs36050885		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5247374delT								LOC339290 (871 upstream) : ZFP161 (41645 downstream)																																			---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5474229	5474231	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5474229_5474231delAAA	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	5782778	5782779	+	Intron	INS	-	G	G	rs145585600	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5782778_5782779insG	uc002kmw.2	+											Homo sapiens chromosome 18 unknown mRNA sequence.																														---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6118171	6118172	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6118171_6118172delCT	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6389514	6389514	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6389514delA	uc010dkt.2	-							NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9216637	9216637	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9216637delT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron|ANKRD12_uc010dkx.1_5'Flank	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9244359	9244359	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9244359delT	uc002knv.2	+						ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron|ANKRD12_uc010dkx.1_Intron	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	9881711	9881712	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9881711_9881712delAA								RAB31 (19158 upstream) : TXNDC2 (4011 downstream)																																			---	---	---	---
VAPA	9218	broad.mit.edu	37	18	9954038	9954038	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9954038delT	uc002kok.2	+						VAPA_uc002koj.2_Intron	NM_194434	NP_919415			vesicle-associated membrane protein-associated						cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10150773	10150773	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10150773delT								VAPA (190756 upstream) : APCDD1 (303852 downstream)																																			---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10548537	10548538	+	Intron	DEL	TT	-	-	rs1662154		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10548537_10548538delTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10697600	10697600	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10697600delA	uc002kor.3	-						FAM38B_uc002koq.2_Intron	NM_022068	NP_071351			family with sequence similarity 38, member B							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10742797	10742798	+	Intron	DEL	TG	-	-	rs71977376		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10742797_10742798delTG	uc002kos.1	-						FAM38B_uc002kot.1_Intron					SubName: Full=cDNA FLJ45725 fis, clone HCHON2009766; Flags: Fragment;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10762647	10762647	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10762647delA	uc002kos.1	-						FAM38B_uc002kou.1_Intron					SubName: Full=cDNA FLJ45725 fis, clone HCHON2009766; Flags: Fragment;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10912964	10912964	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10912964delA								FAM38B (210985 upstream) : GNAL (776172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11090746	11090746	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11090746delA								FAM38B (388767 upstream) : GNAL (598390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11610675	11610676	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11610675_11610676delAA								FAM38B (908696 upstream) : GNAL (78460 downstream)																																			---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11876464	11876464	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11876464delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	12115075	12115075	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12115075delT	uc002kqs.2	+											RecName: Full=UPF0634 protein E;																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	12385180	12385180	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12385180delA								AFG3L2 (7986 upstream) : SLMO1 (22715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	12733086	12733087	+	IGR	DEL	AC	-	-	rs7407063		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12733086_12733087delAC								PSMG2 (7349 upstream) : PTPN2 (52394 downstream)																																			---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13006274	13006274	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13006274delT	uc010xac.1	+						CEP192_uc002krs.1_Intron	NM_032142	NP_115518			centrosomal protein 192kDa											ovary(4)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	13190821	13190821	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13190821delA								CEP192 (65772 upstream) : C18orf1 (27965 downstream)																																			---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13531985	13531985	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13531985delC	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
RNMT	8731	broad.mit.edu	37	18	13742794	13742794	+	Intron	DEL	A	-	-	rs7229786		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13742794delA	uc002ksk.1	+						RNMT_uc002ksl.1_Intron|RNMT_uc002ksm.1_Intron|RNMT_uc010dlk.2_Intron|RNMT_uc010xae.1_Intron	NM_003799	NP_003790			RNA (guanine-7-) methyltransferase						mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	mRNA (guanine-N7-)-methyltransferase activity|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14225639	14225639	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14225639delA								ZNF519 (93210 upstream) : LOC284233 (111783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14927040	14927040	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14927040delT								ANKRD30B (74303 upstream) : LOC644669 (386515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15060272	15060272	+	IGR	DEL	C	-	-	rs4107799		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15060272delC								ANKRD30B (207535 upstream) : LOC644669 (253283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15087487	15087487	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15087487delA								ANKRD30B (234750 upstream) : LOC644669 (226068 downstream)																																			---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18532746	18532747	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18532746_18532747delAA	uc002kte.2	-							NM_005406	NP_005397			Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)																	---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18619417	18619417	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18619417delA	uc002kte.2	-							NM_005406	NP_005397			Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	18744348	18744348	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18744348delT								ROCK1 (52536 upstream) : GREB1L (77855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	18799889	18799889	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18799889delG								ROCK1 (108077 upstream) : GREB1L (22314 downstream)																																			---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	18963670	18963670	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18963670delT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
ABHD3	171586	broad.mit.edu	37	18	19249040	19249040	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19249040delA	uc002ktl.2	-						ABHD3_uc002ktm.2_Intron|ABHD3_uc010xao.1_Intron	NM_138340	NP_612213			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19437239	19437240	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19437239_19437240insT	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	19537283	19537283	+	IGR	DEL	T	-	-	rs77682603		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19537283delT								MIB1 (86373 upstream) : GATA6 (212133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19787620	19787620	+	IGR	DEL	T	-	-	rs57174640	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19787620delT								GATA6 (5393 upstream) : CTAGE1 (205944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20007532	20007532	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20007532delT								CTAGE1 (9654 upstream) : RBBP8 (505763 downstream)																																			---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20539381	20539382	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20539381_20539382delTG	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc002ktx.1_Intron	NM_002894	NP_002885			retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20758178	20758178	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20758178delT	uc002kuc.2	+						CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089			Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20827823	20827824	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20827823_20827824insG	uc002kuc.2	+						C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089			Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	20846067	20846067	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20846067delT	uc010xaq.1	-											Homo sapiens cDNA FLJ41629 fis, clone DFNES2010502.							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)																	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21167742	21167742	+	5'Flank	DEL	T	-	-	rs1788772	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21167742delT	uc002kum.3	-						NPC1_uc010xba.1_5'Flank	NM_000271	NP_000262			Niemann-Pick disease, type C1 precursor						autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21447533	21447533	+	Intron	DEL	G	-	-	rs59733215		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21447533delG	uc002kuq.2	+						LAMA3_uc002kur.2_Intron	NM_198129	NP_937762			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)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	21988574	21988575	+	IGR	INS	-	AT	AT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21988574_21988575insAT								OSBPL1A (10784 upstream) : IMPACT (18034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22635141	22635147	+	IGR	DEL	AAAACAA	-	-	rs33981324		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22635141_22635147delAAAACAA								HRH4 (575221 upstream) : ZNF521 (6741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	23287731	23287731	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23287731delT								ZNF521 (355517 upstream) : SS18 (308488 downstream)																																			---	---	---	---
TAF4B	6875	broad.mit.edu	37	18	23839252	23839252	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23839252delT	uc002kvu.3	+						TAF4B_uc002kvs.3_Intron|TAF4B_uc002kvt.3_Intron	NM_005640	NP_005631			TAF4b RNA polymerase II, TATA box binding						transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)															---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24087665	24087666	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24087665_24087666insT	uc002kvw.2	-						KCTD1_uc010xbj.1_Intron|KCTD1_uc010xbk.1_Intron	NM_001136205	NP_001129677			potassium channel tetramerisation domain						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity			ovary(1)	1	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	24405289	24405292	+	IGR	DEL	GTTG	-	-	rs72033543		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24405289_24405292delGTTG								LOC728606 (121687 upstream) : AQP4 (26718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	25191485	25191486	+	IGR	DEL	AA	-	-	rs148134410		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25191485_25191486delAA								C18orf16 (420835 upstream) : CDH2 (339444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	25296109	25296112	+	IGR	DEL	TTAT	-	-	rs144870797	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25296109_25296112delTTAT								C18orf16 (525459 upstream) : CDH2 (234818 downstream)																																			---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25591733	25591734	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25591733_25591734insA	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25637631	25637633	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25637631_25637633delAAA	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25737756	25737756	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25737756delA	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	26696591	26696591	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26696591delA								CDH2 (939146 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27101768	27101768	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27101768delT								None (None upstream) : MIR302F (777108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27375509	27375510	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27375509_27375510delAA								None (None upstream) : MIR302F (503366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27881350	27881350	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27881350delT								MIR302F (2424 upstream) : DSC3 (688703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28005193	28005194	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28005193_28005194delAA								MIR302F (126267 upstream) : DSC3 (564859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28011148	28011148	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28011148delT								MIR302F (132222 upstream) : DSC3 (558905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28181753	28181754	+	IGR	INS	-	C	C	rs148837398	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28181753_28181754insC								MIR302F (302827 upstream) : DSC3 (388299 downstream)																																			---	---	---	---
DSC3	1825	broad.mit.edu	37	18	28588133	28588133	+	Intron	DEL	A	-	-	rs34151598		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28588133delA	uc002kwj.3	-						DSC3_uc002kwi.3_Intron	NM_001941	NP_001932			desmocollin 3 isoform Dsc3a preproprotein						homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	28874082	28874082	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28874082delT								DSC1 (131263 upstream) : DSG1 (23970 downstream)																																			---	---	---	---
RNF138	51444	broad.mit.edu	37	18	29674572	29674572	+	Intron	DEL	A	-	-	rs59343680	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29674572delA	uc002kxg.2	+						RNF138_uc002kxh.2_Intron	NM_016271	NP_057355			ring finger protein 138 isoform 1						Wnt receptor signaling pathway	intracellular	ligase activity|protein kinase binding|zinc ion binding				0																		---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29770169	29770169	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29770169delT	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30304984	30304984	+	Intron	DEL	T	-	-	rs71982034		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30304984delT	uc002kxm.1	-						KLHL14_uc010dmd.1_Intron	NM_020805	NP_065856			kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30729910	30729910	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30729910delA	uc002kxn.2	-						C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998			hypothetical protein LOC374864 isoform 1											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	31062401	31062401	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31062401delT								C18orf34 (41716 upstream) : ASXL3 (96140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	31146142	31146142	+	IGR	DEL	A	-	-	rs112662632		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31146142delA								C18orf34 (125457 upstream) : ASXL3 (12399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	31948179	31948179	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31948179delT								NOL4 (144733 upstream) : DTNA (125075 downstream)																																			---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32408819	32408819	+	Intron	DEL	T	-	-	rs71962398		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32408819delT	uc010dmn.1	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Intron|DTNA_uc010dmm.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32500341	32500341	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32500341delA								DTNA (28533 upstream) : MAPRE2 (56551 downstream)																																			---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32622889	32622891	+	Intron	DEL	AAA	-	-	rs113315399		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32622889_32622891delAAA	uc002kyg.2	+						MAPRE2_uc010xcb.1_Intron|MAPRE2_uc010xcc.1_Intron|MAPRE2_uc002kyf.2_Intron|MAPRE2_uc002kyh.2_Intron|MAPRE2_uc010xcd.1_Intron	NM_014268	NP_055083			microtubule-associated protein, RP/EB family,						cell division|cell proliferation|mitosis|signal transduction	cytoplasm|microtubule	microtubule binding			ovary(1)	1																		---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32655719	32655719	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32655719delA	uc002kyg.2	+						MAPRE2_uc010xcb.1_Intron|MAPRE2_uc010xcc.1_Intron|MAPRE2_uc002kyf.2_Intron|MAPRE2_uc002kyh.2_Intron|MAPRE2_uc010xcd.1_Intron	NM_014268	NP_055083			microtubule-associated protein, RP/EB family,						cell division|cell proliferation|mitosis|signal transduction	cytoplasm|microtubule	microtubule binding			ovary(1)	1																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33289487	33289488	+	Intron	INS	-	A	A	rs150474982	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33289487_33289488insA	uc010dmu.2	+						GALNT1_uc002kyz.3_Intron|GALNT1_uc002kzb.2_Intron	NM_020474	NP_065207			polypeptide N-acetylgalactosaminyltransferase 1						protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33723066	33723066	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33723066delT	uc002kzk.1	+						ELP2_uc010xcg.1_Intron|ELP2_uc002kzl.1_Intron|ELP2_uc002kzm.1_Intron|ELP2_uc010xch.1_Intron|ELP2_uc002kzn.1_Intron|ELP2_uc002kzo.1_Intron	NM_018255	NP_060725			elongator protein 2						regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33744315	33744315	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33744315delT	uc002kzk.1	+						ELP2_uc010xcg.1_Intron|ELP2_uc002kzl.1_Intron|ELP2_uc002kzm.1_Intron|ELP2_uc010xch.1_Intron|ELP2_uc002kzn.1_Intron|ELP2_uc002kzo.1_Intron	NM_018255	NP_060725			elongator protein 2						regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34204660	34204660	+	Intron	DEL	G	-	-	rs5824029		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34204660delG	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34235453	34235453	+	Intron	DEL	A	-	-	rs138987006	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34235453delA	uc002kzt.1	+						FHOD3_uc002kzr.1_Intron|FHOD3_uc002kzs.1_Intron|FHOD3_uc002kzu.1_Intron|FHOD3_uc010dmz.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
C18orf10	25941	broad.mit.edu	37	18	34408169	34408170	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34408169_34408170insA	uc002kzw.1	-						KIAA1328_uc002kzz.2_5'Flank|C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Intron|C18orf10_uc002kzx.1_Intron|C18orf10_uc002kzy.3_Intron	NM_015476	NP_056291			tubulin polyglutamylase complex subunit 2							cytoplasm|microtubule				skin(1)	1																		---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34734509	34734509	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34734509delC	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
CELF4	56853	broad.mit.edu	37	18	34880192	34880193	+	Intron	DEL	TT	-	-	rs72233735		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34880192_34880193delTT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565			bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35021942	35021978	+	Intron	DEL	CCTAGATGACACAGTGCGTCACCCAAACCGCAAAGAC	-	-	rs4799924	by1000genomes;byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35021942_35021978delCCTAGATGACACAGTGCGTCACCCAAACCGCAAAGAC	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565			bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	35158124	35158124	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35158124delG								CELF4 (12124 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35669392	35669392	+	IGR	DEL	A	-	-	rs35678779		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35669392delA								CELF4 (523392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35734142	35734143	+	IGR	INS	-	GTGC	GTGC	rs143030790	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35734142_35734143insGTGC								CELF4 (588142 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35883528	35883528	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35883528delA								CELF4 (737528 upstream) : LOC647946 (903360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35904456	35904457	+	IGR	INS	-	TG	TG	rs149938499	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35904456_35904457insTG								CELF4 (758456 upstream) : LOC647946 (882431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36542223	36542224	+	IGR	INS	-	C	C	rs78570502		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36542223_36542224insC								None (None upstream) : LOC647946 (244664 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	36911760	36911760	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36911760delT	uc002lak.1	-						LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron					Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	39343565	39343565	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39343565delG								KC6 (243004 upstream) : PIK3C3 (191634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39407155	39407155	+	IGR	DEL	A	-	-	rs5824376		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39407155delA								KC6 (306594 upstream) : PIK3C3 (128044 downstream)																																			---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40618865	40618865	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40618865delT	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	41181654	41181657	+	IGR	DEL	GAAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41181654_41181657delGAAG								SYT4 (324039 upstream) : None (None downstream)																																			---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43253851	43253851	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43253851delT	uc010dnj.2	+						SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A1	6563	broad.mit.edu	37	18	43329109	43329109	+	Intron	DEL	T	-	-	rs28898896		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43329109delT	uc010xcn.1	+						SLC14A1_uc010dnk.2_Intron|SLC14A1_uc002lbf.3_Intron|SLC14A1_uc002lbg.3_Intron|SLC14A1_uc010xco.1_Intron|SLC14A1_uc002lbh.3_Intron|SLC14A1_uc002lbi.3_Intron|SLC14A1_uc002lbj.3_Intron|SLC14A1_uc002lbk.3_Intron	NM_001146036	NP_001139508			solute carrier family 14 (urea transporter),							integral to plasma membrane	urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43529365	43529365	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43529365delT	uc002lbm.2	-						KIAA1632_uc002lbo.1_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43559132	43559133	+	IGR	INS	-	TCTCCC	TCTCCC	rs150640744	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43559132_43559133insTCTCCC								KIAA1632 (11827 upstream) : PSTPIP2 (4370 downstream)																																			---	---	---	---
ATP5A1	498	broad.mit.edu	37	18	43681846	43681847	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43681846_43681847delAA	uc002lbt.1	-						HAUS1_uc002lbv.2_5'Flank|HAUS1_uc002lbu.2_5'Flank	NM_001001937	NP_001001937			ATP synthase, H+ transporting, mitochondrial F1						ATP hydrolysis coupled proton transport|embryo development|lipid metabolic process|negative regulation of endothelial cell proliferation|respiratory electron transport chain	mitochondrial matrix|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism				0																		---	---	---	---
HAUS1	115106	broad.mit.edu	37	18	43702272	43702274	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43702272_43702274delAAA	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452			coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1																		---	---	---	---
HAUS1	115106	broad.mit.edu	37	18	43703177	43703177	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43703177delA	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452			coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43723130	43723130	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43723130delT								HAUS1 (14832 upstream) : C18orf25 (30858 downstream)																																			---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43844699	43844701	+	3'UTR	DEL	TTT	-	-	rs35509991		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43844699_43844701delTTT	uc002lbw.2	+	6					C18orf25_uc002lbx.2_3'UTR	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44526004	44526005	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44526004_44526005delTT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_5'Flank	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44531468	44531468	+	Intron	DEL	T	-	-	rs75960197		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44531468delT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	45226841	45226841	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45226841delA								IER3IP1 (524096 upstream) : SMAD2 (132626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45981525	45981538	+	IGR	DEL	TTTGTGTGTGTATG	-	-	rs36212598		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45981525_45981538delTTTGTGTGTGTATG								ZBTB7C (45862 upstream) : KIAA0427 (83889 downstream)																																			---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46279973	46279973	+	Intron	DEL	A	-	-	rs79862670		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46279973delA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	46543455	46543456	+	IGR	INS	-	GT	GT	rs146768103	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46543455_46543456insGT								SMAD7 (66374 upstream) : DYM (26716 downstream)																																			---	---	---	---
DYM	54808	broad.mit.edu	37	18	46785152	46785155	+	Intron	DEL	ACAC	-	-	rs74174746		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46785152_46785155delACAC	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron|DYM_uc010dov.1_5'Flank	NM_017653	NP_060123			dymeclin							Golgi apparatus					0																		---	---	---	---
DYM	54808	broad.mit.edu	37	18	46790472	46790475	+	Intron	DEL	TTTT	-	-	rs148159481		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46790472_46790475delTTTT	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron	NM_017653	NP_060123			dymeclin							Golgi apparatus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	46994505	46994505	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46994505delT								DYM (7426 upstream) : C18orf32 (13525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47259107	47259107	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47259107delT								LIPG (139831 upstream) : ACAA2 (50768 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47564262	47564262	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47564262delA	uc002leb.2	-						MYO5B_uc002lec.1_Intron	NM_001080467	NP_001073936			myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48102594	48102594	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48102594delA	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48203925	48203925	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48203925delT	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48209824	48209825	+	Intron	DEL	GT	-	-	rs71837682		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48209824_48209825delGT	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
ME2	4200	broad.mit.edu	37	18	48411213	48411216	+	Intron	DEL	TGTG	-	-	rs72001999		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48411213_48411216delTGTG	uc002ley.2	+						ME2_uc010dpd.2_Intron	NM_002396	NP_002387			malic enzyme 2, NAD(+)-dependent, mitochondrial						malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)													---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48554076	48554076	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48554076delA	uc010xdp.1	+						SMAD4_uc010xdo.1_Intron	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48605008	48605008	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48605008delT	uc010xdp.1	+	12					SMAD4_uc002lfb.3_3'UTR	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48609103	48609103	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48609103delT	uc010xdp.1	+	12					SMAD4_uc002lfb.3_3'UTR	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
Unknown	0	broad.mit.edu	37	18	49206349	49206350	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49206349_49206350insA								MEX3C (482659 upstream) : DCC (660221 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50413677	50413678	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50413677_50413678delTT	uc002lfe.1	+						DCC_uc010xdr.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50517309	50517310	+	Intron	INS	-	T	T	rs143725486	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50517309_50517310insT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50817012	50817012	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50817012delA	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50914665	50914666	+	Intron	INS	-	A	A	rs149719950	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50914665_50914666insA	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	51478249	51478250	+	IGR	INS	-	AT	AT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51478249_51478250insAT								DCC (420467 upstream) : MBD2 (202325 downstream)																																			---	---	---	---
C18orf54	162681	broad.mit.edu	37	18	51899102	51899102	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51899102delT	uc002lfn.3	+						C18orf54_uc002lfo.3_Intron	NM_173529	NP_775800			hypothetical protein LOC162681 precursor							extracellular region				ovary(1)|skin(1)	2				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	52437964	52437964	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52437964delT								C18orf26 (171240 upstream) : RAB27B (57876 downstream)																																			---	---	---	---
CCDC68	80323	broad.mit.edu	37	18	52578451	52578452	+	Intron	INS	-	A	A	rs151258696	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52578451_52578452insA	uc002lfs.2	-						CCDC68_uc002lft.2_Intron	NM_001143829	NP_001137301			coiled-coil domain containing 68											skin(1)	1				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	53470778	53470778	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53470778delT								TCF4 (167593 upstream) : TXNL1 (799277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	53713644	53713644	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53713644delT								TCF4 (410459 upstream) : TXNL1 (556411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	53849914	53849914	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53849914delA								TCF4 (546729 upstream) : TXNL1 (420141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54247699	54247700	+	IGR	INS	-	A	A	rs149370813	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54247699_54247700insA								TCF4 (944514 upstream) : TXNL1 (22355 downstream)																																			---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54283634	54283634	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54283634delA	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_Intron|TXNL1_uc002lgj.1_Intron	NM_004786	NP_004777			thioredoxin-like 1						cell redox homeostasis|electron transport chain|glycerol ether metabolic process|transport	cytoplasm	electron carrier activity|protein disulfide oxidoreductase activity				0				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)														---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54327088	54327088	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54327088delT	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54806514	54806514	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54806514delA								WDR7 (109478 upstream) : ST8SIA3 (213207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54979980	54979980	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54979980delC								WDR7 (282944 upstream) : ST8SIA3 (39741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55194857	55194858	+	IGR	INS	-	GC	GC	rs146619137	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55194857_55194858insGC								ONECUT2 (36328 upstream) : FECH (17216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55200988	55200988	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55200988delT								ONECUT2 (42459 upstream) : FECH (11086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55492234	55492237	+	IGR	DEL	CTTC	-	-	rs57269673		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55492234_55492237delCTTC								ATP8B1 (93195 upstream) : NEDD4L (219382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55519259	55519259	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55519259delT								ATP8B1 (120220 upstream) : NEDD4L (192360 downstream)																																			---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55711819	55711820	+	5'UTR	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55711819_55711820insG	uc002lgy.2	+	1					NEDD4L_uc002lgz.2_5'UTR|NEDD4L_uc002lgx.2_5'UTR|NEDD4L_uc010xee.1_5'Flank|NEDD4L_uc002lha.1_5'Flank	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55990672	55990672	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55990672delA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpm.1_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56383364	56383364	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56383364delA	uc002lhm.1	+						MALT1_uc002lhn.1_Intron	NM_006785	NP_006776			mucosa associated lymphoid tissue lymphoma						activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
Unknown	0	broad.mit.edu	37	18	56513158	56513158	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56513158delA								MALT1 (95788 upstream) : ZNF532 (16903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57063843	57063847	+	IGR	DEL	TGTGT	-	-	rs66813723	by1000genomes;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57063843_57063847delTGTGT								LMAN1 (37335 upstream) : CCBE1 (37302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57071089	57071090	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57071089_57071090delTT								LMAN1 (44581 upstream) : CCBE1 (30059 downstream)																																			---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57162841	57162842	+	Intron	DEL	TT	-	-	rs2510620		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57162841_57162842delTT	uc002lib.2	-							NM_133459	NP_597716			collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	57420419	57420419	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57420419delT								CCBE1 (55775 upstream) : PMAIP1 (146773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57801062	57801062	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57801062delT								PMAIP1 (229524 upstream) : MC4R (237502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58136661	58136661	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58136661delT								MC4R (96660 upstream) : CDH20 (864327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58523078	58523078	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58523078delT								MC4R (483077 upstream) : CDH20 (477910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58754776	58754776	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58754776delG								MC4R (714775 upstream) : CDH20 (246212 downstream)																																			---	---	---	---
PIGN	23556	broad.mit.edu	37	18	59735331	59735332	+	Intron	INS	-	TTTG	TTTG	rs140889728	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59735331_59735332insTTTG	uc002lii.3	-						PIGN_uc002lij.3_Intron	NM_176787	NP_789744			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)																---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59894429	59894430	+	Intron	DEL	AA	-	-	rs35190394		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59894429_59894430delAA	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	60262253	60262258	+	IGR	DEL	TTGTTG	-	-	rs143213964		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60262253_60262258delTTGTTG								ZCCHC2 (8291 upstream) : PHLPP1 (120476 downstream)																																			---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60495242	60495245	+	Intron	DEL	TGTG	-	-	rs66515508		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60495242_60495245delTGTG	uc002lis.2	+							NM_194449	NP_919431			PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	60737206	60737206	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60737206delC								PHLPP1 (89541 upstream) : BCL2 (53373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60756754	60756755	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60756754_60756755delTT								PHLPP1 (109089 upstream) : BCL2 (33824 downstream)																																			---	---	---	---
BCL2	596	broad.mit.edu	37	18	60921788	60921789	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60921788_60921789delAA	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624			B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)			T	IGH@	NHL|CLL								---	---	---	---
KDSR	2531	broad.mit.edu	37	18	61008707	61008707	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61008707delA	uc010dpw.2	-						KDSR_uc010xem.1_Intron	NM_002035	NP_002026			3-ketodihydrosphingosine reductase precursor						3-keto-sphinganine metabolic process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	62473336	62473336	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62473336delT								C18orf20 (657076 upstream) : CDH7 (944152 downstream)																																			---	---	---	---
CDH7	1005	broad.mit.edu	37	18	63449318	63449318	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63449318delC	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450			cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)																---	---	---	---
CDH7	1005	broad.mit.edu	37	18	63526785	63526785	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63526785delT	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450			cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	64044632	64044632	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64044632delA								CDH7 (496458 upstream) : CDH19 (126689 downstream)																																			---	---	---	---
CDH19	28513	broad.mit.edu	37	18	64178925	64178925	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64178925delA	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron	NM_021153	NP_066976			cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	64551425	64551425	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64551425delA								CDH19 (280209 upstream) : DSEL (622394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65098692	65098692	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65098692delT								CDH19 (827476 upstream) : DSEL (75127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65847543	65847543	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65847543delT								DSEL (663576 upstream) : TMX3 (493384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66234660	66234661	+	IGR	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66234660_66234661delCT								None (None upstream) : TMX3 (106266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66277948	66277948	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66277948delA								None (None upstream) : TMX3 (62979 downstream)																																			---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66659312	66659312	+	Intron	DEL	T	-	-	rs74362951		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66659312delT	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron	NM_001093729	NP_001087198			coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	67902915	67902915	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67902915delG								RTTN (29953 upstream) : SOCS6 (53222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68018186	68018187	+	IGR	INS	-	TTGTTGTTGTTG	TTGTTGTTGTTG	rs142385373	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68018186_68018187insTTGTTGTTGTTG								SOCS6 (20752 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68614700	68614700	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68614700delA								SOCS6 (617266 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68867928	68867929	+	IGR	DEL	AA	-	-	rs79989833		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68867928_68867929delAA								SOCS6 (870494 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68932815	68932815	+	IGR	DEL	A	-	-	rs142790801		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68932815delA								SOCS6 (935381 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69159479	69159479	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69159479delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69205832	69205833	+	Intron	INS	-	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69205832_69205833insG	uc002lks.1	-						uc002lkt.1_Intron					Homo sapiens cDNA FLJ36657 fis, clone UTERU2001876.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	69873568	69873568	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69873568delC								None (None upstream) : CBLN2 (330347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70077101	70077101	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70077101delA								None (None upstream) : CBLN2 (126814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71181444	71181447	+	IGR	DEL	TCTT	-	-	rs74801771		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71181444_71181447delTCTT								NETO1 (646634 upstream) : FBXO15 (559141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71977806	71977807	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71977806_71977807delTT								CYB5A (18585 upstream) : FAM69C (125157 downstream)																																			---	---	---	---
CNDP2	55748	broad.mit.edu	37	18	72165296	72165296	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72165296delT	uc002llm.1	+						CNDP2_uc002lln.1_5'Flank|CNDP2_uc002llo.2_5'Flank	NM_018235	NP_060705			CNDP dipeptidase 2							cytoplasm	carboxypeptidase activity|metal ion binding|metallopeptidase activity|protein binding|tripeptidase activity			ovary(2)|skin(1)	3		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72641346	72641347	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72641346_72641347delAA	uc002llw.2	+							NM_017757	NP_060227			zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	72872066	72872066	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72872066delA								ZNF407 (94438 upstream) : ZADH2 (37213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73217032	73217033	+	IGR	DEL	TG	-	-	rs113744433		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73217032_73217033delTG								C18orf62 (77443 upstream) : ZNF516 (854586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73423146	73423146	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73423146delT	uc002lmc.2	-											Homo sapiens cDNA clone IMAGE:4830327.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73585411	73585411	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73585411delA								C18orf62 (445822 upstream) : ZNF516 (486208 downstream)																																			---	---	---	---
ZNF516	9658	broad.mit.edu	37	18	74138627	74138627	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74138627delA	uc010dqx.1	-						ZNF516_uc002lme.2_Intron	NM_014643	NP_055458			zinc finger protein 516						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)												OREG0025063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	18	74331233	74331234	+	IGR	INS	-	T	T	rs150995315	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74331233_74331234insT								LOC284276 (59450 upstream) : ZNF236 (204882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74504742	74504742	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74504742delT								LOC284276 (232959 upstream) : ZNF236 (31374 downstream)																																			---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74578380	74578380	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74578380delG	uc002lmi.2	+						ZNF236_uc002lmj.2_Intron|ZNF236_uc002lmk.1_Intron	NM_007345	NP_031371			zinc finger protein 236						cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	74913986	74913986	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74913986delT								MBP (69212 upstream) : GALR1 (48022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75103464	75103471	+	IGR	DEL	TGTGTGTA	-	-	rs57424535		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75103464_75103471delTGTGTGTA								GALR1 (121370 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76089988	76089990	+	IGR	DEL	GGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76089988_76089990delGGA								None (None upstream) : SALL3 (650285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76776475	76776476	+	IGR	INS	-	T	T	rs143149433	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76776475_76776476insT								SALL3 (18284 upstream) : ATP9B (52921 downstream)																																			---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77004435	77004435	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77004435delT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77030300	77030301	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77030300_77030301delCT	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	77519700	77519702	+	IGR	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77519700_77519702delTTT								CTDP1 (5193 upstream) : KCNG2 (103966 downstream)																																			---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77844692	77844692	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77844692delT	uc010dri.1	+											Homo sapiens hypothetical p38 protein mRNA, complete cds.						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)														---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	293103	293103	+	5'Flank	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:293103delG	uc002loi.2	-						PPAP2C_uc002loh.2_5'Flank|PPAP2C_uc002loj.2_5'Flank	NM_003712	NP_003703			phosphatidic acid phosphatase type 2C isoform 1						sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
FGF22	27006	broad.mit.edu	37	19	643528	643528	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:643528delG	uc010xfq.1	+	3	437	c.437delG	c.(436-438)AGGfs	p.R146fs	FGF22_uc010xfr.1_Frame_Shift_Del_p.E138fs	NM_020637	NP_065688	Q9HCT0	FGF22_HUMAN	fibroblast growth factor 22 precursor	146					cell differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	extracellular space	growth factor activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1992270	1992270	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1992270delT	uc002lup.1	-						BTBD2_uc002luo.1_5'Flank	NM_017797	NP_060267			BTB (POZ) domain containing 2							cytoplasmic mRNA processing body	protein binding			ovary(1)|skin(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)														---	---	---	---
TMPRSS9	360200	broad.mit.edu	37	19	2408818	2408819	+	Intron	DEL	AC	-	-	rs113151059		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2408818_2408819delAC	uc010xgx.1	+						TMPRSS9_uc002lvv.1_Intron	NM_182973	NP_892018			transmembrane protease, serine 9						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2				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)														---	---	---	---
ZNF556	80032	broad.mit.edu	37	19	2877213	2877213	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2877213delA	uc002lwp.1	+						ZNF556_uc002lwq.2_Intron	NM_024967	NP_079243			zinc finger protein 556						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				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)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3028804	3028804	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3028804delG	uc002lww.2	-						TLE2_uc010dth.2_Intron|TLE2_uc010xhc.1_Intron|TLE2_uc010dti.2_Intron|TLE2_uc010xhd.1_Intron	NM_003260	NP_003251			transducin-like enhancer protein 2 isoform 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				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)														---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3253100	3253100	+	Intron	DEL	A	-	-	rs112735398		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3253100delA	uc002lxm.2	+						CELF5_uc002lxl.1_Intron|CELF5_uc010dtj.1_Intron|CELF5_uc010xhg.1_Intron	NM_021938	NP_068757			bruno-like 5, RNA binding protein						mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
NFIC	4782	broad.mit.edu	37	19	3451182	3451183	+	Intron	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3451182_3451183delAG	uc010xhi.1	+						NFIC_uc002lxo.2_Intron|NFIC_uc010xhh.1_Intron|NFIC_uc002lxp.2_Intron|NFIC_uc010xhj.1_Intron	NM_205843	NP_995315			nuclear factor I/C isoform 2						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	3877037	3877037	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3877037delA								ZFR2 (8010 upstream) : ATCAY (3581 downstream)																																			---	---	---	---
ZBTB7A	51341	broad.mit.edu	37	19	4055299	4055299	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4055299delG	uc002lzh.2	-						ZBTB7A_uc002lzi.2_Intron	NM_015898	NP_056982			zinc finger and BTB domain containing 7A						cell differentiation|multicellular organismal development|transcription, DNA-dependent	nucleus	DNA binding|histone acetyltransferase binding|zinc ion binding			pancreas(1)|skin(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.014)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
CCDC94	55702	broad.mit.edu	37	19	4261827	4261827	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4261827delA	uc002lzv.3	+							NM_018074	NP_060544			coiled-coil domain containing 94												0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4709243	4709243	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4709243delT	uc002mba.2	-						DPP9_uc002mbb.2_Intron|DPP9_uc002mbc.2_Intron	NM_139159	NP_631898			dipeptidylpeptidase 9						proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)														---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5018860	5018860	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5018860delG	uc002mbq.3	+						KDM4B_uc010xil.1_Intron|KDM4B_uc010xim.1_Intron	NM_015015	NP_055830			jumonji domain containing 2B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5326801	5326804	+	Intron	DEL	GGAG	-	-	rs112523885	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5326801_5326804delGGAG	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841			protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
SAFB2	9667	broad.mit.edu	37	19	5587282	5587282	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5587282delG	uc002mcd.2	-	21	3046	c.2834delC	c.(2833-2835)CCGfs	p.P945fs		NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	945	Interacts with SAFB1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	7107400	7107401	+	IGR	INS	-	GAT	GAT	rs151257692	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7107400_7107401insGAT								ZNF557 (19424 upstream) : INSR (4865 downstream)																																			---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7484262	7484263	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7484262_7484263insT	uc010xjm.1	+						ARHGEF18_uc002mgh.2_Intron	NM_015318	NP_056133			Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)																---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7671043	7671043	+	Intron	DEL	C	-	-	rs71879481		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7671043delC	uc002mgv.3	+						KIAA1543_uc002mgu.3_Intron	NM_020902	NP_065953			NEZHA isoform 2						epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7676981	7676981	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7676981delG	uc002mgv.3	+	11	1703	c.1602delG	c.(1600-1602)GTGfs	p.V534fs	KIAA1543_uc002mgu.3_Frame_Shift_Del_p.V561fs|KIAA1543_uc002mgw.2_5'Flank	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	534	Pro-rich.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
ANGPTL4	51129	broad.mit.edu	37	19	8438288	8438288	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8438288delA	uc002mjq.1	+						ANGPTL4_uc002mjr.1_Intron|ANGPTL4_uc010xkc.1_Intron	NM_139314	NP_647475			angiopoietin-like 4 protein isoform a precursor						angiogenesis|cell differentiation|cellular lipid metabolic process|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|positive regulation of angiogenesis|response to hypoxia|signal transduction|triglyceride homeostasis	extracellular space|proteinaceous extracellular matrix	enzyme inhibitor activity|receptor binding			ovary(1)	1																		---	---	---	---
ACTL9	284382	broad.mit.edu	37	19	8808138	8808138	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8808138delG	uc002mkl.2	-	1	1035	c.914delC	c.(913-915)CCAfs	p.P305fs		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	actin-like 9	305						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9028055	9028063	+	Intron	DEL	AAAAAAAAA	-	-	rs34582719		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9028055_9028063delAAAAAAAAA	uc002mkp.2	-							NM_024690	NP_078966			mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
ZNF699	374879	broad.mit.edu	37	19	9408514	9408514	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9408514delT	uc002mlc.1	-							NM_198535	NP_940937			zinc finger protein 699						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF562	54811	broad.mit.edu	37	19	9768541	9768541	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9768541delT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504			zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10104574	10104574	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10104574delT	uc002mmq.1	-							NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10273296	10273301	+	Intron	DEL	GAAAAA	-	-	rs5827088		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10273296_10273301delGAAAAA	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron|DNMT1_uc002mnk.2_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10570559	10570559	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10570559delT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Intron	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
ATG4D	84971	broad.mit.edu	37	19	10659805	10659805	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10659805delT	uc002mov.2	+						ATG4D_uc010xlh.1_Intron|ATG4D_uc010dxh.2_Intron|ATG4D_uc010dxi.2_Intron|ATG4D_uc010dxj.2_Intron|MIR1238_hsa-mir-1238|MI0006328_5'Flank	NM_032885	NP_116274			APG4 autophagy 4 homolog D						autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)															---	---	---	---
CNN1	1264	broad.mit.edu	37	19	11658537	11658537	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11658537delA	uc002msc.1	+						CNN1_uc010xmb.1_Intron|CNN1_uc010xmc.1_Intron	NM_001299	NP_001290			calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11940914	11940914	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11940914delA	uc002msp.1	+							NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF878	729747	broad.mit.edu	37	19	12155504	12155504	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12155504delA	uc002mta.1	-	5	853	c.853delT	c.(853-855)TCTfs	p.S285fs		NM_001080404	NP_001073873	C9JN71	ZN878_HUMAN	zinc finger protein 878	238	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12410855	12410855	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12410855delA								ZNF44 (5141 upstream) : ZNF563 (17451 downstream)																																			---	---	---	---
CALR	811	broad.mit.edu	37	19	13050676	13050677	+	Intron	DEL	TT	-	-	rs111588637		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13050676_13050677delTT	uc002mvu.2	+							NM_004343	NP_004334			calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14555488	14555489	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14555488_14555489delAC	uc002myp.2	+						PKN1_uc002myq.2_Intron	NM_002741	NP_002732			protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
EMR2	30817	broad.mit.edu	37	19	14882844	14882844	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14882844delT	uc002mzp.1	-						EMR2_uc010xnw.1_Intron|EMR2_uc002mzo.1_Intron|EMR2_uc002mzq.1_Intron|EMR2_uc002mzr.1_Intron|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Intron|EMR2_uc002mzu.1_Intron|EMR2_uc010xnx.1_Intron|EMR2_uc010xny.1_Intron	NM_013447	NP_038475			egf-like module containing, mucin-like, hormone						cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	15594508	15594508	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15594508delC								PGLYRP2 (4193 upstream) : CYP4F22 (24828 downstream)																																			---	---	---	---
CYP4F2	8529	broad.mit.edu	37	19	16008641	16008642	+	Intron	INS	-	AGAG	AGAG	rs139783634	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16008641_16008642insAGAG	uc002nbs.1	-						CYP4F2_uc010xot.1_Intron|CYP4F2_uc010xou.1_Intron	NM_001082	NP_001073			cytochrome P450, family 4, subfamily F,						leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
CIB3	117286	broad.mit.edu	37	19	16275653	16275654	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16275653_16275654insC	uc002nds.2	-	5	417_418	c.417_418insG	c.(415-420)GGGCTGfs	p.G139fs	CIB3_uc010eae.2_Frame_Shift_Ins_p.G78fs|CIB3_uc010eaf.2_RNA|CIB3_uc010eag.2_Frame_Shift_Ins_p.G90fs	NM_054113	NP_473454	Q96Q77	CIB3_HUMAN	DNA-dependent protein kinase catalytic	139_140							calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	16405928	16405930	+	IGR	DEL	GGG	-	-	rs72237667	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16405928_16405930delGGG								AP1M1 (59772 upstream) : KLF2 (29721 downstream)																																			---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16594979	16594979	+	Intron	DEL	C	-	-	rs7252242	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16594979delC	uc002ned.2	-						MED26_uc002nee.2_Intron	NM_145046	NP_659483			calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16872616	16872616	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16872616delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17012123	17012124	+	Intron	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17012123_17012124delGA	uc002nfb.2	-						CPAMD8_uc002nfd.1_Intron	NM_015692	NP_056507			C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17119514	17119514	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17119514delA	uc002nfb.2	-							NM_015692	NP_056507			C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
HAUS8	93323	broad.mit.edu	37	19	17170524	17170524	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17170524delT	uc002nfe.2	-						HAUS8_uc002nff.2_Intron|HAUS8_uc002nfg.1_Intron|HAUS8_uc002nfh.1_Intron	NM_033417	NP_219485			sarcoma antigen NY-SAR-48 isoform a						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole					0																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17753825	17753827	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17753825_17753827delTTT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17759613	17759614	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17759613_17759614delCA	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
IL12RB1	3594	broad.mit.edu	37	19	18193320	18193320	+	Intron	DEL	T	-	-	rs17884870		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18193320delT	uc002nhw.1	-						IL12RB1_uc010xqb.1_Intron|IL12RB1_uc002nhx.1_Intron|IL12RB1_uc002nhy.2_Intron	NM_005535	NP_005526			interleukin 12 receptor, beta 1 isoform 1						cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1																		---	---	---	---
PIK3R2	5296	broad.mit.edu	37	19	18271260	18271260	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18271260delC	uc002nia.1	+						PIK3R2_uc002nib.1_Intron|PIK3R2_uc010ebi.1_Intron	NM_005027	NP_005018			phosphoinositide-3-kinase, regulatory subunit 2						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|negative regulation of anti-apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	GTPase activator activity|phosphatidylinositol 3-kinase regulator activity|protein binding			lung(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
KLHL26	55295	broad.mit.edu	37	19	18779306	18779306	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18779306delG	uc002njz.1	+	3	1126	c.1099delG	c.(1099-1101)GGGfs	p.G367fs		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	367	Kelch 2.									ovary(1)	1																		---	---	---	---
SFRS14	10147	broad.mit.edu	37	19	19121949	19121950	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19121949_19121950delAA	uc002nkx.2	-						SFRS14_uc002nkz.1_Intron|SFRS14_uc002nla.1_Intron|SFRS14_uc002nlb.2_Intron|SFRS14_uc010xqk.1_Intron	NM_014884	NP_055699			splicing factor, arginine/serine-rich 14						mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)															---	---	---	---
ARMC6	93436	broad.mit.edu	37	19	19162185	19162188	+	Intron	DEL	TGTG	-	-	rs72199956		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19162185_19162188delTGTG	uc002nld.2	+						ARMC6_uc002nlc.2_Intron|ARMC6_uc010xql.1_Intron|ARMC6_uc002nle.2_Intron|ARMC6_uc010xqm.1_Intron	NM_033415	NP_219483			armadillo repeat containing 6								protein binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.66e-06)|Epithelial(12;0.000391)															---	---	---	---
GATAD2A	54815	broad.mit.edu	37	19	19617424	19617426	+	3'UTR	DEL	TTT	-	-	rs71739499		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19617424_19617426delTTT	uc010xqt.1	+	12					GATAD2A_uc010xqu.1_3'UTR|GATAD2A_uc010xqv.1_3'UTR|GATAD2A_uc010xqw.1_3'UTR	NM_017660	NP_060130			GATA zinc finger domain containing 2A						DNA methylation|negative regulation of transcription, DNA-dependent	nuclear speck|NuRD complex	protein binding, bridging|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19749401	19749401	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19749401delT	uc002nnd.2	-						GMIP_uc010xrb.1_Intron|GMIP_uc010xrc.1_Intron	NM_016573	NP_057657			GEM interacting protein						negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	21416501	21416501	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21416501delA								ZNF431 (47696 upstream) : ZNF708 (57462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23061761	23061761	+	IGR	DEL	A	-	-	rs139049580		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23061761delA								ZNF99 (108977 upstream) : ZNF91 (459658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23242987	23242988	+	RNA	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23242987_23242988insT	uc002nra.2	-	3		c.578_579insA								Homo sapiens cDNA clone IMAGE:5273406.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	24070559	24070559	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24070559delG								RPSAP58 (59642 upstream) : ZNF254 (145688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27866349	27866349	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27866349delT								None (None upstream) : LOC148189 (415053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27870888	27870889	+	IGR	INS	-	T	T	rs71243293		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27870888_27870889insT								None (None upstream) : LOC148189 (410513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28447093	28447093	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28447093delT								LOC148189 (162245 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29534962	29534963	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29534962_29534963insT								LOC148145 (74907 upstream) : UQCRFS1 (163204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30326994	30326995	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30326994_30326995insA								CCNE1 (11776 upstream) : C19orf2 (87556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31247310	31247310	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31247310delT								ZNF536 (198345 upstream) : DKFZp566F0947 (393473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31557735	31557735	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31557735delG								ZNF536 (508770 upstream) : DKFZp566F0947 (83048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32046784	32046784	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32046784delA								TSHZ3 (206594 upstream) : ZNF507 (789730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32618793	32618794	+	IGR	DEL	AG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32618793_32618794delAG								TSHZ3 (778603 upstream) : ZNF507 (217720 downstream)																																			---	---	---	---
DPY19L3	147991	broad.mit.edu	37	19	32927217	32927217	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32927217delT	uc002ntg.2	+						DPY19L3_uc002nth.1_Intron|DPY19L3_uc002nti.1_5'Flank	NM_207325	NP_997208			dpy-19-like 3							integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33549072	33549072	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33549072delA	uc002nuf.2	-						RHPN2_uc010xro.1_Intron	NM_033103	NP_149094			rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34934950	34934952	+	Intron	DEL	TTT	-	-	rs34669674		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34934950_34934952delTTT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490			SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
USF2	7392	broad.mit.edu	37	19	35761958	35761959	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35761958_35761959insC	uc002nyq.1	+						USF2_uc010xss.1_Intron|USF2_uc002nyr.1_Intron|USF2_uc002nys.1_Intron|USF2_uc002nyt.1_Intron|USF2_uc002nyu.1_Intron|USF2_uc002nyv.1_Intron	NM_003367	NP_003358			upstream stimulatory factor 2 isoform 1						lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose	nucleus	bHLH transcription factor binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity				0	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
ZNF527	84503	broad.mit.edu	37	19	37868937	37868938	+	Intron	DEL	TT	-	-	rs111409931		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37868937_37868938delTT	uc010efk.1	+						ZNF527_uc002ogf.3_Intron|ZNF527_uc010xtq.1_Intron|ZNF527_uc002oge.2_Intron	NM_032453	NP_115829			zinc finger protein 527						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZFP30	22835	broad.mit.edu	37	19	38127290	38127292	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38127290_38127292delAAA	uc002ogv.1	-						ZFP30_uc002ogw.1_Intron|ZFP30_uc002ogx.1_Intron|ZFP30_uc010xtt.1_Intron	NM_014898	NP_055713			zinc finger protein 30 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	38345678	38345679	+	Intron	INS	-	AC	AC	rs139496768	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38345678_38345679insAC	uc002ohi.2	-											Homo sapiens similar to RIKEN cDNA 4930432E11, mRNA (cDNA clone IMAGE:5164439), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	38375469	38375469	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38375469delA								ZNF573 (67529 upstream) : WDR87 (3 downstream)																																			---	---	---	---
DLL3	10683	broad.mit.edu	37	19	39991061	39991061	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39991061delC	uc002olx.2	+						DLL3_uc010egq.2_Intron|DLL3_uc002olw.2_Intron	NM_016941	NP_058637			delta-like 3 protein isoform 1 precursor						Notch signaling pathway|skeletal system development	integral to membrane	Notch binding			central_nervous_system(2)|breast(1)	3	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	40341611	40341611	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40341611delC								FBL (4557 upstream) : FCGBP (12353 downstream)																																			---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40369430	40369431	+	Intron	INS	-	C	C	rs61233386		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40369430_40369431insC	uc002omp.3	-							NM_003890	NP_003881			Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40435838	40435838	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40435838delA	uc002omp.3	-							NM_003890	NP_003881			Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	42107414	42107415	+	IGR	DEL	CA	-	-	rs72172011		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42107414_42107415delCA								CEACAM21 (14218 upstream) : CEACAM4 (17929 downstream)																																			---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42858271	42858273	+	Intron	DEL	TTT	-	-	rs36065839		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42858271_42858273delTTT	uc002otl.3	+						MEGF8_uc002otm.3_Intron	NM_001410	NP_001401			multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
PSG11	5680	broad.mit.edu	37	19	43400684	43400684	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43400684delT	uc002ouw.2	-						PSG3_uc002ouf.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron					RecName: Full=Pregnancy-specific beta-1-glycoprotein 11;          Short=PSBG-11; AltName: Full=Pregnancy-specific beta-1-glycoprotein 13;          Short=PSBG-13; Flags: Precursor;						female pregnancy	extracellular region					0		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43550880	43550880	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43550880delT	uc002ovi.2	-						PSG10_uc002ouv.1_Intron|PSG6_uc010xwk.1_Intron					SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43556931	43556931	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43556931delA	uc002ovi.2	-						PSG10_uc002ouv.1_Intron|PSG6_uc010xwk.1_Intron					SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
CADM4	199731	broad.mit.edu	37	19	44127432	44127432	+	3'UTR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44127432delG	uc002oxc.1	-	9						NM_145296	NP_660339			cell adhesion molecule 4 precursor						cell adhesion	integral to membrane					0		Prostate(69;0.0199)																---	---	---	---
ZNF283	284349	broad.mit.edu	37	19	44335689	44335689	+	Intron	DEL	A	-	-	rs144360678		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44335689delA	uc002oxr.3	+						ZNF283_uc002oxp.3_Intron	NM_181845	NP_862828			zinc finger protein 283						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF180	7733	broad.mit.edu	37	19	44998423	44998423	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44998423delC	uc002ozf.3	-						ZNF180_uc002ozh.3_Intron|ZNF180_uc002ozi.3_Intron|ZNF180_uc002ozg.3_Intron|ZNF180_uc010ejm.2_Intron	NM_013256	NP_037388			zinc finger protein 180						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	45090348	45090348	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45090348delT								CEACAM22P (30198 upstream) : PVR (56750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45265782	45265782	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45265782delT								BCL3 (2482 upstream) : CBLC (15344 downstream)																																			---	---	---	---
SFRS16	11129	broad.mit.edu	37	19	45555226	45555226	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45555226delA	uc002pak.2	+						SFRS16_uc002pal.2_Intron|SFRS16_uc010xxh.1_Intron|SFRS16_uc002pam.2_Intron|SFRS16_uc002pan.1_Intron	NM_007056	NP_008987			splicing factor, arginine/serine-rich 16						mRNA processing|RNA splicing	nucleus					0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45833506	45833507	+	IGR	DEL	TT	-	-	rs71338768		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45833506_45833507delTT								CKM (7372 upstream) : KLC3 (10491 downstream)																																			---	---	---	---
CCDC61	729440	broad.mit.edu	37	19	46513075	46513076	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46513075_46513076delTG	uc002pdw.2	+							NM_001080402	NP_001073871			coiled-coil domain containing 61											ovary(1)	1		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)												OREG0025564	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	19	47002572	47002575	+	IGR	DEL	TGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47002572_47002575delTGTG								PNMAL2 (3403 upstream) : CALM3 (101937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	47339839	47339842	+	IGR	DEL	AAGG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47339839_47339842delAAGG								SNAR-E (5878 upstream) : AP2S1 (1581 downstream)																																			---	---	---	---
SULT2B1	6820	broad.mit.edu	37	19	49094730	49094730	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49094730delA	uc002pjl.2	+						SULT2B1_uc002pjm.2_Intron	NM_177973	NP_814444			sulfotransferase family, cytosolic, 2B, member 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	alcohol sulfotransferase activity|protein binding|steroid sulfotransferase activity			skin(1)	1		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)														---	---	---	---
NUCB1	4924	broad.mit.edu	37	19	49407785	49407785	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49407785delT	uc002plb.3	+						NUCB1_uc002pla.2_Intron|NUCB1_uc002plc.2_Intron	NM_006184	NP_006175			nucleobindin 1 precursor							ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|membrane|microtubule cytoskeleton	calcium ion binding|DNA binding				0		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)														---	---	---	---
FCGRT	2217	broad.mit.edu	37	19	50017856	50017856	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50017856delC	uc002poe.2	+						FCGRT_uc002pod.2_Intron|FCGRT_uc002pog.2_Intron|FCGRT_uc002pof.1_Intron|FCGRT_uc010yax.1_Intron|FCGRT_uc002poh.1_Intron	NM_001136019	NP_001129491			Fc fragment of IgG, receptor, transporter, alpha						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)														---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50102453	50102453	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50102453delT	uc002poo.3	+							NM_020719	NP_065770			proline rich 12								DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)														---	---	---	---
FLJ26850	400710	broad.mit.edu	37	19	50556008	50556014	+	Intron	DEL	AAAAAAA	-	-	rs35329221		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50556008_50556014delAAAAAAA	uc002pro.2	+							NR_027257				Homo sapiens cDNA FLJ26850 fis, clone PRS07964.												0																		---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50880753	50880753	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50880753delA	uc010enw.2	+						NR1H2_uc002prv.3_Intron|NR1H2_uc002prz.3_Intron|NR1H2_uc002psa.3_Intron	NM_007121	NP_009052			nuclear receptor subfamily 1, group H, member 2						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
C19orf63	284361	broad.mit.edu	37	19	50985132	50985132	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50985132delG	uc002psl.2	+						C19orf63_uc002psj.2_Intron|C19orf63_uc002psk.2_Frame_Shift_Del_p.L231fs	NM_206538	NP_996261			hematopoietic signal peptide-containing isoform							extracellular region|integral to membrane					0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00733)|GBM - Glioblastoma multiforme(134;0.0252)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51353908	51353909	+	IGR	INS	-	A	A	rs57268074		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51353908_51353909insA								KLK15 (19129 upstream) : KLK3 (4262 downstream)																																			---	---	---	---
SIGLEC9	27180	broad.mit.edu	37	19	51629582	51629582	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51629582delC	uc002pvu.2	+						SIGLEC9_uc010yct.1_Intron	NM_014441	NP_055256			sialic acid binding Ig-like lectin 9 precursor						cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52682278	52682278	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52682278delT								ZNF836 (7382 upstream) : PPP2R1A (10913 downstream)																																			---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53121520	53121521	+	5'Flank	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53121520_53121521delTT	uc002pzu.3	-						ZNF83_uc002pzv.3_Intron|ZNF83_uc010eps.2_Intron|ZNF83_uc010ept.2_Intron|ZNF83_uc010epu.2_Intron|ZNF83_uc010epv.2_Intron|ZNF83_uc010epw.2_Intron|ZNF83_uc010epx.2_Intron|ZNF83_uc010epy.2_Intron|ZNF83_uc010epz.2_Intron|ZNF83_uc010eqb.1_Intron	NM_018300	NP_060770			zinc finger protein 83 isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)														---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53188049	53188049	+	Intron	DEL	A	-	-	rs7250433	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53188049delA	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024			zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)														---	---	---	---
ZNF331	55422	broad.mit.edu	37	19	54062202	54062203	+	Intron	INS	-	ACAA	ACAA	rs74465035		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54062202_54062203insACAA	uc002qbx.1	+						ZNF331_uc002qby.1_Intron|ZNF331_uc002qbz.1_Intron|ZNF331_uc002qca.1_Intron|ZNF331_uc010eqr.1_Intron|ZNF331_uc002qcb.1_Intron|ZNF331_uc002qcc.1_Intron|ZNF331_uc002qcd.1_Intron	NM_018555	NP_061025			zinc finger protein 331						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)				T	?	follicular thyroid adenoma								---	---	---	---
MIR512-2	574459	broad.mit.edu	37	19	54172143	54172143	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54172143delA	hsa-mir-512-2|MI0003141	+																							0																		---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54308714	54308714	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54308714delA	uc002qch.3	-						NLRP12_uc010eqw.2_Intron|NLRP12_uc002qci.3_Intron|NLRP12_uc002qcj.3_Intron|NLRP12_uc002qck.3_Intron|NLRP12_uc010eqx.2_Intron	NM_144687	NP_653288			NLR family, pyrin domain containing 12 isoform						negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
MBOAT7	79143	broad.mit.edu	37	19	54692246	54692246	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54692246delC	uc002qdq.2	-						MBOAT7_uc010erg.2_5'Flank|MBOAT7_uc010yem.1_5'Flank|MBOAT7_uc002qdr.2_Intron|MBOAT7_uc002qds.2_Intron|MBOAT7_uc010yen.1_Intron|MBOAT7_uc002qdt.3_Intron|TSEN34_uc010yeo.1_5'Flank|TSEN34_uc002qdu.2_5'Flank|TSEN34_uc002qdv.2_5'Flank|TSEN34_uc002qdw.2_5'Flank	NM_024298	NP_077274			membrane bound O-acyltransferase domain						phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
LILRB3	11025	broad.mit.edu	37	19	54726701	54726702	+	Intron	INS	-	TCC	TCC			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54726701_54726702insTCC	uc002qef.1	-						LILRB3_uc002qee.1_Intron|LILRB3_uc002qeh.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qei.1_Intron|LILRA6_uc002qek.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Intron|LILRA6_uc002qem.1_Intron|LILRB3_uc002qen.1_Intron|LILRB3_uc002qeo.1_Intron|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Intron|LILRB3_uc002qer.1_Intron|LILRB3_uc002qes.1_Intron|LILRA6_uc010yep.1_Intron|LILRA6_uc010yeq.1_Intron	NM_006864	NP_006855			leukocyte immunoglobulin-like receptor,						cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	transmembrane receptor activity			skin(2)|ovary(1)	3	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54920078	54920078	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54920078delA								LAIR1 (37914 upstream) : TTYH1 (6557 downstream)																																			---	---	---	---
LENG8	114823	broad.mit.edu	37	19	54972802	54972802	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54972802delT	uc002qfw.2	+	16						NM_052925	NP_443157			leukocyte receptor cluster member 8								protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	56075514	56075515	+	IGR	INS	-	C	C	rs143539582	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56075514_56075515insC								SBK2 (27853 upstream) : ZNF579 (13377 downstream)																																			---	---	---	---
GALP	85569	broad.mit.edu	37	19	56694776	56694776	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56694776delT	uc002qmo.1	+						GALP_uc010eti.2_Intron	NM_033106	NP_149097			galanin-like peptide isoform 1 precursor						neuropeptide signaling pathway	extracellular region	hormone activity				0		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)														---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56769930	56769931	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56769930_56769931delAC	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279			zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	57529219	57529219	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57529219delC								MIMT1 (169297 upstream) : USP29 (102290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	57560939	57560939	+	IGR	DEL	T	-	-	rs35624233		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57560939delT								MIMT1 (201017 upstream) : USP29 (70570 downstream)																																			---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58723517	58723517	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58723517delT	uc002qrq.1	+						ZNF274_uc002qrr.1_Intron|ZNF274_uc002qrs.1_Intron|ZNF274_uc010eum.1_Intron	NM_133502	NP_598009			zinc finger protein 274 isoform c						viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58782968	58782968	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58782968delA	uc002qrx.1	-											Homo sapiens cDNA FLJ32483 fis, clone SKNMC2001503, weakly similar to P-SELECTIN GLYCOPROTEIN LIGAND 1 PRECURSOR.																														---	---	---	---
A1BG	1	broad.mit.edu	37	19	58870088	58870088	+	Intron	DEL	G	-	-	rs11332731		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58870088delG	uc002qsf.1	-						ZNF497_uc002qsh.1_Intron|ZNF497_uc002qsi.1_Intron|uc002qsk.1_Frame_Shift_Del_p.G20fs					Homo sapiens primary hepatoblastoma mRNA for alpha-1-B glycoprotein precursor, partial cds, clone:HYST2477.							extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)														---	---	---	---
SCRT2	85508	broad.mit.edu	37	20	655370	655377	+	Intron	DEL	TGTGTGTA	-	-	rs10580472	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:655370_655377delTGTGTGTA	uc002wec.2	-						SRXN1_uc002web.2_Intron	NM_033129	NP_149120			scratch 2 protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	900979	900979	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:900979delT								ANGPT4 (4019 upstream) : RSPO4 (38119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1713705	1713705	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1713705delT								SIRPG (75280 upstream) : SIRPA (161108 downstream)																																			---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1894522	1894522	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1894522delC	uc002wfq.2	+						SIRPA_uc010zps.1_Intron|SIRPA_uc002wfr.2_Intron|SIRPA_uc002wfs.2_Intron|SIRPA_uc002wft.2_Intron	NM_001040022	NP_001035111			signal-regulatory protein alpha precursor						blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	2056532	2056532	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2056532delA								PDYN (81829 upstream) : STK35 (25996 downstream)																																			---	---	---	---
VPS16	64601	broad.mit.edu	37	20	2835935	2835936	+	Intron	DEL	TT	-	-	rs111722933		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2835935_2835936delTT	uc002whe.2	+						VPS16_uc002whf.2_Intron|VPS16_uc002whd.2_Intron	NM_022575	NP_072097			vacuolar protein sorting 16 isoform 1						intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2977851	2977851	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2977851delT	uc010zqd.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron|PTPRA_uc002who.2_Intron	NM_002836	NP_002827			protein tyrosine phosphatase, receptor type, A						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3313541	3313542	+	Intron	DEL	GC	-	-	rs11468887		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3313541_3313542delGC	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron|C20orf194_uc010gay.1_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3577009	3577009	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3577009delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3600626	3600626	+	Intron	DEL	A	-	-	rs2252335	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3600626delA	uc002wim.2	+							NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
SIGLEC1	6614	broad.mit.edu	37	20	3686964	3686964	+	Intron	DEL	G	-	-	rs73893084	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3686964delG	uc002wja.2	-						SIGLEC1_uc002wiz.3_Intron|SIGLEC1_uc002wjc.2_Intron	NM_023068	NP_075556			sialoadhesin precursor						cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10																		---	---	---	---
PANK2	80025	broad.mit.edu	37	20	3888393	3888393	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3888393delT	uc002wkc.2	+						PANK2_uc002wkb.2_Intron|PANK2_uc010gbd.1_Intron|PANK2_uc002wkd.2_Intron|PANK2_uc002wke.2_Intron|PANK2_uc002wkf.2_Intron	NM_153638	NP_705902			pantothenate kinase 2 isoform 1 preproprotein						cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4261287	4261287	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4261287delT								ADRA1D (31628 upstream) : PRNP (405510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4454324	4454324	+	IGR	DEL	A	-	-	rs75904231		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4454324delA								ADRA1D (224665 upstream) : PRNP (212473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4726386	4726386	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4726386delA								PRNT (5072 upstream) : RASSF2 (34284 downstream)																																			---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4798258	4798258	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4798258delA	uc002wld.2	-						RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron	NM_170774	NP_739580			Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4945478	4945479	+	Intron	INS	-	AA	AA	rs10639211		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4945478_4945479insAA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4945546	4945546	+	Intron	DEL	A	-	-	rs11087663		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4945546delA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5037337	5037337	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5037337delA								SLC23A2 (46398 upstream) : C20orf30 (11793 downstream)																																			---	---	---	---
CDS2	8760	broad.mit.edu	37	20	5165357	5165357	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5165357delT	uc002wls.2	+						CDS2_uc002wlr.1_Intron|CDS2_uc010zqt.1_Intron|CDS2_uc002wlu.2_Intron|CDS2_uc010zqu.1_Intron|CDS2_uc002wlv.2_Intron|CDS2_uc010zqv.1_Intron	NM_003818	NP_003809			phosphatidate cytidylyltransferase 2						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5272907	5272907	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5272907delA								CDS2 (100920 upstream) : PROKR2 (9780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5393549	5393549	+	IGR	DEL	G	-	-	rs148714875		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5393549delG								PROKR2 (96171 upstream) : LOC149837 (85669 downstream)																																			---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5545802	5545802	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5545802delA	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5545874	5545876	+	Intron	DEL	TTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5545874_5545876delTTT	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5963899	5963899	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5963899delA	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_Intron	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5969108	5969109	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5969108_5969109delAA	uc002wmi.2	+						MCM8_uc002wmj.2_Intron|MCM8_uc002wmk.2_Intron|MCM8_uc002wml.2_Intron|MCM8_uc010gbp.2_Intron|MCM8_uc002wmm.2_Intron	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5975125	5975126	+	3'UTR	DEL	AC	-	-	rs145346371		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5975125_5975126delAC	uc002wmi.2	+	19					MCM8_uc002wmj.2_3'UTR|MCM8_uc002wmk.2_3'UTR|MCM8_uc002wml.2_3'UTR|MCM8_uc010gbp.2_3'UTR|MCM8_uc002wmm.2_3'UTR	NM_032485	NP_115874			minichromosome maintenance complex component 8						cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
FERMT1	55612	broad.mit.edu	37	20	6060958	6060959	+	Intron	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6060958_6060959delTG	uc002wmr.2	-						FERMT1_uc002wmq.2_Intron|FERMT1_uc010gbt.2_Intron	NM_017671	NP_060141			kindlin-1						cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
FERMT1	55612	broad.mit.edu	37	20	6078081	6078081	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6078081delA	uc002wmr.2	-						FERMT1_uc010gbt.2_Intron|FERMT1_uc002wms.2_Intron|FERMT1_uc002wmt.2_Intron	NM_017671	NP_060141			kindlin-1						cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	10887039	10887039	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10887039delC								JAG1 (232345 upstream) : BTBD3 (984438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10904165	10904165	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10904165delA								JAG1 (249471 upstream) : BTBD3 (967312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10957607	10957608	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10957607_10957608delTG								JAG1 (302913 upstream) : BTBD3 (913869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11008995	11008995	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11008995delT								JAG1 (354301 upstream) : BTBD3 (862482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11057522	11057522	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11057522delA								JAG1 (402828 upstream) : BTBD3 (813955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11146076	11146076	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11146076delA								JAG1 (491382 upstream) : BTBD3 (725401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11677916	11677916	+	IGR	DEL	G	-	-	rs73615526		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11677916delG								None (None upstream) : BTBD3 (193561 downstream)																																			---	---	---	---
C20orf7	79133	broad.mit.edu	37	20	13789596	13789596	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13789596delA	uc002wom.2	+						C20orf7_uc002won.2_Intron|C20orf7_uc002woo.2_Intron	NM_024120	NP_077025			hypothetical protein LOC79133 isoform 1						mitochondrial respiratory chain complex I assembly	extrinsic to mitochondrial inner membrane	methyltransferase activity				0		Myeloproliferative disorder(85;0.00878)																---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13849643	13849643	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13849643delT	uc010gcf.2	-						SEL1L2_uc002woq.3_Intron|SEL1L2_uc010zrl.1_Intron|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505			sel-1 suppressor of lin-12-like 2 precursor							integral to membrane	binding			ovary(2)	2																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	13992177	13992177	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13992177delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wos.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14704038	14704038	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14704038delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wox.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15291859	15291859	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15291859delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16698488	16698488	+	IGR	DEL	A	-	-	rs72316695		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16698488delA								KIF16B (144410 upstream) : SNRPB2 (12141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	18332940	18332940	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18332940delT	uc002wqn.2	-											Homo sapiens cDNA clone IMAGE:5296922.																														---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19636040	19636040	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19636040delA	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19979923	19979923	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19979923delA	uc002wro.1	+						RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20317987	20317990	+	Intron	DEL	TGGG	-	-	rs138008701	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20317987_20317990delTGGG	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20668959	20668960	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20668959_20668960delAA	uc002wrz.2	-						RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20673343	20673343	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20673343delT	uc002wrz.2	-						RALGAPA2_uc010zsg.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	20864704	20864704	+	IGR	DEL	G	-	-	rs6047125	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20864704delG								RALGAPA2 (171438 upstream) : PLK1S1 (241920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21604269	21604270	+	IGR	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21604269_21604270delCT								NKX2-2 (109605 upstream) : PAX1 (82027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22123915	22123915	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22123915delT								PAX1 (427295 upstream) : LOC284788 (257056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22232194	22232194	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22232194delT								PAX1 (535574 upstream) : LOC284788 (148777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22327455	22327455	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22327455delA								PAX1 (630835 upstream) : LOC284788 (53516 downstream)																																			---	---	---	---
NAPB	63908	broad.mit.edu	37	20	23356142	23356144	+	3'UTR	DEL	TAT	-	-	rs148611575		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23356142_23356144delTAT	uc002wta.2	-	11					NAPB_uc002wtc.2_3'UTR|NAPB_uc002wtb.2_3'UTR|NAPB_uc002wtd.3_RNA	NM_022080	NP_071363			N-ethylmaleimide-sensitive factor attachment						intracellular protein transport|vesicle-mediated transport	membrane				ovary(1)	1	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	23755579	23755580	+	IGR	INS	-	G	G	rs144621360	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23755579_23755580insG								CST1 (24005 upstream) : CST2 (48824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23921925	23921925	+	IGR	DEL	A	-	-	rs6114377	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23921925delA								CST5 (61545 upstream) : GGTLC1 (43766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24228788	24228788	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24228788delA								GGTLC1 (259372 upstream) : TMEM90B (221047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24416121	24416124	+	IGR	DEL	GTGT	-	-	rs34710477		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24416121_24416124delGTGT								GGTLC1 (446705 upstream) : TMEM90B (33711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24745885	24745886	+	IGR	DEL	AC	-	-	rs34141414		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24745885_24745886delAC								TMEM90B (98718 upstream) : CST7 (183980 downstream)																																			---	---	---	---
ABHD12	26090	broad.mit.edu	37	20	25319642	25319642	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25319642delT	uc002wus.1	-						ABHD12_uc002wuq.2_Intron|ABHD12_uc002wur.2_Intron|ABHD12_uc002wut.1_Intron|ABHD12_uc002wuu.1_Intron	NM_001042472	NP_001035937			abhydrolase domain containing 12 isoform a							integral to membrane	acylglycerol lipase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25736314	25736315	+	IGR	DEL	TT	-	-	rs79313128		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25736314_25736315delTT								ZNF337 (58845 upstream) : FAM182B (7787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25868161	25868161	+	IGR	DEL	A	-	-	rs74495154		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25868161delA								FAM182B (19375 upstream) : LOC100134868 (122274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25876583	25876583	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25876583delG								FAM182B (27797 upstream) : LOC100134868 (113852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26128191	26128192	+	IGR	INS	-	AT	AT	rs111751436		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26128191_26128192insAT								C20orf191 (33514 upstream) : MIR663 (60630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29581395	29581395	+	IGR	DEL	G	-	-	rs113529972		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29581395delG								None (None upstream) : FRG1B (30484 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29617843	29617844	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29617843_29617844insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	30041900	30041900	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30041900delA								DEFB123 (3841 upstream) : DEFB124 (11409 downstream)																																			---	---	---	---
XKR7	343702	broad.mit.edu	37	20	30567025	30567026	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30567025_30567026delTT	uc002wxe.2	+							NM_001011718	NP_001011718			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|breast(1)|skin(1)	3			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	31400711	31400711	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31400711delT								DNMT3B (3550 upstream) : MAPRE1 (6988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	31454262	31454262	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31454262delA	uc010zub.1	+							NM_001143967	NP_001137439			EF-hand calcium binding domain 8																														---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32140720	32140720	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32140720delT	uc002wze.1	+						CBFA2T2_uc010zug.1_Intron	NM_001032999	NP_001028171			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
CHMP4B	128866	broad.mit.edu	37	20	32419701	32419701	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32419701delT	uc002xaa.2	+							NM_176812	NP_789782			chromatin modifying protein 4B						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32455330	32455332	+	IGR	DEL	AGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32455330_32455332delAGA								CHMP4B (13161 upstream) : RALY (126400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	32808401	32808402	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32808401_32808402delAA								EIF2S2 (108316 upstream) : ASIP (39769 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33001769	33001769	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33001769delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34089644	34089648	+	Intron	DEL	CCTCT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34089644_34089648delCCTCT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34096147	34096147	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34096147delT	uc002xcm.2	+						CEP250_uc010zve.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
FER1L4	80307	broad.mit.edu	37	20	34185762	34185762	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34185762delT	uc002xcy.3	-							NR_024377				Homo sapiens clone PP3795 unknown mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	34341658	34341660	+	IGR	DEL	AAA	-	-	rs79208525		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34341658_34341660delAAA								RBM39 (11465 upstream) : PHF20 (18263 downstream)																																			---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34459558	34459558	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34459558delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	34643225	34643225	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34643225delT								LOC647979 (4343 upstream) : EPB41L1 (36201 downstream)																																			---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35668766	35668766	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35668766delT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
SRC	6714	broad.mit.edu	37	20	36030406	36030406	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36030406delT	uc002xgx.2	+						SRC_uc002xgy.2_Intron	NM_005417	NP_005408			proto-oncogene tyrosine-protein kinase SRC						axon guidance|bone resorption|cell junction assembly|cellular membrane organization|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular protein kinase cascade|leukocyte migration|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of integrin activation|Ras protein signal transduction|regulation of bone resorption|regulation of vascular permeability|response to interleukin-1|signal complex assembly|T cell costimulation	caveola|cytosol|mitochondrial inner membrane	ATP binding|heme binding|integrin binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|SH3/SH2 adaptor activity			large_intestine(10)|lung(1)|central_nervous_system(1)|endometrium(1)	13		Myeloproliferative disorder(115;0.00878)			Dasatinib(DB01254)													---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36352717	36352717	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36352717delA	uc010zvw.1	+						CTNNBL1_uc010zvv.1_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
DHX35	60625	broad.mit.edu	37	20	37598717	37598720	+	Intron	DEL	TCTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37598717_37598720delTCTG	uc002xjh.2	+						DHX35_uc010zwa.1_Intron|DHX35_uc010zwb.1_Intron|DHX35_uc010zwc.1_Intron	NM_021931	NP_068750			DEAH (Asp-Glu-Ala-His) box polypeptide 35							catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	38048294	38048294	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38048294delT								LOC339568 (194903 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38903738	38903739	+	IGR	DEL	TG	-	-	rs67943649		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38903738_38903739delTG								None (None upstream) : MAFB (410780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39537585	39537588	+	IGR	DEL	AAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39537585_39537588delAAAA								MAFB (219709 upstream) : TOP1 (119874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40271015	40271015	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40271015delA								CHD6 (23882 upstream) : PTPRT (430378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40655401	40655402	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40655401_40655402delTG								CHD6 (408268 upstream) : PTPRT (45991 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41305179	41305184	+	Intron	DEL	CTCTCT	-	-	rs67125859		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41305179_41305184delCTCTCT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41306344	41306344	+	Intron	DEL	C	-	-	rs2425514	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41306344delC	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
HNF4A	3172	broad.mit.edu	37	20	43047140	43047140	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43047140delG	uc002xma.2	+	6	813	c.724delG	c.(724-726)GTGfs	p.V242fs	HNF4A_uc002xlt.2_Frame_Shift_Del_p.V220fs|HNF4A_uc002xlu.2_Frame_Shift_Del_p.V220fs|HNF4A_uc002xlv.2_Frame_Shift_Del_p.V220fs|HNF4A_uc002xly.2_Frame_Shift_Del_p.V242fs|HNF4A_uc002xlz.2_Frame_Shift_Del_p.V242fs|HNF4A_uc010ggq.2_Frame_Shift_Del_p.V235fs	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	242					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43132289	43132289	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43132289delA	uc002xme.2	-						SERINC3_uc002xmf.1_Intron|SERINC3_uc010ggs.1_Intron|SERINC3_uc010zwp.1_Intron	NM_198941	NP_945179			tumor differentially expressed protein 1							integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43162324	43162324	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43162324delA	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521			cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
RIMS4	140730	broad.mit.edu	37	20	43402662	43402662	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43402662delT	uc002xms.2	-						RIMS4_uc010ggu.2_Intron	NM_182970	NP_892015			regulating synaptic membrane exocytosis 4						exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
YWHAB	7529	broad.mit.edu	37	20	43535144	43535153	+	3'UTR	DEL	ATAAAAAAAA	-	-	rs11468357		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43535144_43535153delATAAAAAAAA	uc002xmt.2	+	7					YWHAB_uc002xmu.2_3'UTR	NM_003404	NP_003395			tyrosine 3-monooxygenase/tryptophan						activation of MAPKK activity|activation of pro-apoptotic gene products|axon guidance|cytoplasmic sequestering of protein|epidermal growth factor receptor signaling pathway|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|mRNA metabolic process|negative regulation of protein dephosphorylation|nerve growth factor receptor signaling pathway|Ras protein signal transduction	centrosome|cytosol|melanosome|perinuclear region of cytoplasm	histone deacetylase binding|phosphoserine binding|protein domain specific binding			kidney(2)|ovary(1)|breast(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44590988	44590988	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44590988delG	uc002xqw.2	-						ZNF335_uc010zxk.1_Intron	NM_022095	NP_071378			zinc finger protein 335						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC12A5	57468	broad.mit.edu	37	20	44651583	44651588	+	Intron	DEL	GGAGGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44651583_44651588delGGAGGA	uc010zxl.1	+							NM_001134771	NP_001128243			solute carrier family 12 (potassium-chloride						potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44821224	44821224	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44821224delG	uc002xrm.2	-						CDH22_uc010ghk.1_Intron	NM_021248	NP_067071			cadherin 22 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|skin(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45232630	45232633	+	Intron	DEL	AAAA	-	-	rs78794647		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45232630_45232633delAAAA	uc002xsf.1	-						SLC13A3_uc010ghn.1_Intron|SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	45432173	45432173	+	IGR	DEL	A	-	-	rs112873741		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45432173delA								SLC2A10 (67190 upstream) : EYA2 (91090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	45502691	45502692	+	IGR	DEL	AA	-	-	rs74735132		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45502691_45502692delAA								SLC2A10 (137708 upstream) : EYA2 (20571 downstream)																																			---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46282475	46282476	+	3'UTR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46282475_46282476insT	uc002xtk.2	+	23					NCOA3_uc002xtl.2_3'UTR|NCOA3_uc002xtm.2_3'UTR|NCOA3_uc002xtn.2_3'UTR|NCOA3_uc010zyc.1_3'UTR	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46490356	46490357	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46490356_46490357delCA								SULF2 (74996 upstream) : LOC284749 (498297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46676674	46676674	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46676674delA								SULF2 (261314 upstream) : LOC284749 (311980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46827522	46827523	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46827522_46827523delAA								SULF2 (412162 upstream) : LOC284749 (161131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46944166	46944166	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46944166delC								SULF2 (528806 upstream) : LOC284749 (44488 downstream)																																			---	---	---	---
C20orf199	441951	broad.mit.edu	37	20	47899083	47899086	+	Intron	DEL	TGTT	-	-	rs78029436		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47899083_47899086delTGTT	uc002xuj.2	+						C20orf199_uc002xul.3_Intron|C20orf199_uc002xun.3_Intron|C20orf199_uc002xum.3_Intron|C20orf199_uc002xuo.2_Intron	NR_003605				Homo sapiens cDNA FLJ42181 fis, clone THYMU2031368.												0																		---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48485923	48485923	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48485923delT	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010gic.2_Intron|SLC9A8_uc010gid.2_Intron	NM_015266	NP_056081			sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48875548	48875548	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48875548delC								CEBPB (66336 upstream) : PTPN1 (251343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48998002	48998003	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48998002_48998003delTG								CEBPB (188790 upstream) : PTPN1 (128888 downstream)																																			---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50267442	50267443	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50267442_50267443delAC	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	50437110	50437110	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50437110delA								SALL4 (18062 upstream) : ZFP64 (263441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50907953	50907954	+	IGR	DEL	GC	-	-	rs6096856	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50907953_50907954delGC								ZFP64 (99429 upstream) : TSHZ2 (680923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50920349	50920349	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50920349delT								ZFP64 (111825 upstream) : TSHZ2 (668528 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51729947	51729947	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51729947delT	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	52148908	52148908	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52148908delA								TSHZ2 (44943 upstream) : ZNF217 (34704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52532410	52532410	+	IGR	DEL	A	-	-	rs11479803		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52532410delA								SUMO1P1 (40162 upstream) : BCAS1 (27669 downstream)																																	OREG0026052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53103931	53103931	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53103931delG	uc002xwy.2	+						DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron	NM_018431	NP_060901			docking protein 5								insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
C20orf108	116151	broad.mit.edu	37	20	54937397	54937398	+	Intron	INS	-	CA	CA	rs142367946	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54937397_54937398insCA	uc002xxc.2	+							NM_080821	NP_543011			hypothetical protein LOC116151							integral to membrane					0			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	55490916	55490917	+	IGR	DEL	TG	-	-	rs11468254		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55490916_55490917delTG								TFAP2C (276580 upstream) : BMP7 (252892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55882179	55882179	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55882179delC								BMP7 (40472 upstream) : SPO11 (22652 downstream)																																			---	---	---	---
PMEPA1	56937	broad.mit.edu	37	20	56288102	56288102	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56288102delA	uc002xys.2	-						PMEPA1_uc002xyr.2_5'Flank|PMEPA1_uc002xyt.2_5'Flank	NM_199169	NP_954638			transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1																		---	---	---	---
VAPB	9217	broad.mit.edu	37	20	57001937	57001937	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57001937delA	uc002xza.2	+						VAPB_uc002xzb.2_Intron|VAPB_uc010zzo.1_Intron|VAPB_uc002xzc.2_Intron	NM_004738	NP_004729			VAMP-associated protein B/C						cell death|endoplasmic reticulum unfolded protein response|positive regulation of viral genome replication|sphingolipid metabolic process|virus-host interaction	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	beta-tubulin binding|enzyme binding|protein heterodimerization activity|protein homodimerization activity|structural molecule activity			kidney(1)	1	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)															---	---	---	---
VAPB	9217	broad.mit.edu	37	20	57002518	57002518	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57002518delT	uc002xza.2	+						VAPB_uc002xzb.2_Intron|VAPB_uc010zzo.1_Intron|VAPB_uc002xzc.2_Intron	NM_004738	NP_004729			VAMP-associated protein B/C						cell death|endoplasmic reticulum unfolded protein response|positive regulation of viral genome replication|sphingolipid metabolic process|virus-host interaction	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	beta-tubulin binding|enzyme binding|protein heterodimerization activity|protein homodimerization activity|structural molecule activity			kidney(1)	1	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	57022793	57022793	+	RNA	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57022793delT	uc002xzd.1	+	1		c.72delT								Homo sapiens cDNA FLJ41394 fis, clone BRCAN2026197.																												OREG0026077	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	20	59107009	59107009	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59107009delG	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59477028	59477029	+	IGR	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59477028_59477029delCT								MIR646 (593403 upstream) : CDH4 (350530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59494936	59494939	+	IGR	DEL	CTCT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59494936_59494939delCTCT								MIR646 (611311 upstream) : CDH4 (332620 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60436631	60436632	+	Intron	INS	-	AACCCAACCACAGAG	AACCCAACCACAGAG	rs141040334	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60436631_60436632insAACCCAACCACAGAG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60499206	60499206	+	Intron	DEL	G	-	-	rs71927224		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60499206delG	uc002ybn.1	+						CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	60532332	60532333	+	IGR	INS	-	TAGATAGATAGA	TAGATAGATAGA	rs146511572	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60532332_60532333insTAGATAGATAGA								MIR1257 (3614 upstream) : TAF4 (17522 downstream)																																			---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60573017	60573020	+	Intron	DEL	TGTT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60573017_60573020delTGTT	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
TAF4	6874	broad.mit.edu	37	20	60589973	60589973	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60589973delA	uc002ybs.2	-							NM_003185	NP_003176			TBP-associated factor 4						interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)															---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60720374	60720375	+	Intron	INS	-	G	G	rs143133978	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60720374_60720375insG	uc002ycb.2	+						PSMA7_uc002ybx.1_5'Flank|PSMA7_uc002yby.1_5'Flank|SS18L1_uc011aaa.1_Intron|SS18L1_uc002ybz.1_Intron|SS18L1_uc002yca.1_Intron	NM_198935	NP_945173			SS18-like protein 1						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60754515	60754515	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60754515delT	uc002ycb.2	+	11					SS18L1_uc002ybz.1_Intron|SS18L1_uc002yca.1_Intron|SS18L1_uc002ycc.1_Intron	NM_198935	NP_945173			SS18-like protein 1						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61536692	61536692	+	Intron	DEL	A	-	-	rs71693950		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61536692delA	uc002ydr.1	-						DIDO1_uc002yds.1_Intron|DIDO1_uc002ydt.1_Intron|DIDO1_uc002ydu.1_Intron|DIDO1_uc002ydv.1_3'UTR|DIDO1_uc002ydw.1_3'UTR|DIDO1_uc002ydx.1_3'UTR|DIDO1_uc011aao.1_3'UTR	NM_033081	NP_149072			death inducer-obliterator 1 isoform c						apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61555629	61555630	+	Intron	INS	-	AG	AG	rs139584103	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61555629_61555630insAG	uc002ydr.1	-						DIDO1_uc002yds.1_Intron|DIDO1_uc002ydt.1_Intron|DIDO1_uc002ydu.1_Intron|DIDO1_uc002ydv.1_Intron|DIDO1_uc002ydw.1_Intron|DIDO1_uc002ydx.1_Intron	NM_033081	NP_149072			death inducer-obliterator 1 isoform c						apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
SLC17A9	63910	broad.mit.edu	37	20	61598425	61598426	+	Intron	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61598425_61598426insC	uc002yea.3	+						SLC17A9_uc002ydz.3_Intron|SLC17A9_uc011aap.1_3'UTR	NM_022082	NP_071365			vesicular nucleotide transporter SLC17A9						exocytosis|transmembrane transport	integral to membrane	transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
YTHDF1	54915	broad.mit.edu	37	20	61827842	61827842	+	3'UTR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61827842delA	uc002yeh.2	-	5					YTHDF1_uc011aaq.1_3'UTR	NM_017798	NP_060268			YTH domain family, member 1											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	61853002	61853010	+	IGR	DEL	TGCAGGGAC	-	-	rs71195499	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61853002_61853010delTGCAGGGAC								YTHDF1 (5464 upstream) : BIRC7 (14266 downstream)																																			---	---	---	---
KCNQ2	3785	broad.mit.edu	37	20	62038661	62038661	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62038661delG	uc002yey.1	-	17	2132	c.1955delC	c.(1954-1956)CCGfs	p.P652fs	KCNQ2_uc002yez.1_Frame_Shift_Del_p.P621fs|KCNQ2_uc002yfa.1_Frame_Shift_Del_p.P634fs|KCNQ2_uc002yfb.1_Frame_Shift_Del_p.P624fs	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein	652	Cytoplasmic (Potential).				axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)													---	---	---	---
TPD52L2	7165	broad.mit.edu	37	20	62516802	62516802	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62516802delG	uc002yhc.2	+						TPD52L2_uc002ygy.2_Intron|TPD52L2_uc002ygz.2_Intron|TPD52L2_uc002yha.2_Intron|TPD52L2_uc002yhb.2_Intron|TPD52L2_uc002yhd.2_Intron|TPD52L2_uc011abk.1_Intron|TPD52L2_uc011abl.1_Intron|TPD52L2_uc002yhe.2_Intron	NM_003288	NP_003279			tumor protein D52-like 2 isoform e						regulation of cell proliferation	perinuclear region of cytoplasm	protein binding|protein homodimerization activity			ovary(1)|skin(1)	2	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62626924	62626924	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62626924delT	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601			PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62789607	62789620	+	Intron	DEL	CCCCACCTGCTCCA	-	-	rs141958784	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62789607_62789620delCCCCACCTGCTCCA	uc002yih.2	+							NM_004535	NP_004526			myelin transcription factor 1						cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	62918179	62918180	+	5'Flank	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62918179_62918180insT	uc002yin.2	+											DQ590432																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	62918180	62918181	+	5'Flank	INS	-	C	C	rs142978887		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62918180_62918181insC	uc002yin.2	+											DQ590432																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	62947577	62947578	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62947577_62947578insT								PCMTD2 (39999 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9414350	9414351	+	IGR	DEL	AT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9414350_9414351delAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10503733	10503733	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10503733delT	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10601010	10601010	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10601010delA								None (None upstream) : TPTE (305733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10729080	10729081	+	IGR	INS	-	TT	TT	rs138121719		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10729080_10729081insTT								None (None upstream) : TPTE (177662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10845797	10845798	+	IGR	INS	-	TGGAA	TGGAA	rs28970804		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10845797_10845798insTGGAA								None (None upstream) : TPTE (60945 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10912348	10912350	+	Intron	DEL	AAT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10912348_10912350delAAT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10968790	10968790	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10968790delA	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11074104	11074106	+	Intron	DEL	TAG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11074104_11074106delTAG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	11144769	11144772	+	IGR	DEL	TGTC	-	-	rs55756166		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11144769_11144772delTGTC								BAGE (45832 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	11187952	11187954	+	IGR	DEL	ATA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11187952_11187954delATA								BAGE (89015 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14343637	14343639	+	IGR	DEL	AAA	-	-	rs144497465	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14343637_14343639delAAA								None (None upstream) : C21orf99 (66848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14360853	14360853	+	IGR	DEL	A	-	-	rs113034034		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360853delA								None (None upstream) : C21orf99 (49634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14375639	14375639	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14375639delT								None (None upstream) : C21orf99 (34848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14804372	14804372	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14804372delG								C21orf99 (313803 upstream) : POTED (178126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16815033	16815034	+	IGR	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16815033_16815034delAA								NRIP1 (377907 upstream) : USP25 (287462 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17203605	17203606	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17203605_17203606delAA	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	18570225	18570226	+	IGR	INS	-	GAAGGAAG	GAAGGAAG			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18570225_18570226insGAAGGAAG								C21orf34 (588131 upstream) : CXADR (315104 downstream)																																			---	---	---	---
C21orf91	54149	broad.mit.edu	37	21	19178298	19178299	+	Intron	INS	-	A	A	rs143716630	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19178298_19178299insA	uc002yko.3	-						C21orf91_uc002ykq.3_Intron|C21orf91_uc002ykp.3_Intron	NM_001100420	NP_001093890			early undifferentiated retina and lens isoform											ovary(1)	1				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	19264349	19264349	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19264349delT								NCRNA00157 (6424 upstream) : CHODL (9231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21762641	21762641	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21762641delT								None (None upstream) : C21orf131 (352273 downstream)																																			---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22881130	22881143	+	Intron	DEL	TTTTTTTTTTTTTT	-	-	rs72167467		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22881130_22881143delTTTTTTTTTTTTTT	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531			neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	26358722	26358722	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26358722delA								None (None upstream) : NCRNA00158 (399412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26560276	26560276	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26560276delA								None (None upstream) : NCRNA00158 (197858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28032939	28032939	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28032939delG								CYYR1 (87358 upstream) : ADAMTS1 (175669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28481823	28481823	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28481823delT								ADAMTS5 (142384 upstream) : NCRNA00113 (612875 downstream)																																			---	---	---	---
NCRNA00189	193629	broad.mit.edu	37	21	30659329	30659330	+	Intron	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30659329_30659330delCA	uc002ynh.2	+						NCRNA00189_uc002yni.2_Intron	NR_027072				Homo sapiens chromosome 21 open reading frame 109 (C21orf109) mRNA, complete cds.												0																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	30949206	30949206	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30949206delT	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron	NM_000830	NP_000821			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)													---	---	---	---
KRTAP13-2	337959	broad.mit.edu	37	21	31744777	31744777	+	5'Flank	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31744777delT	uc002ynz.3	-							NM_181621	NP_853652			keratin associated protein 13-2							intermediate filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	31945362	31945363	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31945362_31945363delCA								KRTAP19-7 (11754 upstream) : KRTAP6-3 (19396 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32876171	32876173	+	Intron	DEL	AAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32876171_32876173delAAA	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33057345	33057345	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33057345delA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_Frame_Shift_Del_p.F509fs	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33807540	33807540	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33807540delG	uc002ypr.1	+						C21orf63_uc002ypq.1_Intron|C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron	NM_058187	NP_478067			hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																		---	---	---	---
DONSON	29980	broad.mit.edu	37	21	34953532	34953532	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34953532delT	uc002ysk.2	-						DONSON_uc002ysi.1_Intron|DONSON_uc002ysj.2_Intron|DONSON_uc002ysl.2_Intron|DONSON_uc010gme.2_Intron|DONSON_uc002ysm.2_Intron	NM_017613	NP_060083			downstream neighbor of SON						multicellular organismal development	nucleus				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	35529472	35529473	+	IGR	INS	-	TG	TG	rs147597208	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35529472_35529473insTG								MRPS6 (14138 upstream) : C21orf82 (23505 downstream)																																			---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37324609	37324610	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37324609_37324610delAA	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
ERG	2078	broad.mit.edu	37	21	39774635	39774639	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39774635_39774639delAAAAA	uc010gnw.2	-						ERG_uc002yxa.2_Intron|ERG_uc011aek.1_Intron|ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc011aem.1_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gny.1_Intron	NM_001136155	NP_001129627			ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40871691	40871691	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40871691delT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367			SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	41041849	41041849	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41041849delT								B3GALT5 (7034 upstream) : IGSF5 (75485 downstream)																																			---	---	---	---
IGSF5	150084	broad.mit.edu	37	21	41128722	41128722	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41128722delG	uc002yyo.2	+							NM_001080444	NP_001073913			immunoglobulin superfamily 5 like							integral to membrane|tight junction					0		Prostate(19;5.35e-06)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41451648	41451648	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41451648delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
PLAC4	191585	broad.mit.edu	37	21	42551242	42551243	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42551242_42551243delGA	uc002yyz.2	-	1	5924_5925	c.313_314delTC	c.(313-315)TCAfs	p.S105fs	BACE2_uc002yyw.2_Intron|BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_182832	NP_878252	Q8WY50	PLAC4_HUMAN	placenta-specific 4	105											0		Prostate(19;2.29e-06)																---	---	---	---
MX1	4599	broad.mit.edu	37	21	42794577	42794577	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42794577delA	uc002yzh.2	+							NM_001144925	NP_001138397			myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)																---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43541382	43541382	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43541382delT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.1_Intron	NM_001004416	NP_001004416			uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	43604311	43604312	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43604311_43604312delTG								UMODL1 (41206 upstream) : ABCG1 (15487 downstream)																																			---	---	---	---
RSPH1	89765	broad.mit.edu	37	21	43899836	43899837	+	Intron	INS	-	AC	AC	rs141751119	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43899836_43899837insAC	uc002zbg.2	-							NM_080860	NP_543136			testis-specific gene A2						meiosis	cytosol|nucleus				ovary(1)	1																		---	---	---	---
SLC37A1	54020	broad.mit.edu	37	21	43930701	43930701	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43930701delA	uc002zbi.2	+						SLC37A1_uc002zbh.1_Intron	NM_018964	NP_061837			solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44035366	44035367	+	5'Flank	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44035366_44035367delAC	uc002zbk.1	-											Homo sapiens, clone IMAGE:5189363, mRNA.																														---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44118958	44118958	+	Intron	DEL	T	-	-	rs1515755	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44118958delT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44593850	44593851	+	IGR	DEL	CC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44593850_44593851delCC								CRYAA (937 upstream) : SIK1 (240547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	45201542	45201543	+	IGR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45201542_45201543delTT								CSTB (5283 upstream) : RRP1 (7875 downstream)																																			---	---	---	---
C21orf33	8209	broad.mit.edu	37	21	45564932	45564932	+	3'UTR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45564932delT	uc002zec.3	+	7					C21orf33_uc002zed.3_3'UTR	NM_004649	NP_004640			es1 protein isoform Ia precursor							mitochondrion				ovary(1)	1				STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191)														---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45719080	45719081	+	5'Flank	INS	-	AC	AC	rs141850593	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45719080_45719081insAC	uc002zel.2	+						PFKL_uc002zek.2_5'Flank|PFKL_uc011afd.1_5'Flank	NM_002626	NP_002617			liver phosphofructokinase						fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)														---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46345334	46345345	+	Intron	DEL	GGAGGGAAGGAA	-	-	rs71836178		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46345334_46345345delGGAGGGAAGGAA	uc002zgg.2	-						uc002zgh.2_Intron	NM_001127491	NP_001120963			integrin, beta 2 precursor						apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)													---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46828347	46828347	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46828347delT	uc002zhg.2	+							NM_130445	NP_569712			alpha 1 type XVIII collagen isoform 2 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46880031	46880033	+	Intron	DEL	AAG	-	-	rs140975224		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46880031_46880033delAAG	uc011afs.1	+						COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Intron	NM_130444	NP_569711			alpha 1 type XVIII collagen isoform 3 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46917558	46917559	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46917558_46917559insC	uc011afs.1	+	31	3932_3933	c.3911_3912insC	c.(3910-3912)GGCfs	p.G1304fs	COL18A1_uc002zhg.2_Frame_Shift_Ins_p.G889fs|COL18A1_uc002zhi.2_Frame_Shift_Ins_p.G1069fs	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	1304	Triple-helical region 7 (COL7).				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	47436409	47436409	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47436409delT								COL6A1 (11446 upstream) : COL6A2 (81624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	47463388	47463388	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47463388delT								COL6A1 (38425 upstream) : COL6A2 (54645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17054210	17054211	+	IGR	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17054210_17054211insA								OR11H1 (604406 upstream) : CCT8L2 (17437 downstream)																																			---	---	---	---
CCT8L2	150160	broad.mit.edu	37	22	17075185	17075185	+	5'Flank	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17075185delA	uc002zlp.1	-							NM_014406	NP_055221			T-complex protein 1						cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	17504999	17504999	+	IGR	DEL	A	-	-	rs35368678		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17504999delA								GAB4 (15887 upstream) : CECR7 (12461 downstream)																																			---	---	---	---
CECR1	51816	broad.mit.edu	37	22	17689127	17689127	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17689127delA	uc002zmk.1	-						CECR1_uc010gqu.1_Intron|CECR1_uc011agi.1_Intron|CECR1_uc011agj.1_Intron	NM_017424	NP_059120			cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)																---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17848600	17848600	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17848600delA	uc010gqv.1	+							NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17898546	17898557	+	Intron	DEL	GAGGAAGAGGAG	-	-	rs55821121		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17898546_17898557delGAGGAAGAGGAG	uc010gqv.1	+							NM_031413	NP_113601			cat eye syndrome chromosome region, candidate 2						chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
GGT3P	2679	broad.mit.edu	37	22	18767407	18767408	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18767407_18767408delTT	uc010gri.1	-						GGT3P_uc011ago.1_Intron|GGT3P_uc011agp.1_Intron|GGT3P_uc002zob.1_Intron					Homo sapiens cDNA clone IMAGE:5761295, **** WARNING: chimeric clone ****.												0																		---	---	---	---
MED15	51586	broad.mit.edu	37	22	20926926	20926927	+	Intron	INS	-	C	C	rs149925804	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20926926_20926927insC	uc002zsp.2	+						MED15_uc002zsq.2_Intron|MED15_uc010gso.2_Intron|MED15_uc002zsr.2_Intron|MED15_uc011ahs.1_Intron|MED15_uc002zss.2_Intron|MED15_uc011ahu.1_Intron|MED15_uc002zst.2_5'Flank	NM_001003891	NP_001003891			mediator complex subunit 15 isoform a						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding			skin(1)	1	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	20973452	20973452	+	Intron	DEL	T	-	-	rs111447457		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20973452delT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	20975200	20975200	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20975200delT	uc002zsv.2	-											Homo sapiens, clone IMAGE:5171202, mRNA.																														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22620538	22620541	+	Intron	DEL	TTTC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22620538_22620541delTTTC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23025520	23025523	+	Intron	DEL	TGTG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23025520_23025523delTGTG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23651482	23651482	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23651482delG	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	24000098	24000101	+	Intron	DEL	TTTC	-	-	rs57713026		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24000098_24000101delTTTC	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
SMARCB1	6598	broad.mit.edu	37	22	24145725	24145726	+	Intron	INS	-	T	T	rs34300355	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24145725_24145726insT	uc002zyb.2	+						SMARCB1_uc002zya.2_Intron|SMARCB1_uc002zyc.2_Intron|SMARCB1_uc002zyd.2_Intron	NM_003073	NP_003064			SWI/SNF related, matrix associated, actin						cell cycle|chromatin remodeling|DNA integration|interspecies interaction between organisms|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|retroviral genome replication|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleolus|nucleoplasm|SWI/SNF complex	p53 binding			soft_tissue(193)|central_nervous_system(172)|haematopoietic_and_lymphoid_tissue(23)|meninges(5)|skin(5)|bone(4)|ovary(2)|endometrium(1)|lung(1)|pancreas(1)	407		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)						D|N|F|S		malignant rhabdoid 	malignant rhabdoid			Rhabdoid_Predisposition_syndrome|Schwannomatosis				---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24803683	24803683	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24803683delT	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145			cytospin A						cell cycle|cell division						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25734629	25734632	+	IGR	DEL	TTTT	-	-	rs148054088		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25734629_25734632delTTTT								IGLL3 (18438 upstream) : LRP5L (12754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25938799	25938799	+	IGR	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25938799delC								LRP5L (161255 upstream) : ADRBK2 (22062 downstream)																																			---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26291892	26291893	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26291892_26291893delTT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26402277	26402277	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26402277delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26666511	26666511	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26666511delG	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26709569	26709570	+	Intron	DEL	CG	-	-	rs35545563		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26709569_26709570delCG	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26769543	26769543	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26769543delA	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_Intron|SEZ6L_uc011ake.1_Intron	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
ASPHD2	57168	broad.mit.edu	37	22	26839054	26839054	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26839054delC	uc003acg.2	+							NM_020437	NP_065170			aspartate beta-hydroxylase domain containing 2						peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1																		---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26894669	26894669	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26894669delA	uc003acr.2	-						TFIP11_uc003acs.2_Intron|TFIP11_uc003act.2_Intron	NM_012143	NP_036275			tuftelin interacting protein 11						biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27755437	27755438	+	IGR	DEL	TG	-	-	rs71704118		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27755437_27755438delTG								MIAT (640488 upstream) : MN1 (388828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27848130	27848133	+	IGR	DEL	TGGA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27848130_27848133delTGGA								MIAT (733181 upstream) : MN1 (296133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27969425	27969425	+	IGR	DEL	C	-	-	rs35207321		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27969425delC								MIAT (854476 upstream) : MN1 (174841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28121551	28121552	+	IGR	INS	-	CAT	CAT			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28121551_28121552insCAT								None (None upstream) : MN1 (22714 downstream)																																			---	---	---	---
MN1	4330	broad.mit.edu	37	22	28146770	28146770	+	3'UTR	DEL	A	-	-	rs28501997		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28146770delA	uc003adj.2	-	2					MN1_uc010gvg.2_RNA	NM_002430	NP_002421			meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10								T	ETV6	AML|meningioma								---	---	---	---
MN1	4330	broad.mit.edu	37	22	28177445	28177446	+	Intron	INS	-	G	G	rs146620151	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28177445_28177446insG	uc003adj.2	-						MN1_uc010gvg.2_Intron	NM_002430	NP_002421			meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10								T	ETV6	AML|meningioma								---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28838104	28838104	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28838104delT	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
EMID1	129080	broad.mit.edu	37	22	29626944	29626944	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29626944delA	uc003aen.2	+						EMID1_uc003aem.2_Intron|EMID1_uc003aeo.2_Intron|EMID1_uc003aep.2_Intron	NM_133455	NP_597712			EMI domain containing 1							collagen					0																		---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29745510	29745510	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29745510delT	uc003afj.2	-						AP1B1_uc003afi.2_Intron|AP1B1_uc003afk.2_Intron|AP1B1_uc003afl.2_Intron|AP1B1_uc011ako.1_Intron	NM_001127	NP_001118			adaptor-related protein complex 1 beta 1 subunit						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
THOC5	8563	broad.mit.edu	37	22	29938753	29938753	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29938753delA	uc003afr.2	-						THOC5_uc003afs.2_Intron|THOC5_uc003aft.2_Intron|THOC5_uc003afu.2_Intron|THOC5_uc010gvo.2_Intron|THOC5_uc003afv.1_Intron|THOC5_uc003afw.1_Intron	NM_001002878	NP_001002878			THO complex 5						intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			breast(3)	3																		---	---	---	---
HORMAD2	150280	broad.mit.edu	37	22	30507905	30507905	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30507905delT	uc003agy.2	+							NM_152510	NP_689723			HORMA domain containing 2						meiosis|mitosis	chromosome|nucleus					0			Epithelial(10;0.125)															---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31943153	31943154	+	Intron	DEL	AC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31943153_31943154delAC	uc003ale.2	+						SFI1_uc003ald.1_Intron|SFI1_uc003alf.2_Intron|SFI1_uc003alg.2_Intron|SFI1_uc011alp.1_Intron|SFI1_uc011alq.1_Intron|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468			spindle assembly associated Sfi1 homolog isoform						G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32232567	32232568	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32232567_32232568insT	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			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33324752	33324752	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33324752delT	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
LARGE	9215	broad.mit.edu	37	22	33806657	33806657	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33806657delT	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.1_Intron	NM_004737	NP_004728			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)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	35541668	35541669	+	IGR	DEL	CA	-	-	rs67039080		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35541668_35541669delCA								ISX (58290 upstream) : HMGXB4 (111776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36449876	36449876	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36449876delT								RBM9 (25291 upstream) : APOL3 (86496 downstream)																																			---	---	---	---
APOL2	23780	broad.mit.edu	37	22	36632865	36632865	+	Intron	DEL	G	-	-	rs35090400		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36632865delG	uc003aoz.2	-						APOL2_uc011amm.1_Intron|APOL2_uc003apa.2_Intron	NM_030882	NP_112092			apolipoprotein L2						acute-phase response|cholesterol metabolic process|lipid transport|lipoprotein metabolic process|maternal process involved in female pregnancy|multicellular organismal development	endoplasmic reticulum membrane|extracellular region	high-density lipoprotein particle binding|lipid binding|receptor binding				0																		---	---	---	---
APOL1	8542	broad.mit.edu	37	22	36662142	36662143	+	3'UTR	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36662142_36662143delTT	uc003apf.2	+	6					APOL1_uc011amn.1_3'UTR|APOL1_uc003apc.2_RNA|APOL1_uc003ape.2_3'UTR|APOL1_uc011amo.1_3'UTR|APOL1_uc011amp.1_3'UTR|APOL1_uc011amq.1_3'UTR|APOL1_uc010gwx.2_3'UTR	NM_003661	NP_003652			apolipoprotein L1 isoform a precursor						cholesterol metabolic process|cytolysis|innate immune response|killing of cells of other organism|lipid transport|lipoprotein metabolic process	high-density lipoprotein particle|very-low-density lipoprotein particle	chloride channel activity|lipid binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36712414	36712414	+	Intron	DEL	C	-	-	rs5756151		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36712414delC	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37779019	37779019	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37779019delC	uc003asq.3	-							NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
ANKRD54	129138	broad.mit.edu	37	22	38242188	38242188	+	5'Flank	DEL	A	-	-	rs71324883		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38242188delA	uc003auc.2	-						ANKRD54_uc003aud.2_5'Flank|MIR658_hsa-mir-658|MI0003682_5'Flank	NM_138797	NP_620152			ankyrin repeat domain 54												0	Melanoma(58;0.045)																	---	---	---	---
PLA2G6	8398	broad.mit.edu	37	22	38536711	38536711	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38536711delT	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc011ano.1_Intron	NM_003560	NP_003551			phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)													---	---	---	---
PLA2G6	8398	broad.mit.edu	37	22	38548976	38548976	+	Intron	DEL	A	-	-	rs112507836		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38548976delA	uc003auy.1	-						PLA2G6_uc003auz.1_Intron|PLA2G6_uc003ava.1_Intron|PLA2G6_uc003avb.2_Intron|PLA2G6_uc010gxk.1_Intron|PLA2G6_uc011ano.1_Intron	NM_003560	NP_003551			phospholipase A2, group VI isoform a						cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)													---	---	---	---
DDX17	10521	broad.mit.edu	37	22	38895223	38895224	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38895223_38895224insA	uc003avy.3	-						DDX17_uc003avx.3_Intron|DDX17_uc011anu.1_Intron	NM_001098504	NP_001091974			DEAD box polypeptide 17 isoform 3						RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)																	---	---	---	---
APOBEC3G	60489	broad.mit.edu	37	22	39474726	39474726	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39474726delT	uc003awx.2	+						APOBEC3G_uc003awy.2_5'Flank	NM_021822	NP_068594			apolipoprotein B mRNA editing enzyme, catalytic						base conversion or substitution editing|DNA cytosine deamination|innate immune response|interspecies interaction between organisms|negative regulation of retroviral genome replication|negative regulation of transposition|positive regulation of defense response to virus by host|response to virus|viral reproduction	apolipoprotein B mRNA editing enzyme complex|cytosol|mitochondrion	cytidine deaminase activity|dCTP deaminase activity|protein homodimerization activity|RNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2	Melanoma(58;0.04)																	---	---	---	---
TAB1	10454	broad.mit.edu	37	22	39788662	39788662	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39788662delG	uc003axr.2	+							NM_006116	NP_006107			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB 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|endosome membrane	catalytic activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	39961048	39961049	+	IGR	DEL	CA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39961048_39961049delCA								RPS19BP1 (32188 upstream) : CACNA1I (5709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	41424171	41424171	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41424171delA								RBX1 (55505 upstream) : MIR1281 (64346 downstream)																																			---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41720075	41720075	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41720075delA	uc003azw.2	+						ZC3H7B_uc003azv.1_Intron|ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060			zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41943193	41943193	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41943193delA								POLR3H (2714 upstream) : CSDC2 (13821 downstream)																																			---	---	---	---
TTLL1	25809	broad.mit.edu	37	22	43442684	43442684	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43442684delT	uc003bdi.2	-						TTLL1_uc010gzh.2_Intron|TTLL1_uc003bdj.2_Intron|TTLL1_uc003bdh.2_Intron	NM_012263	NP_036395			tubulin tyrosine ligase-like family, member 1						protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)														---	---	---	---
MPPED1	758	broad.mit.edu	37	22	43816415	43816416	+	Intron	DEL	TT	-	-	rs34894717		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43816415_43816416delTT	uc011apv.1	+						MPPED1_uc011apw.1_Intron|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Intron|MPPED1_uc011apz.1_Intron	NM_001044370	NP_001037835			metallophosphoesterase domain containing 1								hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	45476158	45476160	+	IGR	DEL	CAT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45476158_45476160delCAT								PHF21B (70349 upstream) : NUP50 (83566 downstream)																																			---	---	---	---
RIBC2	26150	broad.mit.edu	37	22	45828138	45828138	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45828138delT	uc011aqs.1	+							NM_015653	NP_056468			RIB43A domain with coiled-coils 2												0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49131686	49131686	+	Intron	DEL	G	-	-	rs10716843		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49131686delG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	X	1920829	1920830	+	IGR	DEL	TC	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1920829_1920830delTC								ASMT (158856 upstream) : DHRSX (216727 downstream)																																			---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2248563	2248563	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2248563delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	5947478	5947478	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5947478delA	uc010ndh.2	-						NLGN4X_uc004crp.2_Intron|NLGN4X_uc004crq.2_Intron|NLGN4X_uc010ndi.2_Intron|NLGN4X_uc004crr.2_Intron|NLGN4X_uc010ndj.2_Intron	NM_181332	NP_851849			X-linked neuroligin 4 precursor						brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
WWC3	55841	broad.mit.edu	37	X	9989155	9989155	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9989155delT	uc004csx.3	+						WWC3_uc010nds.2_Intron	NM_015691	NP_056506			WWC family member 3											ovary(4)	4																		---	---	---	---
TMEM27	57393	broad.mit.edu	37	X	15657921	15657921	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15657921delA	uc004cxc.1	-							NM_020665	NP_065716			transmembrane protein 27 precursor						proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16871713	16871713	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16871713delA	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron|RBBP7_uc010nez.2_3'UTR	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
SCML2	10389	broad.mit.edu	37	X	18275161	18275161	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18275161delA	uc004cyl.2	-						SCML2_uc004cyk.3_Intron|SCML2_uc010nfd.1_Intron|SCML2_uc011miz.1_Intron|SCML2_uc010nfc.2_Intron	NM_006089	NP_006080			sex comb on midleg-like 2						anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18597856	18597856	+	Intron	DEL	A	-	-	rs12013924		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18597856delA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19055764	19055764	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19055764delA	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
RPS6KA3	6197	broad.mit.edu	37	X	20174513	20174513	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20174513delA	uc004czu.2	-						RPS6KA3_uc011mjk.1_Intron|RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8																		---	---	---	---
RPS6KA3	6197	broad.mit.edu	37	X	20205736	20205737	+	Intron	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20205736_20205737insT	uc004czu.2	-						RPS6KA3_uc011mjk.1_Intron|RPS6KA3_uc004czv.2_Intron|RPS6KA3_uc011mjl.1_Intron|RPS6KA3_uc011mjm.1_Intron	NM_004586	NP_004577			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|central nervous system development|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|skeletal system development|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(4)|stomach(1)|ovary(1)|lung(1)|breast(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	22547098	22547098	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22547098delA								ZNF645 (254524 upstream) : DDX53 (470989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	23335396	23335397	+	IGR	DEL	TT	-	-	rs5901730		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23335396_23335397delTT								DDX53 (315192 upstream) : PTCHD1 (17588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	24459440	24459440	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24459440delT								FAM48B1 (75900 upstream) : PDK3 (23904 downstream)																																			---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24763696	24763696	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24763696delA	uc004dbl.2	+							NM_016937	NP_058633			DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)													---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29368547	29368548	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29368547_29368548insA	uc004dby.2	+							NM_014271	NP_055086			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																		---	---	---	---
CXorf59	286464	broad.mit.edu	37	X	36117799	36117799	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36117799delA	uc004ddk.1	+							NM_173695	NP_775966			hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
CYBB	1536	broad.mit.edu	37	X	37668788	37668788	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37668788delT	uc004ddr.2	+						CYBB_uc011mkf.1_Intron|CYBB_uc011mkg.1_Intron	NM_000397	NP_000388			cytochrome b-245 beta polypeptide						electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	40915591	40915591	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40915591delA								LOC100132831 (223142 upstream) : USP9X (29297 downstream)																																			---	---	---	---
CASK	8573	broad.mit.edu	37	X	41437798	41437798	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41437798delA	uc004dfl.3	-						CASK_uc004dfj.3_Intron|CASK_uc004dfk.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron	NM_003688	NP_003679			calcium/calmodulin-dependent serine protein						cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6																		---	---	---	---
MAOB	4129	broad.mit.edu	37	X	43741511	43741511	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43741511delC	uc004dfz.3	-	1	211	c.35delG	c.(34-36)GGCfs	p.G12fs	MAOB_uc011mky.1_5'UTR|MAOB_uc010nhj.2_Frame_Shift_Del_p.G12fs	NM_000898	NP_000889	P27338	AOFB_HUMAN	monoamine oxidase B	12	Cytoplasmic.				xenobiotic metabolic process	integral to membrane|mitochondrial outer membrane	electron carrier activity|primary amine oxidase activity			ovary(1)|central_nervous_system(1)	2					Amantadine(DB00915)|Bupropion(DB01156)|Carbidopa(DB00190)|Citalopram(DB00215)|Dopamine(DB00988)|Entacapone(DB00494)|Furazolidone(DB00614)|Ginkgo biloba(DB01381)|Ibuprofen(DB01050)|Imipramine(DB00458)|Iproniazid(DB04818)|Isocarboxazid(DB01247)|Levodopa(DB01235)|Maprotiline(DB00934)|Meclizine(DB00737)|Moclobemide(DB01171)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Rasagiline(DB01367)|Selegiline(DB01037)|Tranylcypromine(DB00752)													---	---	---	---
CXorf36	79742	broad.mit.edu	37	X	45057591	45057591	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45057591delA	uc004dgg.2	-						CXorf36_uc004dgi.3_Intron	NM_176819	NP_789789			hypothetical protein LOC79742 isoform 1							extracellular region				lung(1)	1																		---	---	---	---
RBM10	8241	broad.mit.edu	37	X	47035887	47035887	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47035887delT	uc004dhf.2	+						RBM10_uc004dhe.1_Intron|RBM10_uc004dhg.2_Intron|RBM10_uc004dhh.2_Intron|RBM10_uc010nhq.2_Intron|RBM10_uc004dhi.2_Intron	NM_005676	NP_005667			RNA binding motif protein 10 isoform 1						mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			ovary(1)|large_intestine(1)|prostate(1)|breast(1)|pancreas(1)	5																		---	---	---	---
SSX5	6758	broad.mit.edu	37	X	48046901	48046901	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48046901delA	uc004dja.1	-						SSX5_uc004diz.1_Intron	NM_175723	NP_783729			synovial sarcoma, X breakpoint 5 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	53834859	53834859	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53834859delA								HUWE1 (121186 upstream) : PHF8 (128255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61685673	61685673	+	IGR	DEL	G	-	-	rs76464288		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61685673delG								None (None upstream) : SPIN4 (881435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61708580	61708580	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61708580delA								None (None upstream) : SPIN4 (858528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61731833	61731833	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61731833delG								None (None upstream) : SPIN4 (835275 downstream)																																			---	---	---	---
MSN	4478	broad.mit.edu	37	X	64945276	64945276	+	Intron	DEL	C	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64945276delC	uc004dwf.2	+						MSN_uc010nkp.1_Intron	NM_002444	NP_002435			moesin						leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10								T	ALK	ALCL								---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69623948	69623948	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69623948delA	uc004dyg.2	+						KIF4A_uc010nkw.2_Intron	NM_012310	NP_036442			kinesin family member 4						anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
NHSL2	340527	broad.mit.edu	37	X	71291649	71291650	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71291649_71291650delCT	uc011mqa.1	+							NM_001013627	NP_001013649			NHS-like 2												0	Renal(35;0.156)																	---	---	---	---
ERCC6L	54821	broad.mit.edu	37	X	71428555	71428555	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71428555delA	uc004eaq.1	-						PIN4_uc004eao.1_Intron|ERCC6L_uc004eap.1_Intron	NM_017669	NP_060139			excision repair protein ERCC6-like						cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol	ATP binding|DNA binding|helicase activity|protein binding			ovary(3)	3	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	72441064	72441065	+	IGR	INS	-	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72441064_72441065insT								NAP1L2 (6380 upstream) : CDX4 (226025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	72674451	72674451	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72674451delT								CDX4 (31 upstream) : CHIC1 (108533 downstream)																																			---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74649036	74649036	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74649036delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
CHM	1121	broad.mit.edu	37	X	85134074	85134074	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85134074delA	uc004eet.2	-						CHM_uc011mqz.1_Intron	NM_000390	NP_000381			choroideremia isoform a						intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)																---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91652468	91652469	+	Intron	DEL	TT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91652468_91652469delTT	uc004efk.1	+						PCDH11X_uc004efl.1_Intron|PCDH11X_uc004efo.1_Intron|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Intron|PCDH11X_uc004efn.1_Intron	NM_032968	NP_116750			protocadherin 11 X-linked isoform c						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100057725	100057725	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100057725delA								SYTL4 (70594 upstream) : CSTF2 (17623 downstream)																																			---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100381989	100381989	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100381989delA	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724			centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100591863	100591863	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100591863delT								TAF7L (43818 upstream) : TIMM8A (8781 downstream)																																			---	---	---	---
NXF5	55998	broad.mit.edu	37	X	101093566	101093566	+	Intron	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101093566delG	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564			nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
NXF3	56000	broad.mit.edu	37	X	102344108	102344109	+	Intron	INS	-	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102344108_102344109insA	uc004eju.2	-						NXF3_uc011mrw.1_Intron|NXF3_uc011mrx.1_Intron	NM_022052	NP_071335			nuclear RNA export factor 3							cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107512391	107512391	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107512391delA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc004enx.2_Intron|COL4A6_uc004eny.2_Intron	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
Unknown	0	broad.mit.edu	37	X	108812483	108812483	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108812483delA								NXT2 (24570 upstream) : KCNE1L (54448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	110756334	110756334	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110756334delT	uc004eph.2	+											Homo sapiens mRNA; cDNA DKFZp686D0853 (from clone DKFZp686D0853).																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	113396408	113396409	+	IGR	DEL	TG	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:113396408_113396409delTG								None (None upstream) : HTR2C (422142 downstream)																																			---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114868272	114868272	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114868272delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
PLS3	5358	broad.mit.edu	37	X	114877477	114877477	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114877477delT	uc004eqd.2	+						PLS3_uc010nqg.2_Intron|PLS3_uc011mtf.1_Intron|PLS3_uc004eqe.2_Intron|PLS3_uc011mtg.1_Intron|PLS3_uc011mth.1_Intron|PLS3_uc011mti.1_Intron|PLS3_uc011mtj.1_Intron|PLS3_uc011mtk.1_5'Flank|PLS3_uc011mtl.1_5'Flank	NM_005032	NP_005023			plastin 3							cytoplasm	actin binding|calcium ion binding			lung(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	115339944	115339944	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:115339944delA								AGTR2 (33721 upstream) : SLC6A14 (227830 downstream)																																			---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117761355	117761355	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117761355delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
LAMP2	3920	broad.mit.edu	37	X	119577955	119577956	+	Intron	DEL	AT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119577955_119577956delAT	uc004est.3	-						LAMP2_uc004ess.3_Intron|LAMP2_uc011mtz.1_Intron|LAMP2_uc011mua.1_Intron|LAMP2_uc010nqp.1_Intron	NM_002294	NP_002285			lysosomal-associated membrane protein 2 isoform						platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	119866953	119866953	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119866953delG								C1GALT1C1 (103012 upstream) : CT47B1 (139501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121074309	121074309	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121074309delA								GLUD2 (890515 upstream) : None (None downstream)																																			---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122564879	122564880	+	Intron	DEL	AC	-	-	rs67925408		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122564879_122564880delAC	uc004etq.3	+						GRIA3_uc004etr.3_Intron|GRIA3_uc004ets.3_Intron	NM_007325	NP_015564			glutamate receptor, ionotrophic, AMPA 3 isoform						glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	124028293	124028293	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:124028293delA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	132420144	132420145	+	IGR	INS	-	TGA	TGA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132420144_132420145insTGA								TFDP3 (67768 upstream) : GPC4 (14919 downstream)																																			---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132779620	132779620	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132779620delT	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron	NM_004484	NP_004475			glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)							T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	X	133126161	133126161	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133126161delT								GPC3 (6495 upstream) : MIR363 (177247 downstream)																																			---	---	---	---
FAM122C	159091	broad.mit.edu	37	X	133963451	133963452	+	Intron	INS	-	A	A	rs72454255		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133963451_133963452insA	uc004exz.1	+						FAM122C_uc011mvq.1_Intron|FAM122C_uc004exy.1_Intron	NM_138819	NP_620174			hypothetical protein LOC159091												0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
DDX26B	203522	broad.mit.edu	37	X	134710982	134710982	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134710982delA	uc004eyw.3	+						DDX26B_uc004eyx.3_Intron	NM_182540	NP_872346			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide												0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135481957	135481958	+	Intron	DEL	AA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135481957_135481958delAA	uc004ezu.1	+						GPR112_uc010nsb.1_Intron	NM_153834	NP_722576			G-protein coupled receptor 112						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138840030	138840030	+	Intron	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138840030delA	uc004faz.2	-						ATP11C_uc004fax.2_Intron|ATP11C_uc004fay.2_Intron|ATP11C_uc004fba.2_Intron	NM_173694	NP_775965			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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	138989987	138989987	+	IGR	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138989987delT								ATP11C (75540 upstream) : MIR505 (16320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	141325469	141325469	+	IGR	DEL	G	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141325469delG								MAGEC2 (32393 upstream) : SPANXN4 (788235 downstream)																																			---	---	---	---
AFF2	2334	broad.mit.edu	37	X	147744323	147744323	+	Intron	DEL	T	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147744323delT	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron	NM_002025	NP_002016			fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149637879	149637880	+	Intron	DEL	CT	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149637879_149637880delCT	uc004fee.1	+						MAMLD1_uc011mxt.1_Intron|MAMLD1_uc011mxu.1_Intron|MAMLD1_uc011mxv.1_Intron|MAMLD1_uc011mxw.1_5'Flank	NM_005491	NP_005482			mastermind-like domain containing 1						male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150162649	150162649	+	IGR	DEL	A	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150162649delA								HMGB3 (3403 upstream) : GPR50 (182410 downstream)																																			---	---	---	---
G6PD	2539	broad.mit.edu	37	X	153774052	153774061	+	Intron	DEL	AAAAAAAAAA	-	-			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153774052_153774061delAAAAAAAAAA	uc004fly.1	-						G6PD_uc004flx.1_Intron|IKBKG_uc011mzr.1_Intron|IKBKG_uc010nva.2_5'Flank|IKBKG_uc004fmb.3_5'Flank|IKBKG_uc011mzs.1_5'Flank|IKBKG_uc004fma.3_5'Flank|IKBKG_uc004fmc.3_5'Flank|IKBKG_uc004fmd.2_5'Flank	NM_001042351	NP_001035810			glucose-6-phosphate dehydrogenase isoform b						cellular response to oxidative stress|cholesterol biosynthetic process|cytokine production|erythrocyte maturation|glucose 6-phosphate metabolic process|glutathione metabolic process|negative regulation of protein glutathionylation|pentose-phosphate shunt, oxidative branch|ribose phosphate biosynthetic process	centrosome|cytosol|internal side of plasma membrane|intracellular membrane-bounded organelle	glucose binding|glucose-6-phosphate dehydrogenase activity|NADP binding|protein homodimerization activity			ovary(4)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13430917	13430918	+	IGR	INS	-	AA	AA			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13430917_13430918insAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	58976118	58976127	+	IGR	DEL	TCCAATCCAT	-	-	rs111262396		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58976118_58976127delTCCAATCCAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	58976952	58976961	+	IGR	DEL	CACTCCACTC	-	-	rs113422656		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:58976952_58976961delCACTCCACTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59009655	59009656	+	IGR	INS	-	A	A	rs71218032		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59009655_59009656insA								None (None upstream) : None (None downstream)																																			---	---	---	---
MXRA8	54587	broad.mit.edu	37	1	1293893	1293893	+	5'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1293893C>T	uc001aew.2	-	1					MXRA8_uc001aex.3_5'UTR|MXRA8_uc001aey.3_5'UTR|MXRA8_uc010nyl.1_5'UTR|MXRA8_uc001aez.2_5'UTR|MXRA8_uc001afa.2_Intron	NM_032348	NP_115724			matrix-remodelling associated 8 precursor							integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-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)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
ATAD3A	55210	broad.mit.edu	37	1	1455959	1455959	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1455959C>A	uc001afz.1	+	7	950	c.856C>A	c.(856-858)CGT>AGT	p.R286S	ATAD3A_uc001aga.1_Missense_Mutation_p.R238S|ATAD3A_uc001agb.1_Missense_Mutation_p.R159S	NM_018188	NP_060658	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	286							ATP binding|nucleoside-triphosphatase activity|protein binding			skin(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-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)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)														---	---	---	---
NADK	65220	broad.mit.edu	37	1	1687948	1687948	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1687948G>A	uc009vkw.2	-	5	614	c.493C>T	c.(493-495)CGA>TGA	p.R165*	NADK_uc001aic.2_Nonsense_Mutation_p.R165*|NADK_uc001aid.3_Nonsense_Mutation_p.R165*|NADK_uc001aie.2_Nonsense_Mutation_p.R310*|NADK_uc010nyv.1_Nonsense_Mutation_p.R133*|NADK_uc009vkx.1_Nonsense_Mutation_p.R43*	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	165					ATP metabolic process|NAD metabolic process|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|NAD+ kinase activity|protein binding				0	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;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3342751	3342751	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3342751T>C	uc001akf.2	+	14	3326	c.3246T>C	c.(3244-3246)AAT>AAC	p.N1082N	PRDM16_uc001akc.2_Silent_p.N1081N|PRDM16_uc001akd.2_Silent_p.N1081N|PRDM16_uc001ake.2_Silent_p.N1082N|PRDM16_uc009vlh.2_Silent_p.N782N	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	1082	Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
KIAA0562	9731	broad.mit.edu	37	1	3755627	3755627	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3755627T>C	uc001aky.2	-	8	1151	c.792A>G	c.(790-792)GAA>GAG	p.E264E	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Silent_p.E264E	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	264	Potential.					centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8421436	8421436	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8421436T>C	uc001ape.2	-	19	2941	c.2131A>G	c.(2131-2133)ACG>GCG	p.T711A	RERE_uc001apf.2_Missense_Mutation_p.T711A|RERE_uc010nzx.1_Missense_Mutation_p.T443A|RERE_uc001apd.2_Missense_Mutation_p.T157A	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	711					multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
APITD1	378708	broad.mit.edu	37	1	10502436	10502436	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10502436G>A	uc001are.2	+	5	807	c.391G>A	c.(391-393)GCT>ACT	p.A131T	APITD1_uc001arf.2_Intron|APITD1_uc001arg.2_Intron|APITD1_uc001arh.2_Missense_Mutation_p.A92T	NM_199294	NP_954988	Q8N2Z9	CENPS_HUMAN	apoptosis-inducing, TAF9-like domain 1 isoform	131					DNA repair|mitotic prometaphase|transcription initiation, DNA-dependent	chromosome, centromeric region|cytosol|Fanconi anaemia nuclear complex	chromatin binding|DNA binding|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.31e-07)|COAD - Colon adenocarcinoma(227;7.32e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
FBXO44	93611	broad.mit.edu	37	1	11716005	11716005	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11716005G>A	uc001asm.2	+	2	239	c.113G>A	c.(112-114)CGG>CAG	p.R38Q	FBXO2_uc001asj.2_5'Flank|FBXO2_uc009vna.2_5'Flank|FBXO2_uc009vnb.1_5'Flank|FBXO44_uc001ask.2_Missense_Mutation_p.R38Q|FBXO44_uc010oaq.1_Missense_Mutation_p.R38Q|FBXO44_uc001asl.2_Missense_Mutation_p.R38Q|FBXO44_uc001asn.2_Missense_Mutation_p.R38Q|FBXO44_uc010oar.1_Missense_Mutation_p.R38Q|FBXO44_uc010oas.1_5'UTR	NM_033182	NP_149438	Q9H4M3	FBX44_HUMAN	F-box protein 44 isoform 1	38	F-box.				protein catabolic process	SCF ubiquitin ligase complex	protein binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CLCN6	1185	broad.mit.edu	37	1	11894557	11894557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11894557G>A	uc001ate.3	+	17	1816	c.1703G>A	c.(1702-1704)GGG>GAG	p.G568E	CLCN6_uc010oat.1_Missense_Mutation_p.G284E|CLCN6_uc010oau.1_Missense_Mutation_p.G546E	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	568	Helical; (By similarity).				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12198276	12198276	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12198276C>T	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron|TNFRSF8_uc001atr.2_Intron|TNFRSF8_uc001ats.2_Intron	NM_001243	NP_001234			tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPHA2	1969	broad.mit.edu	37	1	16459802	16459802	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16459802C>T	uc001aya.1	-	11	2063	c.1926G>A	c.(1924-1926)CCG>CCA	p.P642P		NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	642	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase.|Cytoplasmic (Potential).				activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)													---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19471342	19471342	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19471342T>C	uc001bbi.2	-	54	8009	c.8005A>G	c.(8005-8007)ACC>GCC	p.T2669A	UBR4_uc001bbk.1_Missense_Mutation_p.T351A	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	2669					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21546439	21546439	+	3'UTR	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21546439G>A	uc001bek.2	-	19					ECE1_uc001bem.2_3'UTR|ECE1_uc001bej.2_3'UTR|ECE1_uc001bei.2_3'UTR|ECE1_uc010odl.1_3'UTR	NM_001397	NP_001388			endothelin converting enzyme 1 isoform 1						bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
CNKSR1	10256	broad.mit.edu	37	1	26506988	26506988	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26506988C>T	uc001bln.3	+	2	155	c.97C>T	c.(97-99)CTG>TTG	p.L33L	CNKSR1_uc010oex.1_RNA|CNKSR1_uc001blm.3_Silent_p.L33L|CNKSR1_uc009vsd.2_5'UTR|CNKSR1_uc009vse.2_5'UTR|CNKSR1_uc001blo.2_5'UTR	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	33	SAM.				Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			lung(1)|kidney(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NUDC	10726	broad.mit.edu	37	1	27269258	27269258	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27269258G>A	uc001bng.1	+	5	653	c.537G>A	c.(535-537)TCG>TCA	p.S179S	NUDC_uc001bnh.1_Silent_p.S236S|NUDC_uc009vsq.1_Silent_p.S153S	NM_006600	NP_006591	Q9Y266	NUDC_HUMAN	nuclear distribution gene C homolog	179	CS.				cell proliferation|cytokinesis|mitotic prometaphase|multicellular organismal development	cytosol|microtubule|nucleoplasm	protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)														---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32086581	32086581	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32086581G>A	uc009vtx.2	+	5	901	c.516G>A	c.(514-516)TCG>TCA	p.S172S	HCRTR1_uc001btb.2_5'UTR|HCRTR1_uc001btc.3_Silent_p.S86S|HCRTR1_uc001btd.2_Silent_p.S172S|HCRTR1_uc010ogl.1_Silent_p.S172S	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1	172	Helical; Name=4; (Potential).				feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32150143	32150143	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32150143G>A	uc001btk.1	-	31	2506	c.2141C>T	c.(2140-2142)GCG>GTG	p.A714V	COL16A1_uc001btj.1_Missense_Mutation_p.A543V|COL16A1_uc001btl.3_Missense_Mutation_p.A714V	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	714	Triple-helical region 6 (COL6) with 1 imperfection.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
BAI2	576	broad.mit.edu	37	1	32193865	32193865	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32193865C>T	uc001btn.2	-	31	4787	c.4433G>A	c.(4432-4434)CGG>CAG	p.R1478Q	BAI2_uc001btm.2_Missense_Mutation_p.R472Q|BAI2_uc001btp.1_Missense_Mutation_p.R472Q|BAI2_uc010ogn.1_Missense_Mutation_p.R448Q|BAI2_uc010ogo.1_Missense_Mutation_p.R1087Q|BAI2_uc010ogp.1_Missense_Mutation_p.R1411Q|BAI2_uc010ogq.1_Missense_Mutation_p.R1444Q|BAI2_uc001bto.2_Missense_Mutation_p.R1477Q	NM_001703	NP_001694	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1478	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(5)|breast(4)|ovary(2)|central_nervous_system(1)|skin(1)	13		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)														---	---	---	---
LCK	3932	broad.mit.edu	37	1	32745576	32745576	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32745576C>T	uc001bux.2	+	11	1314	c.1176C>T	c.(1174-1176)AAC>AAT	p.N392N	LCK_uc001buy.2_Silent_p.N392N|LCK_uc001buz.2_Silent_p.N422N|LCK_uc010ohc.1_Silent_p.N436N|LCK_uc001bva.2_Silent_p.N399N	NM_005356	NP_005347	P06239	LCK_HUMAN	lymphocyte-specific protein tyrosine kinase	392	Protein kinase.				activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)			T	TRB@	T-ALL								---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34180274	34180274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34180274G>A	uc001bxn.1	-	21	3228	c.3199C>T	c.(3199-3201)CCC>TCC	p.P1067S	CSMD2_uc001bxm.1_Missense_Mutation_p.P1107S	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1067	Sushi 6.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
EIF2C1	26523	broad.mit.edu	37	1	36354182	36354182	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36354182G>T	uc001bzl.2	+	2	393	c.180G>T	c.(178-180)AAG>AAT	p.K60N	EIF2C1_uc001bzk.2_5'UTR	NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1	60					negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
LSM10	84967	broad.mit.edu	37	1	36859607	36859607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36859607G>A	uc001cao.1	-	2	274	c.124C>T	c.(124-126)CGC>TGC	p.R42C		NM_032881	NP_116270	Q969L4	LSM10_HUMAN	LSM10, U7 small nuclear RNA associated	42					histone mRNA metabolic process|mRNA processing|RNA splicing|S phase of mitotic cell cycle|termination of RNA polymerase II transcription	Cajal body|U7 snRNP	histone pre-mRNA DCP binding|protein binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
C1orf109	54955	broad.mit.edu	37	1	38148841	38148841	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38148841G>T	uc001cbp.2	-						C1orf109_uc001cbn.2_Intron|C1orf109_uc010oig.1_Intron|C1orf109_uc001cbo.2_Intron	NM_017850	NP_060320			hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
SF3A3	10946	broad.mit.edu	37	1	38433787	38433787	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38433787C>T	uc001cci.2	-	15	1425	c.1301G>A	c.(1300-1302)GGC>GAC	p.G434D	SF3A3_uc010oik.1_Missense_Mutation_p.G381D	NM_006802	NP_006793	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3	434	Matrin-type.				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39900152	39900152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39900152C>T	uc010oiu.1	+	33	13083	c.12952C>T	c.(12952-12954)CGC>TGC	p.R4318C	MACF1_uc010ois.1_Missense_Mutation_p.R3816C|MACF1_uc001cda.1_Missense_Mutation_p.R3703C|MACF1_uc001cdc.1_Missense_Mutation_p.R2773C	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44474178	44474178	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44474178T>C	uc001cll.2	-	5	848	c.656A>G	c.(655-657)TAC>TGC	p.Y219C	SLC6A9_uc009vxe.2_Missense_Mutation_p.Y75C|SLC6A9_uc010okm.1_Missense_Mutation_p.Y146C|SLC6A9_uc001clm.2_Missense_Mutation_p.Y165C|SLC6A9_uc009vxd.2_RNA|SLC6A9_uc010okn.1_Missense_Mutation_p.Y150C|SLC6A9_uc001cln.2_Missense_Mutation_p.Y146C|SLC6A9_uc010oko.1_Missense_Mutation_p.Y35C|SLC6A9_uc010okp.1_RNA	NM_201649	NP_964012	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 2	219	Extracellular (Potential).					integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)													---	---	---	---
UROD	7389	broad.mit.edu	37	1	45479413	45479413	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45479413C>A	uc001cna.1	+	5	532	c.424C>A	c.(424-426)CGA>AGA	p.R142R	HECTD3_uc009vxk.2_5'Flank|HECTD3_uc010olh.1_5'Flank|UROD_uc010oli.1_3'UTR|UROD_uc001cnb.1_Silent_p.R107R|UROD_uc010olj.1_Silent_p.R86R|UROD_uc001cnc.1_Silent_p.R47R	NM_000374	NP_000365	P06132	DCUP_HUMAN	uroporphyrinogen decarboxylase	142			R -> Q (in FPCT).			cytosol|microtubule cytoskeleton|nucleus	uroporphyrinogen decarboxylase activity				0	Acute lymphoblastic leukemia(166;0.155)													Porphyria_Cutanea_Tarda_Type_II				---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45553698	45553698	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45553698G>T	uc001cnd.2	-	2	1035	c.807C>A	c.(805-807)TCC>TCA	p.S269S		NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM domain containing 5	269							zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MKNK1	8569	broad.mit.edu	37	1	47046273	47046273	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47046273G>A	uc001cqb.2	-	4	407	c.163C>T	c.(163-165)CTT>TTT	p.L55F	MKNK1_uc010omd.1_5'UTR|MKNK1_uc001cqc.2_Missense_Mutation_p.L55F|MKNK1_uc009vyi.2_Missense_Mutation_p.L55F|MKNK1_uc010ome.1_5'UTR|MKNK1_uc009vyj.2_Intron|MKNK1_uc001cqd.2_Missense_Mutation_p.L43F|MKNK1_uc010omf.1_Missense_Mutation_p.L55F	NM_003684	NP_003675	Q9BUB5	MKNK1_HUMAN	MAP kinase-interacting serine/threonine kinase 1	55	Protein kinase.|ATP (By similarity).				intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
BTF3L4	91408	broad.mit.edu	37	1	52551842	52551842	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52551842A>G	uc001ctk.2	+	5	637	c.429A>G	c.(427-429)CCA>CCG	p.P143P	BTF3L4_uc001ctl.2_Silent_p.P85P|BTF3L4_uc010onh.1_RNA|BTF3L4_uc001ctm.2_Silent_p.P143P	NM_152265	NP_689478	Q96K17	BT3L4_HUMAN	basic transcription factor 3-like 4 isoform 1	143										large_intestine(1)	1																		---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53722913	53722913	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53722913G>A	uc001cvi.1	-	15	2575	c.2433C>T	c.(2431-2433)CAC>CAT	p.H811H	LRP8_uc001cvh.1_Silent_p.H364H|LRP8_uc001cvk.1_Silent_p.H641H|LRP8_uc001cvj.1_Silent_p.H811H|LRP8_uc001cvl.1_Intron|LRP8_uc001cvm.1_Silent_p.H396H	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein	811	Extracellular (Potential).				cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0																		---	---	---	---
C1orf83	127428	broad.mit.edu	37	1	54554360	54554360	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54554360A>G	uc001cwt.1	+	4	535	c.335A>G	c.(334-336)GAA>GGA	p.E112G	C1orf83_uc001cwu.1_RNA	NM_153035	NP_694580	Q96MN5	TEAN2_HUMAN	hypothetical protein LOC127428	112	TFIIS N-terminal.				transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
C8A	731	broad.mit.edu	37	1	57347128	57347128	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57347128C>A	uc001cyo.2	+	5	607	c.475C>A	c.(475-477)CTG>ATG	p.L159M		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	159	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62261242	62261242	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62261242G>A	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
DNAJC6	9829	broad.mit.edu	37	1	65830386	65830386	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65830386G>T	uc001dcd.1	+	2	255	c.91G>T	c.(91-93)GGG>TGG	p.G31W	DNAJC6_uc001dcc.1_Missense_Mutation_p.G62W|DNAJC6_uc010opc.1_Missense_Mutation_p.G18W|DNAJC6_uc001dce.1_Missense_Mutation_p.G88W	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	31					cellular membrane organization|post-Golgi vesicle-mediated transport	cytosol	heat shock protein binding|protein tyrosine phosphatase activity|SH3 domain binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70502240	70502240	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70502240C>A	uc001dep.2	+	18	2137	c.2107C>A	c.(2107-2109)CGG>AGG	p.R703R	LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	703						centrosome|focal adhesion|nucleolus	protein binding	p.R703P(1)		ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75108700	75108700	+	Intron	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75108700T>A	uc001dgg.2	-							NM_001002912	NP_001002912			hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75108701	75108701	+	Intron	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75108701A>T	uc001dgg.2	-							NM_001002912	NP_001002912			hypothetical protein LOC127254											ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
PRKACB	5567	broad.mit.edu	37	1	84679841	84679841	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84679841A>G	uc001djj.2	+	9	1035	c.771A>G	c.(769-771)CGA>CGG	p.R257R	PRKACB_uc001djl.2_Silent_p.R304R|PRKACB_uc010ort.1_Silent_p.R264R|PRKACB_uc001djn.2_Silent_p.R261R|PRKACB_uc010oru.1_Silent_p.R245R|PRKACB_uc001djp.2_Silent_p.R263R|PRKACB_uc001djq.2_Silent_p.R227R|PRKACB_uc010orv.1_Silent_p.R244R	NM_002731	NP_002722	P22694	KAPCB_HUMAN	cAMP-dependent protein kinase catalytic subunit	257	Protein kinase.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|gluconeogenesis|intracellular protein kinase cascade|nerve growth factor receptor signaling pathway|regulation of insulin secretion|synaptic transmission|transmembrane transport|triglyceride catabolic process|water transport	cAMP-dependent protein kinase complex|centrosome|cytosol|nucleoplasm|plasma membrane	ATP binding|cAMP-dependent protein kinase activity|magnesium ion binding|protein binding			lung(2)|ovary(1)	3				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86590960	86590960	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86590960A>G	uc001dlj.2	-	3	1101	c.1059T>C	c.(1057-1059)ACT>ACC	p.T353T	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA|COL24A1_uc009wcq.2_Silent_p.T353T	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	353					cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
LRRC8B	23507	broad.mit.edu	37	1	90049770	90049770	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90049770G>A	uc001dni.2	+	7	2068	c.1561G>A	c.(1561-1563)GTT>ATT	p.V521I	LRRC8B_uc001dnh.2_Missense_Mutation_p.V521I|LRRC8B_uc001dnj.2_Missense_Mutation_p.V521I	NM_001134476	NP_001127948	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member	521	LRR 3.					integral to membrane				ovary(2)	2		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)														---	---	---	---
ZNF326	284695	broad.mit.edu	37	1	90473078	90473078	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90473078C>T	uc001dnq.2	+	5	523	c.384C>T	c.(382-384)GGC>GGT	p.G128G	ZNF326_uc009wda.1_Intron|ZNF326_uc001dnr.2_Intron	NM_182976	NP_892021	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326 isoform 1	128	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	DNA binding			ovary(1)	1		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)														---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92568094	92568094	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92568094A>G	uc001doo.2	+	3	679	c.412A>G	c.(412-414)ATG>GTG	p.M138V	BTBD8_uc010otc.1_RNA	NM_183242	NP_899065	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	138						nucleus				ovary(1)	1		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)														---	---	---	---
CCDC18	343099	broad.mit.edu	37	1	93698101	93698101	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93698101C>G	uc001dpq.2	+	18	2933	c.2765C>G	c.(2764-2766)ACA>AGA	p.T922R	CCDC18_uc009wdl.1_Missense_Mutation_p.T439R	NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41	803	Potential.									ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)														---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97243163	97243163	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97243163C>G	uc001drq.2	+	6	701	c.455C>G	c.(454-456)GCT>GGT	p.A152G	PTBP2_uc001drn.2_Missense_Mutation_p.A152G|PTBP2_uc001dro.2_Missense_Mutation_p.A152G|PTBP2_uc010otz.1_Missense_Mutation_p.A163G|PTBP2_uc001drp.2_RNA|PTBP2_uc009wdw.2_Missense_Mutation_p.A100G|PTBP2_uc001drr.2_Missense_Mutation_p.A152G|PTBP2_uc010oua.1_Missense_Mutation_p.A160G|PTBP2_uc001dru.2_RNA	NM_021190	NP_067013	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	152							nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110134705	110134705	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110134705C>T	uc001dxz.2	+	8	1072	c.915C>T	c.(913-915)TGC>TGT	p.C305C		NM_006496	NP_006487	P08754	GNAI3_HUMAN	guanine nucleotide binding protein (G protein),	305					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			ovary(1)	1		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)														---	---	---	---
KCNA10	3744	broad.mit.edu	37	1	111060871	111060871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111060871C>T	uc001dzt.1	-	1	927	c.539G>A	c.(538-540)CGG>CAG	p.R180Q		NM_005549	NP_005540	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related	180						voltage-gated potassium channel complex	intracellular cyclic nucleotide activated cation channel activity|voltage-gated potassium channel activity			ovary(3)|large_intestine(1)	4		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)														---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113057636	113057636	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113057636A>G	uc001ecb.2	+	2	838	c.323A>G	c.(322-324)CAG>CGG	p.Q108R	WNT2B_uc001eca.2_Missense_Mutation_p.Q89R|WNT2B_uc009wgg.2_Missense_Mutation_p.Q16R	NM_024494	NP_078613	Q93097	WNT2B_HUMAN	wingless-type MMTV integration site family,	108					chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(2)|breast(2)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113666514	113666514	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113666514G>A	uc001edf.1	+	18	3187	c.2989G>A	c.(2989-2991)GTG>ATG	p.V997M	LRIG2_uc009wgn.1_Missense_Mutation_p.V894M	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	997	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114201800	114201800	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114201800T>C	uc001edk.2	+	16	2909	c.2728T>C	c.(2728-2730)TCC>CCC	p.S910P	MAGI3_uc001edh.3_Missense_Mutation_p.S935P|MAGI3_uc001edi.3_Missense_Mutation_p.S910P|MAGI3_uc010owm.1_Missense_Mutation_p.S935P|MAGI3_uc001edj.2_Missense_Mutation_p.S631P	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	935	Interaction with LPAR2 and GRIN2B.|PDZ 5.				apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114247302	114247302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114247302G>A	uc009wgp.1	-	13	2241	c.1789C>T	c.(1789-1791)CGT>TGT	p.R597C	PHTF1_uc001edn.2_Missense_Mutation_p.R597C|PHTF1_uc001edm.2_Missense_Mutation_p.R354C	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	597						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PIAS3	10401	broad.mit.edu	37	1	145580520	145580520	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145580520G>A	uc001eoc.1	+	7	911	c.820G>A	c.(820-822)GTG>ATG	p.V274M	NBPF10_uc001emp.3_Intron|PIAS3_uc010oyy.1_3'UTR|PIAS3_uc001eod.1_Translation_Start_Site	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	274	PINIT.				positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding			ovary(1)	1	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150307612	150307612	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150307612A>G	uc001eum.3	+	7	1097	c.935A>G	c.(934-936)GAC>GGC	p.D312G	PRPF3_uc009wlp.2_RNA|PRPF3_uc010pca.1_Missense_Mutation_p.D271G|PRPF3_uc010pcb.1_Missense_Mutation_p.D263G|PRPF3_uc009wlq.1_RNA	NM_004698	NP_004689	O43395	PRPF3_HUMAN	PRP3 pre-mRNA processing factor 3 homolog	312					nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding	p.D312E(1)		ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)														---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150444651	150444651	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150444651A>G	uc009wlr.2	+	11	3428	c.3227A>G	c.(3226-3228)GAT>GGT	p.D1076G	RPRD2_uc010pcc.1_3'UTR|RPRD2_uc001eup.3_Missense_Mutation_p.D1050G	NM_015203	NP_056018	Q5VT52	RPRD2_HUMAN	Regulation of nuclear pre-mRNA domain containing	1076							protein binding			ovary(1)	1																		---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151546737	151546737	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151546737G>A	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512			tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)													OREG0003906	type=REGULATORY REGION|Gene=TUFT1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082386	152082386	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152082386G>A	uc001ezp.2	-	2	3307	c.3307C>T	c.(3307-3309)CGC>TGC	p.R1103C	TCHH_uc009wne.1_Missense_Mutation_p.R1103C	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1103	10 X 30 AA tandem repeats.|4-7.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152283156	152283156	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152283156T>C	uc001ezu.1	-	3	4242	c.4206A>G	c.(4204-4206)TCA>TCG	p.S1402S	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1402	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
CRNN	49860	broad.mit.edu	37	1	152383276	152383276	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152383276C>A	uc001ezx.2	-	3	356	c.282G>T	c.(280-282)GAG>GAT	p.E94D		NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	cornulin	94					cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
SPRR2E	6704	broad.mit.edu	37	1	153066064	153066064	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153066064G>T	uc001fbh.2	-	2	225	c.164C>A	c.(163-165)CCT>CAT	p.P55H	SPRR2D_uc009wnz.2_Intron|SPRR2A_uc001fbf.2_Intron|SPRR2A_uc009woa.2_Intron	NM_001024209	NP_001019380	P22531	SPR2E_HUMAN	small proline-rich protein 2E	55					keratinization	cornified envelope|cytoplasm	protein binding|structural molecule activity			ovary(1)	1	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
S100A16	140576	broad.mit.edu	37	1	153580105	153580105	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153580105G>A	uc001fcc.2	-	3	350	c.217C>T	c.(217-219)CGC>TGC	p.R73C	S100A16_uc001fcd.1_Missense_Mutation_p.R73C	NM_080388	NP_525127	Q96FQ6	S10AG_HUMAN	S100 calcium binding protein A16	73	2; high affinity.|EF-hand 2.					cytosol|nucleolus	calcium ion binding|protein homodimerization activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154242685	154242685	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154242685G>A	uc001fep.3	+	27	3345	c.3178G>A	c.(3178-3180)GGG>AGG	p.G1060R	UBAP2L_uc010pel.1_Intron|UBAP2L_uc001feq.2_Intron|UBAP2L_uc001fer.2_Missense_Mutation_p.G273R|HAX1_uc001fet.2_5'Flank|HAX1_uc001fes.2_5'Flank|HAX1_uc010peo.1_5'Flank|HAX1_uc009wou.2_5'Flank|HAX1_uc009wov.2_5'Flank	NM_014847	NP_055662	Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like isoform a	1060					binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
THBS3	7059	broad.mit.edu	37	1	155165843	155165843	+	Missense_Mutation	SNP	C	T	T	rs140469044		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155165843C>T	uc001fix.2	-	22	2770	c.2747G>A	c.(2746-2748)CGT>CAT	p.R916H	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Missense_Mutation_p.R907H|THBS3_uc001fiz.2_Missense_Mutation_p.R879H|THBS3_uc001fiy.2_Missense_Mutation_p.R445H|THBS3_uc010pfu.1_Missense_Mutation_p.R796H	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	916	TSP C-terminal.				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
GBA	2629	broad.mit.edu	37	1	155206085	155206085	+	Missense_Mutation	SNP	C	T	T	rs11558184		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155206085C>T	uc001fjh.2	-	8	1325	c.1175G>A	c.(1174-1176)CGG>CAG	p.R392Q	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Missense_Mutation_p.R279Q|GBA_uc010pfx.1_Missense_Mutation_p.R343Q|GBA_uc001fji.2_Missense_Mutation_p.R392Q|GBA_uc001fjj.2_Missense_Mutation_p.R392Q|GBA_uc001fjk.2_Missense_Mutation_p.R392Q|GBA_uc001fjl.2_Missense_Mutation_p.R392Q|GBA_uc010pfy.1_Missense_Mutation_p.R305Q	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	392			R -> G (in GD).|R -> W (in GD; 5% of normal activity).		carbohydrate metabolic process|cell death|cellular response to tumor necrosis factor|ceramide biosynthetic process|glucosylceramide catabolic process|lysosome organization|negative regulation of interleukin-6 production|negative regulation of MAP kinase activity|positive regulation of protein dephosphorylation|sphingosine biosynthetic process|termination of signal transduction	lysosomal lumen|lysosomal membrane	cation binding|glucosylceramidase activity|receptor binding			ovary(1)|skin(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)									Gaucher_disease_type_I				---	---	---	---
GBA	2629	broad.mit.edu	37	1	155206139	155206139	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155206139A>G	uc001fjh.2	-	8	1271	c.1121T>C	c.(1120-1122)ATG>ACG	p.M374T	RAG1AP1_uc010pey.1_Intron|GBA_uc010pfw.1_Missense_Mutation_p.M261T|GBA_uc010pfx.1_Missense_Mutation_p.M325T|GBA_uc001fji.2_Missense_Mutation_p.M374T|GBA_uc001fjj.2_Missense_Mutation_p.M374T|GBA_uc001fjk.2_Missense_Mutation_p.M374T|GBA_uc001fjl.2_Missense_Mutation_p.M374T|GBA_uc010pfy.1_Missense_Mutation_p.M287T	NM_000157	NP_000148	P04062	GLCM_HUMAN	glucocerebrosidase precursor	374					carbohydrate metabolic process|cell death|cellular response to tumor necrosis factor|ceramide biosynthetic process|glucosylceramide catabolic process|lysosome organization|negative regulation of interleukin-6 production|negative regulation of MAP kinase activity|positive regulation of protein dephosphorylation|sphingosine biosynthetic process|termination of signal transduction	lysosomal lumen|lysosomal membrane	cation binding|glucosylceramidase activity|receptor binding			ovary(1)|skin(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Alglucerase(DB00088)|Imiglucerase(DB00053)									Gaucher_disease_type_I				---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155324299	155324299	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155324299T>C	uc009wqq.2	-	16	7673	c.7193A>G	c.(7192-7194)AAT>AGT	p.N2398S	RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Missense_Mutation_p.N2393S	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	2398					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
PAQR6	79957	broad.mit.edu	37	1	156213673	156213673	+	3'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156213673C>T	uc001fnu.1	-	8					PAQR6_uc010phf.1_Silent_p.E277E|PAQR6_uc001fny.1_Silent_p.E205E|PAQR6_uc001fnv.1_3'UTR|PAQR6_uc010phg.1_3'UTR|PAQR6_uc001fnx.1_3'UTR|PAQR6_uc001fnw.1_Silent_p.E345E|PAQR6_uc001fnz.1_Silent_p.E345E|PAQR6_uc010phh.1_3'UTR|PAQR6_uc001foa.1_3'UTR|PAQR6_uc001fob.1_RNA	NM_198406	NP_940798			progestin and adipoQ receptor family member VI							integral to membrane	receptor activity				0	Hepatocellular(266;0.158)																	---	---	---	---
SMG5	23381	broad.mit.edu	37	1	156230321	156230321	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156230321C>T	uc001foc.3	-	15	2353	c.2204G>A	c.(2203-2205)CGT>CAT	p.R735H	SMG5_uc009wrv.2_Missense_Mutation_p.R220H	NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay	735					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)																	---	---	---	---
C1orf85	112770	broad.mit.edu	37	1	156264628	156264628	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156264628T>C	uc001foh.2	-	2	313	c.300A>G	c.(298-300)CTA>CTG	p.L100L	C1orf85_uc001fof.3_5'Flank|C1orf85_uc001fog.1_RNA|C1orf85_uc001foi.2_Silent_p.L100L|C1orf85_uc009wrx.2_Silent_p.L100L|C1orf85_uc001foj.2_Intron	NM_144580	NP_653181	Q8WWB7	NCUG1_HUMAN	kidney predominant protein NCU-G1 precursor	100	Lumenal (Potential).				positive regulation of transcription from RNA polymerase II promoter	cytosol|integral to membrane|lysosomal membrane|nucleus	ligand-dependent nuclear receptor activity|protein binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)	2	Hepatocellular(266;0.158)																	---	---	---	---
VHLL	391104	broad.mit.edu	37	1	156268937	156268937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156268937G>A	uc001fok.2	-	1	492	c.44C>T	c.(43-45)GCG>GTG	p.A15V		NM_001004319	NP_001004319	Q6RSH7	VHLL_HUMAN	von Hippel-Lindau tumor suppressor-like	15					protein ubiquitination	nucleus				ovary(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
BCAN	63827	broad.mit.edu	37	1	156616821	156616821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156616821G>A	uc001fpp.2	+	3	656	c.320G>A	c.(319-321)CGC>CAC	p.R107H	BCAN_uc001fpo.2_Missense_Mutation_p.R107H	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	107	Ig-like V-type.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
BCAN	63827	broad.mit.edu	37	1	156622146	156622146	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156622146A>G	uc001fpp.2	+	8	1740	c.1404A>G	c.(1402-1404)GAA>GAG	p.E468E	BCAN_uc001fpo.2_Silent_p.E468E	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	468	Glu-rich.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156909341	156909341	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156909341T>C	uc001fqo.2	-	36	5015	c.3975A>G	c.(3973-3975)AAA>AAG	p.K1325K	ARHGEF11_uc010phu.1_Silent_p.K741K|ARHGEF11_uc001fqn.2_Silent_p.K1365K	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1325					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
FCRL4	83417	broad.mit.edu	37	1	157548310	157548310	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157548310C>T	uc001fqw.2	-	10	1519	c.1383G>A	c.(1381-1383)TTG>TTA	p.L461L	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	461	Cytoplasmic (Potential).|ITIM motif 2.					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)																---	---	---	---
FCRL2	79368	broad.mit.edu	37	1	157738406	157738406	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157738406T>C	uc001fre.2	-	5	740	c.681A>G	c.(679-681)TCA>TCG	p.S227S	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Silent_p.S227S|FCRL2_uc009wsp.2_Intron	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	227	Ig-like C2-type 3.|Extracellular (Potential).				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)															---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158615094	158615094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158615094G>A	uc001fst.1	-	29	4277	c.4078C>T	c.(4078-4080)CAC>TAC	p.H1360Y		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1360	Spectrin 13.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
NHLH1	4807	broad.mit.edu	37	1	160340833	160340833	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160340833G>A	uc001fwa.2	+	2	754	c.312G>A	c.(310-312)ACG>ACA	p.T104T		NM_005598	NP_005589	Q02575	HEN1_HUMAN	nescient helix loop helix 1	104	Helix-loop-helix motif.				cell differentiation|central nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_cancers(52;7.11e-19)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
SLAMF7	57823	broad.mit.edu	37	1	160718187	160718187	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160718187G>T	uc001fwq.2	+	2	274	c.259G>T	c.(259-261)GGC>TGC	p.G87C	SLAMF7_uc010pjn.1_Intron|SLAMF7_uc001fws.2_Intron|SLAMF7_uc001fwr.2_Missense_Mutation_p.G87C|SLAMF7_uc010pjo.1_Missense_Mutation_p.G87C|SLAMF7_uc010pjp.1_Intron|SLAMF7_uc010pjq.1_Missense_Mutation_p.G87C|SLAMF7_uc010pjr.1_Intron	NM_021181	NP_067004	Q9NQ25	SLAF7_HUMAN	SLAM family member 7	87	Extracellular (Potential).				cell adhesion|natural killer cell activation|natural killer cell mediated cytotoxicity	integral to membrane	receptor activity			skin(2)|ovary(1)	3	all_cancers(52;2.63e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)															---	---	---	---
CD244	51744	broad.mit.edu	37	1	160803894	160803894	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160803894T>C	uc009wtq.2	-	7	1100	c.922A>G	c.(922-924)ACG>GCG	p.T308A	CD244_uc001fxa.2_Missense_Mutation_p.T303A|CD244_uc009wtp.2_RNA|CD244_uc009wtr.2_Missense_Mutation_p.T211A	NM_016382	NP_057466	Q9BZW8	CD244_HUMAN	CD244 natural killer cell receptor 2B4	308	Cytoplasmic (Potential).				blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
USF1	7391	broad.mit.edu	37	1	161011148	161011148	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161011148G>A	uc001fxi.2	-	7	721	c.526C>T	c.(526-528)CGC>TGC	p.R176C	F11R_uc010pjw.1_5'Flank|F11R_uc001fxf.3_5'Flank|TSTD1_uc010pjx.1_5'Flank|TSTD1_uc009wtw.2_5'Flank|TSTD1_uc001fxh.3_5'Flank|USF1_uc001fxj.2_Missense_Mutation_p.R117C	NM_007122	NP_009053	P22415	USF1_HUMAN	upstream stimulatory factor 1 isoform 1	176					cellular response to insulin stimulus|glucose homeostasis|late viral mRNA transcription|lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter by glucose|response to hypoxia|response to UV	transcription factor complex	bHLH transcription factor binding|histone deacetylase binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)															---	---	---	---
USF1	7391	broad.mit.edu	37	1	161012379	161012379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161012379A>G	uc001fxi.2	-	4	335	c.140T>C	c.(139-141)GTC>GCC	p.V47A	USF1_uc001fxj.2_5'UTR	NM_007122	NP_009053	P22415	USF1_HUMAN	upstream stimulatory factor 1 isoform 1	47					cellular response to insulin stimulus|glucose homeostasis|late viral mRNA transcription|lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter by glucose|response to hypoxia|response to UV	transcription factor complex	bHLH transcription factor binding|histone deacetylase binding|protein heterodimerization activity|protein homodimerization activity|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)															---	---	---	---
USP21	27005	broad.mit.edu	37	1	161134845	161134845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161134845C>T	uc010pke.1	+	13	1896	c.1519C>T	c.(1519-1521)CTT>TTT	p.L507F	USP21_uc010pkf.1_Missense_Mutation_p.L507F|PPOX_uc001fyj.2_5'Flank|PPOX_uc001fyn.2_5'Flank|PPOX_uc001fyg.2_5'Flank|PPOX_uc001fyl.2_5'Flank|PPOX_uc001fym.2_5'Flank|PPOX_uc001fyk.2_5'Flank|PPOX_uc001fyh.2_5'Flank|PPOX_uc010pkg.1_5'Flank|PPOX_uc009wuc.1_5'Flank|PPOX_uc010pkh.1_5'Flank|PPOX_uc001fyi.2_5'Flank	NM_001014443	NP_001014443	Q9UK80	UBP21_HUMAN	ubiquitin-specific protease 21	507					histone deubiquitination|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding|NEDD8-specific protease activity|protein binding|transcription coactivator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)|prostate(1)|breast(1)	5	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)															---	---	---	---
HSPA6	3310	broad.mit.edu	37	1	161494672	161494672	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161494672T>C	uc001gap.2	+	2	884	c.224T>C	c.(223-225)CTG>CCG	p.L75P	HSPA6_uc001gaq.2_Missense_Mutation_p.L75P	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	75					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
HSPA6	3310	broad.mit.edu	37	1	161495689	161495689	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161495689C>T	uc001gap.2	+	2	1901	c.1241C>T	c.(1240-1242)ACG>ATG	p.T414M	HSPA6_uc001gaq.2_Missense_Mutation_p.T414M	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	414					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
NUF2	83540	broad.mit.edu	37	1	163310207	163310207	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163310207C>T	uc001gcq.1	+	9	960	c.660C>T	c.(658-660)ACC>ACT	p.T220T	NUF2_uc001gcp.2_Silent_p.T220T|NUF2_uc001gcr.1_Silent_p.T220T|NUF2_uc009wvc.1_Silent_p.T220T	NM_145697	NP_663735	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	220	Interaction with the N-terminus of NDC80.|Potential.				cell division|chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			ovary(3)|skin(1)	4	all_hematologic(923;0.101)																	---	---	---	---
MGST3	4259	broad.mit.edu	37	1	165623555	165623555	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165623555C>T	uc001gdf.2	+	5	377	c.289C>T	c.(289-291)CGA>TGA	p.R97*	MGST3_uc001gdg.2_Nonsense_Mutation_p.R111*	NM_004528	NP_004519	O14880	MGST3_HUMAN	microsomal glutathione S-transferase 3	97					leukotriene biosynthetic process|leukotriene production involved in inflammatory response|signal transduction|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glutathione peroxidase activity|glutathione transferase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Glutathione(DB00143)													---	---	---	---
ADCY10	55811	broad.mit.edu	37	1	167871248	167871248	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167871248C>A	uc001ger.2	-						ADCY10_uc009wvk.2_Intron|ADCY10_uc010plj.1_Intron|ADCY10_uc009wvl.2_Intron|ADCY10_uc009wvm.2_Intron	NM_018417	NP_060887			adenylate cyclase 10						intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
DCAF6	55827	broad.mit.edu	37	1	167971802	167971802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167971802G>A	uc001gew.2	+	8	1228	c.986G>A	c.(985-987)CGA>CAA	p.R329Q	DCAF6_uc001gev.2_Missense_Mutation_p.R329Q|DCAF6_uc001gex.2_Missense_Mutation_p.R329Q|DCAF6_uc010plk.1_Missense_Mutation_p.R298Q|DCAF6_uc001gey.2_Missense_Mutation_p.R182Q	NM_001017977	NP_001017977	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform b	329					positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
METTL13	51603	broad.mit.edu	37	1	171763553	171763553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171763553G>A	uc001ghz.2	+	7	2058	c.1711G>A	c.(1711-1713)GTC>ATC	p.V571I	METTL13_uc001gia.2_Missense_Mutation_p.V485I|METTL13_uc001gib.2_Missense_Mutation_p.V415I|METTL13_uc010pml.1_Missense_Mutation_p.V570I|METTL13_uc001gic.1_5'Flank	NM_015935	NP_057019	Q8N6R0	MTL13_HUMAN	CGI-01 protein isoform 1	571							methyltransferase activity|protein binding			kidney(1)	1																		---	---	---	---
GAS5	60674	broad.mit.edu	37	1	173833499	173833499	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173833499A>G	uc001gji.2	-						GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_RNA|SNORD81_uc009wwi.1_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175049293	175049293	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175049293C>A	uc001gkl.1	+						TNN_uc010pmx.1_Intron	NM_022093	NP_071376			tenascin N precursor						cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)														---	---	---	---
TNR	7143	broad.mit.edu	37	1	175325505	175325505	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175325505G>A	uc001gkp.1	-	14	3149	c.3068C>T	c.(3067-3069)GCC>GTC	p.A1023V	TNR_uc009wwu.1_Missense_Mutation_p.A1023V	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1023	Fibronectin type-III 8.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178427415	178427415	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178427415A>G	uc001glr.2	+	12	2690	c.2565A>G	c.(2563-2565)ATA>ATG	p.I855M	RASAL2_uc001glq.2_Missense_Mutation_p.I996M|RASAL2_uc009wxc.2_Missense_Mutation_p.I369M	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	855					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
MR1	3140	broad.mit.edu	37	1	181021588	181021588	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181021588C>T	uc001goq.1	+	4	827	c.822C>T	c.(820-822)AAC>AAT	p.N274N	MR1_uc001gor.1_Silent_p.N229N|MR1_uc001gos.1_Intron|MR1_uc010pns.1_Intron	NM_001531	NP_001522	Q95460	HMR1_HUMAN	major histocompatibility complex, class	274	Extracellular (Potential).|Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I|immune response	endoplasmic reticulum|extracellular region|integral to membrane|MHC class I protein complex	MHC class I receptor activity			skin(1)	1																		---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183190061	183190061	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183190061A>G	uc001gqa.2	+	5	919	c.605A>G	c.(604-606)TAC>TGC	p.Y202C	LAMC2_uc001gpz.3_Missense_Mutation_p.Y202C|LAMC2_uc010poa.1_Translation_Start_Site	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	202					cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183511236	183511236	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183511236G>T	uc001gqg.2	+	14	1563	c.1441G>T	c.(1441-1443)GGG>TGG	p.G481W	SMG7_uc010pob.1_Missense_Mutation_p.G510W|SMG7_uc001gqf.2_Missense_Mutation_p.G481W|SMG7_uc001gqh.2_Missense_Mutation_p.G481W|SMG7_uc001gqi.2_Missense_Mutation_p.G439W|SMG7_uc010poc.1_Missense_Mutation_p.G439W	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	481					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
NCF2	4688	broad.mit.edu	37	1	183533129	183533129	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183533129A>G	uc001gqj.3	-						NCF2_uc010pod.1_Intron|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Intron	NM_000433	NP_000424			neutrophil cytosolic factor 2						cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185964206	185964206	+	Silent	SNP	G	A	A	rs112519612		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185964206G>A	uc001grq.1	+	24	3994	c.3765G>A	c.(3763-3765)ACG>ACA	p.T1255T		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1255	Ig-like C2-type 9.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186120322	186120322	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186120322C>T	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186276818	186276818	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276818C>T	uc001gru.3	+	7	2018	c.1967C>T	c.(1966-1968)CCC>CTC	p.P656L	PRG4_uc001grt.3_Missense_Mutation_p.P615L|PRG4_uc009wyl.2_Missense_Mutation_p.P563L|PRG4_uc009wym.2_Missense_Mutation_p.P522L|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	656	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186276820	186276820	+	Missense_Mutation	SNP	A	G	G	rs142325425		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276820A>G	uc001gru.3	+	7	2020	c.1969A>G	c.(1969-1971)ACA>GCA	p.T657A	PRG4_uc001grt.3_Missense_Mutation_p.T616A|PRG4_uc009wyl.2_Missense_Mutation_p.T564A|PRG4_uc009wym.2_Missense_Mutation_p.T523A|PRG4_uc010poo.1_Intron	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	657	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186300667	186300667	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186300667T>C	uc001grv.2	-	39	5948	c.5651A>G	c.(5650-5652)CAG>CGG	p.Q1884R		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1884					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
RGS21	431704	broad.mit.edu	37	1	192335240	192335240	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192335240C>A	uc001gsh.2	+	5	619	c.445C>A	c.(445-447)CTC>ATC	p.L149I		NM_001039152	NP_001034241	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	149					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2																		---	---	---	---
TROVE2	6738	broad.mit.edu	37	1	193050593	193050593	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193050593G>A	uc001gss.2	+	6	1361	c.1186G>A	c.(1186-1188)GCT>ACT	p.A396T	TROVE2_uc001gst.1_Missense_Mutation_p.A121T|TROVE2_uc001gsu.1_Missense_Mutation_p.A121T|TROVE2_uc001gsv.1_Missense_Mutation_p.A396T|TROVE2_uc001gsw.2_Missense_Mutation_p.A396T|TROVE2_uc009wyp.2_Missense_Mutation_p.A396T|TROVE2_uc009wyq.2_Missense_Mutation_p.A396T|TROVE2_uc001gsx.1_Missense_Mutation_p.A396T	NM_004600	NP_004591	P10155	RO60_HUMAN	TROVE domain family, member 2 isoform 2	396					transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198682089	198682089	+	Silent	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198682089A>T	uc001gur.1	+	12	1353	c.1173A>T	c.(1171-1173)GGA>GGT	p.G391G	PTPRC_uc001gus.1_Silent_p.G343G|PTPRC_uc001gut.1_Silent_p.G230G|PTPRC_uc009wzf.1_Silent_p.G279G|PTPRC_uc010ppg.1_Silent_p.G327G	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	391	Extracellular (Potential).|Fibronectin type-III 1.				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																		---	---	---	---
ZNF281	23528	broad.mit.edu	37	1	200376939	200376939	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200376939C>T	uc001gve.2	-	2	2002	c.1895G>A	c.(1894-1896)CGA>CAA	p.R632Q	ZNF281_uc001gvf.1_Missense_Mutation_p.R632Q|ZNF281_uc001gvg.1_Missense_Mutation_p.R596Q	NM_012482	NP_036614	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	632					negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200628222	200628222	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200628222C>T	uc009wzk.2	-	4	1238	c.995G>A	c.(994-996)CGA>CAA	p.R332Q	DDX59_uc010ppl.1_Missense_Mutation_p.R332Q	NM_001031725	NP_001026895	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	332	Helicase ATP-binding.					intracellular	ATP binding|ATP-dependent helicase activity|metal ion binding|RNA binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200801853	200801853	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200801853T>C	uc001gvl.2	+	7	1110	c.840T>C	c.(838-840)ACT>ACC	p.T280T	CAMSAP1L1_uc001gvk.2_Silent_p.T269T|CAMSAP1L1_uc001gvm.2_Silent_p.T269T	NM_203459	NP_982284	Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein	280	CH.					cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
C1orf106	55765	broad.mit.edu	37	1	200867455	200867455	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200867455C>A	uc001gvo.2	+	2	212	c.182C>A	c.(181-183)CCT>CAT	p.P61H	C1orf106_uc010ppm.1_5'UTR	NM_018265	NP_060735	Q3KP66	CA106_HUMAN	hypothetical protein LOC55765 isoform 1	61										skin(2)|ovary(1)	3																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201031583	201031583	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201031583C>A	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201824899	201824899	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201824899T>C	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
CHI3L1	1116	broad.mit.edu	37	1	203149635	203149635	+	Missense_Mutation	SNP	C	T	T	rs76446715	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203149635C>T	uc001gzi.2	-	8	1028	c.857G>A	c.(856-858)CGG>CAG	p.R286Q	FMOD_uc010pqi.1_Intron|CHI3L1_uc001gzk.1_Intron|CHI3L1_uc001gzj.2_Intron|CHI3L1_uc001gzl.3_5'Flank	NM_001276	NP_001267	P36222	CH3L1_HUMAN	chitinase 3-like 1 precursor	286					chitin catabolic process	extracellular space|proteinaceous extracellular matrix	cation binding|chitinase activity|extracellular matrix structural constituent|sugar binding			pancreas(1)	1																		---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203317092	203317092	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203317092C>T	uc001gzr.2	-	2	443	c.307G>A	c.(307-309)GTT>ATT	p.V103I	FMOD_uc010pqi.1_RNA	NM_002023	NP_002014	Q06828	FMOD_HUMAN	fibromodulin precursor	103	LRRNT.				transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
ZC3H11A	9877	broad.mit.edu	37	1	203821387	203821387	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203821387C>T	uc001hac.2	+	20	2909	c.2293C>T	c.(2293-2295)CCC>TCC	p.P765S	ZC3H11A_uc001had.2_Missense_Mutation_p.P765S|ZC3H11A_uc001hae.2_Missense_Mutation_p.P765S|ZC3H11A_uc001haf.2_Missense_Mutation_p.P765S|ZC3H11A_uc010pqm.1_Missense_Mutation_p.P711S	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	765							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204438278	204438278	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204438278C>G	uc001haw.2	-	3	1132	c.653G>C	c.(652-654)GGT>GCT	p.G218A	PIK3C2B_uc010pqv.1_Missense_Mutation_p.G218A|PIK3C2B_uc001hax.1_Missense_Mutation_p.G218A|PIK3C2B_uc009xbd.1_RNA	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	218	Interaction with GRB2.				cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204985644	204985644	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204985644A>G	uc001hbj.2	+	30	4028	c.3700A>G	c.(3700-3702)AAT>GAT	p.N1234D	NFASC_uc010pra.1_Missense_Mutation_p.N1168D|NFASC_uc001hbi.2_Missense_Mutation_p.N1163D|NFASC_uc010prb.1_Missense_Mutation_p.N1183D|NFASC_uc010prc.1_Missense_Mutation_p.N734D|NFASC_uc001hbl.1_Missense_Mutation_p.N310D|NFASC_uc001hbm.1_Missense_Mutation_p.N257D|NFASC_uc009xbh.1_Silent_p.S88S|NFASC_uc001hbo.1_Silent_p.S109S	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	1341	Cytoplasmic (Potential).				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
CNTN2	6900	broad.mit.edu	37	1	205041113	205041113	+	Silent	SNP	G	A	A	rs115143667	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205041113G>A	uc001hbr.2	+	20	2852	c.2583G>A	c.(2581-2583)GCG>GCA	p.A861A	CNTN2_uc001hbq.1_Silent_p.A752A|CNTN2_uc001hbs.2_Silent_p.A649A	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor	861	Fibronectin type-III 3.				axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
DSTYK	25778	broad.mit.edu	37	1	205116774	205116774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205116774A>G	uc001hbw.2	-	13	2766	c.2702T>C	c.(2701-2703)ATT>ACT	p.I901T	DSTYK_uc001hbx.2_Missense_Mutation_p.I856T	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1	901	Protein kinase.					cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1																		---	---	---	---
TMCC2	9911	broad.mit.edu	37	1	205211172	205211172	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205211172G>T	uc001hbz.1	+	3	1191	c.747G>T	c.(745-747)AAG>AAT	p.K249N	TMCC2_uc010prf.1_Missense_Mutation_p.K171N	NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	249				TALLLADGSNVYLLAEEAEGIGDK -> MNQVVQPLMSRHS ACRGSQAHLSW (in Ref. 6).		integral to membrane	protein binding			pancreas(1)	1	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
PFKFB2	5208	broad.mit.edu	37	1	207241025	207241025	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207241025T>G	uc001hfg.2	+	9	923	c.814T>G	c.(814-816)TCT>GCT	p.S272A	PFKFB2_uc010psc.1_Missense_Mutation_p.S174A|PFKFB2_uc001hfh.2_Missense_Mutation_p.S272A|PFKFB2_uc009xcc.2_Missense_Mutation_p.S230A|PFKFB2_uc010psd.1_Missense_Mutation_p.S86A	NM_006212	NP_006203	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,	272	Fructose-2,6-bisphosphatase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			ovary(1)	1	Prostate(682;0.19)																	---	---	---	---
CR1	1378	broad.mit.edu	37	1	207679272	207679272	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207679272C>T	uc001hfy.2	+	2	285	c.145C>T	c.(145-147)CTT>TTT	p.L49F	CR1_uc009xcl.1_Missense_Mutation_p.L49F|CR1_uc001hfx.2_Missense_Mutation_p.L49F|CR1_uc010psg.1_Missense_Mutation_p.L49F|CR1_uc009xcj.1_Missense_Mutation_p.L49F|CR1_uc009xck.1_Missense_Mutation_p.L49F	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	49	Sushi 1.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1	1378	broad.mit.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207787831G>T	uc001hfy.2	+	32	5448	c.5308G>T	c.(5308-5310)GAA>TAA	p.E1770*	CR1_uc001hfx.2_Nonsense_Mutation_p.E2220*	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1770	Extracellular (Potential).|Sushi 27.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
CR1L	1379	broad.mit.edu	37	1	207818592	207818592	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207818592T>A	uc001hga.3	+	1	135	c.14T>A	c.(13-15)GTC>GAC	p.V5D	CR1L_uc001hfz.2_RNA	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	5						cytoplasm|extracellular region|membrane					0																		---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208216416	208216416	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208216416C>A	uc001hgz.2	-	21	4765	c.4007G>T	c.(4006-4008)CGG>CTG	p.R1336L		NM_025179	NP_079455	O75051	PLXA2_HUMAN	plexin A2 precursor	1336	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215812576	215812576	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215812576G>T	uc001hku.1	-	69	15360	c.14973C>A	c.(14971-14973)TTC>TTA	p.F4991L		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4991	Fibronectin type-III 35.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215814033	215814033	+	Silent	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215814033A>C	uc001hku.1	-	68	15222	c.14835T>G	c.(14833-14835)TCT>TCG	p.S4945S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4945	Fibronectin type-III 35.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215847625	215847625	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215847625C>A	uc001hku.1	-	63	14015	c.13628G>T	c.(13627-13629)AGG>ATG	p.R4543M		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4543	Fibronectin type-III 31.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220363814	220363814	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220363814A>G	uc010puk.1	-	15	1700	c.1536T>C	c.(1534-1536)AGT>AGC	p.S512S	RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_Silent_p.S92S	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	512					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
MOSC2	54996	broad.mit.edu	37	1	220928413	220928413	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220928413C>T	uc001hmq.2	+	2	595	c.397C>T	c.(397-399)CTG>TTG	p.L133L	MOSC2_uc001hmr.2_Silent_p.L133L|MOSC2_uc009xdx.2_Silent_p.L133L	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2	133						mitochondrial outer membrane|peroxisome	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)														---	---	---	---
FAM177B	400823	broad.mit.edu	37	1	222919899	222919899	+	Silent	SNP	C	T	T	rs141453662	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222919899C>T	uc001hnt.2	+	3	278	c.12C>T	c.(10-12)GAC>GAT	p.D4D	uc001hnr.1_Intron|FAM177B_uc009xeb.2_RNA	NM_207468	NP_997351	A6PVY3	F177B_HUMAN	hypothetical protein LOC400823	4										ovary(1)	1																		---	---	---	---
NVL	4931	broad.mit.edu	37	1	224424208	224424208	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224424208G>A	uc001hok.2	-	20	2409	c.2366C>T	c.(2365-2367)ACG>ATG	p.T789M	NVL_uc001hol.2_Missense_Mutation_p.T683M|NVL_uc010pvd.1_Missense_Mutation_p.T698M|NVL_uc010pve.1_Missense_Mutation_p.T600M|NVL_uc010pvf.1_RNA	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1	789						aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
EPHX1	2052	broad.mit.edu	37	1	226027630	226027630	+	Missense_Mutation	SNP	A	G	G	rs35073925	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226027630A>G	uc001hpk.2	+	6	903	c.823A>G	c.(823-825)ACT>GCT	p.T275A	EPHX1_uc001hpl.2_Missense_Mutation_p.T275A	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	275					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)																	---	---	---	---
C1orf55	163859	broad.mit.edu	37	1	226175749	226175749	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226175749C>A	uc001hpu.3	-	6	1035	c.982G>T	c.(982-984)GAA>TAA	p.E328*	C1orf55_uc001hpv.2_Nonsense_Mutation_p.E328*	NM_152608	NP_689821	Q6IQ49	CA055_HUMAN	hypothetical protein LOC163859	328										lung(1)	1	Breast(184;0.197)																	---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226426761	226426761	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226426761G>A	uc001hqa.2	-	12	1514	c.1204C>T	c.(1204-1206)CGG>TGG	p.R402W	LIN9_uc001hqb.2_Missense_Mutation_p.R367W|LIN9_uc001hqc.2_Missense_Mutation_p.R334W|LIN9_uc009xel.1_Missense_Mutation_p.R367W	NM_173083	NP_775106	Q5TKA1	LIN9_HUMAN	lin-9 homolog	386	Potential.				cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227239649	227239649	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227239649C>T	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Missense_Mutation_p.S245N|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqu.1_Missense_Mutation_p.S153N	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
WNT3A	89780	broad.mit.edu	37	1	228210365	228210365	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228210365C>T	uc001hrq.1	+						WNT3A_uc001hrp.1_Intron	NM_033131	NP_149122			wingless-type MMTV integration site family,						axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of neuron projection development|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|positive regulation of transcription from RNA polymerase II promoter|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)																---	---	---	---
TAF5L	27097	broad.mit.edu	37	1	229737984	229737984	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229737984G>A	uc001htq.2	-	4	1096	c.930C>T	c.(928-930)GAC>GAT	p.D310D	TAF5L_uc001htr.2_Silent_p.D310D	NM_014409	NP_055224	O75529	TAF5L_HUMAN	PCAF associated factor 65 beta isoform a	310					histone H3 acetylation|transcription from RNA polymerase II promoter	STAGA complex|transcription factor TFTC complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
C1orf124	83932	broad.mit.edu	37	1	231488454	231488454	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231488454A>T	uc001hur.2	+	5	1265	c.817A>T	c.(817-819)ATC>TTC	p.I273F	C1orf124_uc001hus.2_3'UTR|C1orf124_uc001hut.2_3'UTR	NM_032018	NP_114407	Q9H040	CA124_HUMAN	hypothetical protein LOC83932 isoform a	273					DNA repair	nuclear speck	DNA binding|metal ion binding				0	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233120166	233120166	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233120166G>A	uc001hvl.2	-	34	6533	c.6298C>T	c.(6298-6300)CGA>TGA	p.R2100*	PCNXL2_uc001hvk.1_3'UTR|PCNXL2_uc001hvm.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	2100						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236740226	236740226	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236740226G>T	uc001hyd.1	-	21	2904	c.2779C>A	c.(2779-2781)CTG>ATG	p.L927M	HEATR1_uc009xgh.1_Missense_Mutation_p.L170M	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	927					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236925910	236925910	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236925910C>T	uc001hyf.2	+	21	2880	c.2676C>T	c.(2674-2676)AGC>AGT	p.S892S	ACTN2_uc001hyg.2_Silent_p.S684S|ACTN2_uc009xgi.1_Silent_p.S892S|ACTN2_uc010pxu.1_Silent_p.S581S|ACTN2_uc001hyh.2_Silent_p.S580S	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	892					focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237732550	237732550	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237732550C>T	uc001hyl.1	+	29	3649	c.3529C>T	c.(3529-3531)CTG>TTG	p.L1177L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1177	Cytoplasmic (By similarity).|4 X approximate repeats.|B30.2/SPRY 2.				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)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237791158	237791158	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237791158C>T	uc001hyl.1	+	41	6338	c.6218C>T	c.(6217-6219)TCT>TTT	p.S2073F		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2073	Cytoplasmic (By similarity).|4 X approximate repeats.				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)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241875194	241875194	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241875194G>A	uc001hze.1	+						WDR64_uc001hzf.1_Intron					RecName: Full=WD repeat-containing protein 64;											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241912901	241912901	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241912901G>T	uc001hzf.1	+	8	930	c.777G>T	c.(775-777)CCG>CCT	p.P259P	WDR64_uc001hzg.1_Silent_p.P5P	NM_144625	NP_653226	B1ANS9	WDR64_HUMAN	WD repeat domain 64	539	WD 7.									skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
MAP1LC3C	440738	broad.mit.edu	37	1	242159681	242159681	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242159681G>A	uc001hzk.2	-	4	303	c.228C>T	c.(226-228)CGC>CGT	p.R76R		NM_001004343	NP_001004343	Q9BXW4	MLP3C_HUMAN	microtubule-associated protein 1 light chain 3	76					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(106;0.0188)															---	---	---	---
CEP170	9859	broad.mit.edu	37	1	243303325	243303325	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243303325C>T	uc001hzs.2	-	16	4552	c.4144G>A	c.(4144-4146)GGT>AGT	p.G1382S	CEP170_uc001hzt.2_Missense_Mutation_p.G1258S|CEP170_uc001hzu.2_Missense_Mutation_p.G1284S|CEP170_uc001hzr.2_5'UTR|CEP170_uc001hzv.1_Missense_Mutation_p.G734S	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	1382	Targeting to microtubules.|Targeting to centrosomes.					centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)															---	---	---	---
ZNF496	84838	broad.mit.edu	37	1	247464263	247464263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247464263C>T	uc001ico.2	-	9	1787	c.1322G>A	c.(1321-1323)GGG>GAG	p.G441E	ZNF496_uc009xgv.2_Missense_Mutation_p.G477E|ZNF496_uc001icp.2_Missense_Mutation_p.G441E	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	441	C2H2-type 2.				positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)															---	---	---	---
OR2G2	81470	broad.mit.edu	37	1	247751877	247751877	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247751877G>A	uc010pyy.1	+	1	216	c.216G>A	c.(214-216)CTG>CTA	p.L72L		NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)															---	---	---	---
OR2G3	81469	broad.mit.edu	37	1	247769166	247769166	+	Silent	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247769166T>G	uc010pyz.1	+	1	279	c.279T>G	c.(277-279)ACT>ACG	p.T93T		NM_001001914	NP_001001914	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G,	93	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)															---	---	---	---
TRIM58	25893	broad.mit.edu	37	1	248031365	248031365	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248031365G>T	uc001ido.2	+	5	919	c.871G>T	c.(871-873)GTG>TTG	p.V291L	OR2W3_uc001idp.1_5'UTR	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	291	B30.2/SPRY.					intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
OR2M5	127059	broad.mit.edu	37	1	248308964	248308964	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248308964G>A	uc010pze.1	+	1	515	c.515G>A	c.(514-516)CGG>CAG	p.R172Q		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)															---	---	---	---
TMEM18	129787	broad.mit.edu	37	2	675560	675560	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:675560C>T	uc002qwl.2	-	2	222	c.128G>A	c.(127-129)TGC>TAC	p.C43Y	TMEM18_uc002qwk.2_RNA|uc002qwm.1_5'Flank	NM_152834	NP_690047	Q96B42	TMM18_HUMAN	transmembrane protein 18	43	Helical; (Potential).				cell migration	integral to membrane|nuclear membrane				ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)														---	---	---	---
ALLC	55821	broad.mit.edu	37	2	3730671	3730671	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3730671G>A	uc010ewt.2	+							NM_018436	NP_060906			allantoicase isoform a								allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)											HNSCC(21;0.051)			---	---	---	---
SOX11	6664	broad.mit.edu	37	2	5833022	5833022	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5833022A>G	uc002qyj.2	+	1	224	c.169A>G	c.(169-171)ATG>GTG	p.M57V		NM_003108	NP_003099	P35716	SOX11_HUMAN	SRY-box 11	57	HMG box.				cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis	cytoplasm|nucleolus	enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding			central_nervous_system(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)														---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10140759	10140759	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10140759A>G	uc002raa.2	+	16	1952	c.1781A>G	c.(1780-1782)TAC>TGC	p.Y594C	GRHL1_uc002rab.2_RNA|GRHL1_uc002rad.2_Missense_Mutation_p.Y405C|GRHL1_uc010yjb.1_Missense_Mutation_p.Y443C	NM_198182	NP_937825	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1	594					cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11750919	11750919	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11750919G>A	uc002rbk.1	+	18	3072	c.2772G>A	c.(2770-2772)ACG>ACA	p.T924T	GREB1_uc002rbo.1_Silent_p.T558T|GREB1_uc002rbp.1_5'Flank	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	924						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)														---	---	---	---
DDX1	1653	broad.mit.edu	37	2	15736846	15736846	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15736846C>T	uc002rce.2	+						DDX1_uc010yjq.1_Intron	NM_004939	NP_004930			DEAD (Asp-Glu-Ala-Asp) box polypeptide 1						DNA duplex unwinding|double-strand break repair|multicellular organismal development|regulation of transcription, DNA-dependent|regulation of translational initiation|spliceosome assembly|transcription, DNA-dependent	cleavage body|stress granule|tRNA-splicing ligase complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|DNA/RNA helicase activity|exonuclease activity|poly(A) RNA binding|protein binding|RNA helicase activity|transcription cofactor activity			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	all_epithelial(98;2.96e-07)|Acute lymphoblastic leukemia(84;4.24e-05)|Ovarian(717;0.0694)	GBM - Glioblastoma multiforme(3;0.00969)	Epithelial(75;4.35e-05)|OV - Ovarian serous cystadenocarcinoma(76;0.133)														---	---	---	---
MATN3	4148	broad.mit.edu	37	2	20194089	20194089	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20194089C>A	uc002rdl.2	-	7	1439	c.1376G>T	c.(1375-1377)AGC>ATC	p.S459I	MATN3_uc010exu.1_Missense_Mutation_p.S417I	NM_002381	NP_002372	O15232	MATN3_HUMAN	matrilin 3 precursor	459	By similarity.				skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
MFSD2B	388931	broad.mit.edu	37	2	24247037	24247037	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24247037C>T	uc002reo.1	+	13	1400	c.1386C>T	c.(1384-1386)GGC>GGT	p.G462G		NM_001080473	NP_001073942	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing	462	Helical; (Potential).				transport	integral to membrane				ovary(2)	2																		---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24483988	24483988	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24483988G>T	uc002rfe.2	-	22	2927	c.2669C>A	c.(2668-2670)CCT>CAT	p.P890H	ITSN2_uc002rff.2_Missense_Mutation_p.P863H|ITSN2_uc002rfg.2_Missense_Mutation_p.P890H	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	890					endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26683555	26683555	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26683555C>A	uc002rhk.2	-	45	5900	c.5773G>T	c.(5773-5775)GGC>TGC	p.G1925C	OTOF_uc010yla.1_Missense_Mutation_p.G655C|OTOF_uc002rhh.2_Missense_Mutation_p.G1158C|OTOF_uc002rhi.2_Missense_Mutation_p.G1235C|OTOF_uc002rhj.2_Missense_Mutation_p.G1158C	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1925	Cytoplasmic (Potential).				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
GTF3C2	2976	broad.mit.edu	37	2	27556591	27556591	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27556591C>T	uc002rjv.1	-	13	2026	c.1663G>A	c.(1663-1665)GGT>AGT	p.G555S	GTF3C2_uc010eyy.1_Missense_Mutation_p.G10S|GTF3C2_uc002rju.1_Missense_Mutation_p.G566S|GTF3C2_uc002rjw.1_Missense_Mutation_p.G555S|GTF3C2_uc010eyz.1_Missense_Mutation_p.G555S|uc002rjy.1_5'Flank	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	555	WD 2.					transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
IFT172	26160	broad.mit.edu	37	2	27683894	27683894	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27683894C>T	uc002rku.2	-	23	2560	c.2509G>A	c.(2509-2511)GCA>ACA	p.A837T		NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	837	TPR 3.				cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31178502	31178502	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31178502C>T	uc002rnr.2	-	6	1255	c.636G>A	c.(634-636)CTG>CTA	p.L212L	GALNT14_uc002rnq.2_Silent_p.L192L|GALNT14_uc002rns.2_Silent_p.L217L|GALNT14_uc010ymr.1_Silent_p.L177L|GALNT14_uc010ezo.1_Silent_p.L179L|GALNT14_uc010ezp.1_Silent_p.L183L	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	212	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
XDH	7498	broad.mit.edu	37	2	31560626	31560626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31560626C>T	uc002rnv.1	-	35	3911	c.3832G>A	c.(3832-3834)GCC>ACC	p.A1278T		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	1278					purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33623607	33623607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33623607G>A	uc002ros.2	+	34	5164	c.5164G>A	c.(5164-5166)GAG>AAG	p.E1722K	LTBP1_uc002rot.2_Missense_Mutation_p.E1396K|LTBP1_uc002rou.2_Missense_Mutation_p.E1395K|LTBP1_uc002rov.2_Missense_Mutation_p.E1342K|LTBP1_uc010ymz.1_Missense_Mutation_p.E1353K|LTBP1_uc010yna.1_Missense_Mutation_p.E1300K|LTBP1_uc010ynb.1_Missense_Mutation_p.E619K	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1721					negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36740836	36740836	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36740836C>T	uc002rpd.2	+	11	1957	c.1918C>T	c.(1918-1920)CTG>TTG	p.L640L		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	640	VWFC 3.|Extracellular (Potential).				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44203369	44203369	+	Splice_Site	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44203369C>A	uc002rtr.2	-	6	709	c.651_splice	c.e6-1	p.S217_splice	LRPPRC_uc010yob.1_Splice_Site_p.S117_splice|LRPPRC_uc010faw.1_Splice_Site_p.S191_splice	NM_133259	NP_573566			leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
SIX3	6496	broad.mit.edu	37	2	45169338	45169338	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45169338G>A	uc002run.1	+	1	302	c.95G>A	c.(94-96)AGC>AAC	p.S32N		NM_005413	NP_005404	O95343	SIX3_HUMAN	SIX homeobox 3	32					visual perception	nucleus					0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47705414	47705414	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47705414T>C	uc002rvy.1	+	14	2282	c.2214T>C	c.(2212-2214)TCT>TCC	p.S738S	MSH2_uc010yoh.1_Silent_p.S672S|MSH2_uc002rvz.2_Silent_p.S738S|MSH2_uc010fbg.2_Silent_p.S548S	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2	738					B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		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)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
RTN4	57142	broad.mit.edu	37	2	55252334	55252334	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55252334T>C	uc002rye.2	-	3	3199	c.2901A>G	c.(2899-2901)ATA>ATG	p.I967M	RTN4_uc002ryd.2_Missense_Mutation_p.I761M|RTN4_uc002ryf.2_Intron|RTN4_uc002ryg.2_Intron	NM_020532	NP_065393	Q9NQC3	RTN4_HUMAN	reticulon 4 isoform A	967	Cytoplasmic (Potential).				apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
PELI1	57162	broad.mit.edu	37	2	64322041	64322041	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64322041G>A	uc002scs.3	-	6	5091	c.1052C>T	c.(1051-1053)GCT>GTT	p.A351V	PELI1_uc002sct.3_Missense_Mutation_p.A351V|PELI1_uc002scr.3_Missense_Mutation_p.A172V	NM_020651	NP_065702	Q96FA3	PELI1_HUMAN	pellino protein	351					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol				ovary(1)	1																		---	---	---	---
CEP68	23177	broad.mit.edu	37	2	65296924	65296924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65296924G>A	uc002sdl.3	+	2	560	c.346G>A	c.(346-348)GGG>AGG	p.G116R	CEP68_uc002sdj.2_Missense_Mutation_p.G116R|CEP68_uc010yqb.1_Missense_Mutation_p.G116R|CEP68_uc002sdk.3_Missense_Mutation_p.G116R|CEP68_uc010yqc.1_Missense_Mutation_p.G116R|CEP68_uc010yqd.1_Missense_Mutation_p.G116R	NM_015147	NP_055962	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	116					centrosome organization	centrosome				skin(1)	1																		---	---	---	---
PCBP1	5093	broad.mit.edu	37	2	70315822	70315822	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70315822C>T	uc002sgf.2	+	1	1238	c.947C>T	c.(946-948)GCC>GTC	p.A316V	ASPRV1_uc002sga.2_5'Flank|uc002sgb.1_5'Flank|uc002sgd.2_5'Flank|uc002sge.1_5'Flank	NM_006196	NP_006187	Q15365	PCBP1_HUMAN	poly(rC) binding protein 1	316	KH 3.				nuclear mRNA splicing, via spliceosome	cytoplasm|nucleoplasm|ribonucleoprotein complex	protein binding|RNA binding|single-stranded DNA binding				0																		---	---	---	---
ATP6V1B1	525	broad.mit.edu	37	2	71189997	71189997	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71189997G>A	uc002shj.2	+	9	963	c.876G>A	c.(874-876)ACG>ACA	p.T292T	ATP6V1B1_uc010fdv.2_Silent_p.T292T|ATP6V1B1_uc010fdw.2_RNA|ATP6V1B1_uc010fdx.2_Silent_p.T250T	NM_001692	NP_001683	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1	292					ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport	apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			skin(1)	1																		---	---	---	---
EMX1	2016	broad.mit.edu	37	2	73160979	73160979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73160979C>T	uc002sin.1	+	3	1147	c.769C>T	c.(769-771)CCT>TCT	p.P257S	EMX1_uc002sim.1_Missense_Mutation_p.A209V	NM_004097	NP_004088	Q04741	EMX1_HUMAN	empty spiracles homolog 1	224						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
CAPG	822	broad.mit.edu	37	2	85628347	85628347	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85628347G>A	uc002spl.1	-	5	707	c.457C>T	c.(457-459)CGG>TGG	p.R153W	CAPG_uc002spm.1_Missense_Mutation_p.R153W|CAPG_uc010ysq.1_Missense_Mutation_p.R153W|CAPG_uc010fgi.1_Missense_Mutation_p.R153W|CAPG_uc010fgj.1_Missense_Mutation_p.R47W	NM_001747	NP_001738	P40121	CAPG_HUMAN	gelsolin-like capping protein	153	Gelsolin-like 2.				barbed-end actin filament capping|protein complex assembly	F-actin capping protein complex|melanosome|nuclear membrane|nucleolus	actin binding				0																		---	---	---	---
EIF2AK3	9451	broad.mit.edu	37	2	88890059	88890059	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88890059A>T	uc002stc.3	-	6	1269	c.1067T>A	c.(1066-1068)TTT>TAT	p.F356Y		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	356	Lumenal (Potential).				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3																		---	---	---	---
ASTL	431705	broad.mit.edu	37	2	96789597	96789597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96789597C>T	uc010yui.1	-	9	1288	c.1288G>A	c.(1288-1290)GAA>AAA	p.E430K		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase precursor	430					proteolysis		metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
ASTL	431705	broad.mit.edu	37	2	96798442	96798442	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96798442C>T	uc010yui.1	-	6	474	c.474G>A	c.(472-474)GGG>GGA	p.G158G		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase precursor	158					proteolysis		metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96945296	96945296	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96945296A>G	uc002svu.2	-	36	5112	c.5026T>C	c.(5026-5028)TAT>CAT	p.Y1676H	SNRNP200_uc002svt.2_Missense_Mutation_p.Y286H|SNRNP200_uc010yuj.1_RNA	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1676	Helicase C-terminal 2.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
ANKRD39	51239	broad.mit.edu	37	2	97514112	97514112	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97514112G>A	uc002sxd.3	-	4	510	c.478C>T	c.(478-480)CGG>TGG	p.R160W		NM_016466	NP_057550	Q53RE8	ANR39_HUMAN	ankyrin repeat domain 39	160											0																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99688288	99688288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99688288G>A	uc002szg.3	-	12	1616	c.988C>T	c.(988-990)CGT>TGT	p.R330C	TSGA10_uc002szh.3_Missense_Mutation_p.R330C|TSGA10_uc002szi.3_Missense_Mutation_p.R330C|TSGA10_uc010fin.1_Missense_Mutation_p.R330C|TSGA10_uc010yvn.1_3'UTR	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	330					spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105924423	105924423	+	Silent	SNP	C	A	A	rs149165498	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105924423C>A	uc002tcq.2	-	2	420	c.336G>T	c.(334-336)TCG>TCT	p.S112S	TGFBRAP1_uc002tcr.3_Silent_p.S112S	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	112	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																		---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109300406	109300406	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109300406A>C	uc002teg.2	+	10	1048	c.929A>C	c.(928-930)GAG>GCG	p.E310A	LIMS1_uc002tef.2_Missense_Mutation_p.E322A|LIMS1_uc002teh.2_Missense_Mutation_p.E310A|LIMS1_uc002tei.2_Missense_Mutation_p.E310A|LIMS1_uc002tej.2_Missense_Mutation_p.E347A|LIMS1_uc002tek.3_Missense_Mutation_p.E372A|uc002tel.2_5'Flank	NM_004987	NP_004978	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	310					cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112541976	112541976	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112541976C>T	uc002thi.2	-	41	5166	c.4919G>A	c.(4918-4920)GGC>GAC	p.G1640D		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1640					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112614266	112614266	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112614266C>A	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120677688	120677688	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120677688A>G	uc002tmf.1	+	12	1643	c.872A>G	c.(871-873)TAC>TGC	p.Y291C	PTPN4_uc010flj.1_Missense_Mutation_p.Y4C	NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type	291	FERM.					cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)													---	---	---	---
PTPN18	26469	broad.mit.edu	37	2	131116512	131116512	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131116512A>G	uc002trc.2	+	2	267	c.166A>G	c.(166-168)AAC>GAC	p.N56D	PTPN18_uc002trd.2_Missense_Mutation_p.N56D|PTPN18_uc002trb.2_Intron	NM_014369	NP_055184	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type	56	Tyrosine-protein phosphatase.					cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)																	---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133402818	133402818	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133402818A>G	uc002ttl.2	+	2	1470	c.1001A>G	c.(1000-1002)TAC>TGC	p.Y334C	LYPD1_uc002ttm.3_3'UTR|LYPD1_uc002ttn.2_3'UTR|LYPD1_uc002tto.2_3'UTR	NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39	334	Helical; Name=7; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141816614	141816614	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141816614G>T	uc002tvj.1	-	9	2218	c.1246C>A	c.(1246-1248)CTT>ATT	p.L416I	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	416	Extracellular (Potential).|LDL-receptor class B 4.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153399319	153399319	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153399319G>A	uc002tye.2	+	3	635	c.268G>A	c.(268-270)GCT>ACT	p.A90T		NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2	90	GBD/FH3.				actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160027037	160027037	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160027037C>T	uc002uag.2	+	10	1346	c.1072C>T	c.(1072-1074)CGA>TGA	p.R358*	TANC1_uc010fol.1_Nonsense_Mutation_p.R252*|TANC1_uc010zcm.1_Nonsense_Mutation_p.R350*|TANC1_uc010fom.1_Nonsense_Mutation_p.R164*	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	358						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162930006	162930006	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162930006G>A	uc002ubz.2	-						DPP4_uc010fpb.2_Intron|DPP4_uc002uca.1_5'Flank|DPP4_uc002ucb.1_5'Flank	NM_001935	NP_001926			dipeptidylpeptidase IV						cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166223736	166223736	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166223736G>T	uc002udc.2	+	19	3820	c.3530G>T	c.(3529-3531)CGG>CTG	p.R1177L	SCN2A_uc002udd.2_Missense_Mutation_p.R1177L|SCN2A_uc002ude.2_Missense_Mutation_p.R1177L	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	1177					myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166535659	166535659	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166535659A>G	uc002udf.2	+	7	1530	c.1154A>G	c.(1153-1155)GAC>GGC	p.D385G	CSRNP3_uc002udg.2_Missense_Mutation_p.D385G	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	385					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																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168102239	168102239	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168102239A>C	uc002udx.2	+	8	4355	c.4337A>C	c.(4336-4338)AAG>ACG	p.K1446T	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.K1271T|XIRP2_uc010fpq.2_Missense_Mutation_p.K1224T|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1271					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168102522	168102522	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168102522T>C	uc002udx.2	+	8	4638	c.4620T>C	c.(4618-4620)ACT>ACC	p.T1540T	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Silent_p.T1365T|XIRP2_uc010fpq.2_Silent_p.T1318T|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1365					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171376034	171376034	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171376034G>A	uc002ufy.2	+	30	3702	c.3559G>A	c.(3559-3561)GTC>ATC	p.V1187I	MYO3B_uc002ufv.2_Missense_Mutation_p.V1174I|MYO3B_uc010fqb.1_Missense_Mutation_p.V1174I|MYO3B_uc002ufz.2_Missense_Mutation_p.V1160I|MYO3B_uc002ufw.2_RNA|MYO3B_uc002ufx.2_RNA|MYO3B_uc002ugb.2_RNA	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	1187					response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173852994	173852994	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173852994C>T	uc002uhv.3	+	13	1408	c.1221C>T	c.(1219-1221)TAC>TAT	p.Y407Y	RAPGEF4_uc002uhw.3_Silent_p.Y263Y|RAPGEF4_uc010zec.1_Silent_p.Y254Y|RAPGEF4_uc010zed.1_Silent_p.Y236Y|RAPGEF4_uc010zee.1_Silent_p.Y254Y|RAPGEF4_uc010fqo.2_Silent_p.Y236Y|RAPGEF4_uc010zef.1_Silent_p.Y187Y|RAPGEF4_uc010zeg.1_Silent_p.Y234Y|RAPGEF4_uc010fqp.1_Silent_p.Y187Y|RAPGEF4_uc010zeh.1_Silent_p.Y187Y	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	407	cAMP 2.				blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
CDCA7	83879	broad.mit.edu	37	2	174228609	174228609	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174228609C>A	uc002uid.1	+	4	579	c.448C>A	c.(448-450)CCA>ACA	p.P150T	CDCA7_uc002uic.1_Missense_Mutation_p.P229T|CDCA7_uc010zej.1_Missense_Mutation_p.P185T|CDCA7_uc010zek.1_Missense_Mutation_p.P108T	NM_145810	NP_665809	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7 isoform 2	150					regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)															---	---	---	---
HOXD11	3237	broad.mit.edu	37	2	176972255	176972255	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176972255G>A	uc002uki.2	+	1	172	c.172G>A	c.(172-174)GTG>ATG	p.V58M	HOXD11_uc010fqx.2_Intron	NM_021192	NP_067015	P31277	HXD11_HUMAN	homeobox D11	58						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)				T	NUP98	AML								---	---	---	---
TTC30A	92104	broad.mit.edu	37	2	178481542	178481542	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178481542T>C	uc002ulo.2	-	1	2153	c.1888A>G	c.(1888-1890)ATT>GTT	p.I630V		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	630					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179396464	179396464	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179396464G>A	uc010zfg.1	-	307	97398	c.97174C>T	c.(97174-97176)CGT>TGT	p.R32392C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R26087C|TTN_uc010zfi.1_Missense_Mutation_p.R26020C|TTN_uc010zfj.1_Missense_Mutation_p.R25895C|TTN_uc002umq.2_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	33319							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)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179474047	179474047	+	Silent	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179474047T>A	uc010zfg.1	-	222	44510	c.44286A>T	c.(44284-44286)GGA>GGT	p.G14762G	uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G8457G|TTN_uc010zfi.1_Silent_p.G8390G|TTN_uc010zfj.1_Silent_p.G8265G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	15689							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)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179594261	179594261	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179594261C>T	uc010zfg.1	-	61	15114	c.14890G>A	c.(14890-14892)GTG>ATG	p.V4964M	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.V1625M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	5891							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)															---	---	---	---
SSFA2	6744	broad.mit.edu	37	2	182774703	182774703	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182774703G>A	uc002uoi.2	+						SSFA2_uc002uoh.2_Intron|SSFA2_uc002uoj.2_Intron|SSFA2_uc002uok.2_Intron|SSFA2_uc010zfo.1_Intron|SSFA2_uc002uol.2_Intron	NM_001130445	NP_001123917			sperm specific antigen 2 isoform 1							cytoplasm|plasma membrane	actin binding			breast(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0856)															---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185801763	185801763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185801763G>A	uc002uph.2	+	4	2234	c.1640G>A	c.(1639-1641)AGG>AAG	p.R547K		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	547						intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201846082	201846082	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201846082C>T	uc002uws.3	-	12	1692	c.1504G>A	c.(1504-1506)GAA>AAA	p.E502K	FAM126B_uc002uwu.2_Missense_Mutation_p.E476K|FAM126B_uc002uwv.2_Missense_Mutation_p.E502K	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN	hypothetical protein LOC285172	502						intracellular				ovary(1)	1																		---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203420873	203420873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203420873A>G	uc002uzf.3	+	12	3633	c.2485A>G	c.(2485-2487)ACA>GCA	p.T829A	BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	829	Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206592721	206592721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206592721G>A	uc002vaw.2	+	7	1888	c.1097G>A	c.(1096-1098)AGC>AAC	p.S366N	NRP2_uc002vat.2_Missense_Mutation_p.S366N|NRP2_uc002vau.2_Missense_Mutation_p.S366N|NRP2_uc002vav.2_Missense_Mutation_p.S366N|NRP2_uc002vax.2_Missense_Mutation_p.S366N|NRP2_uc002vay.2_Missense_Mutation_p.S366N|NRP2_uc010fud.2_Missense_Mutation_p.S366N	NM_201266	NP_957718	O60462	NRP2_HUMAN	neuropilin 2 isoform 1 precursor	366	Extracellular (Potential).|F5/8 type C 1.				angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207171007	207171007	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207171007T>C	uc002vbp.2	+	5	2005	c.1755T>C	c.(1753-1755)TGT>TGC	p.C585C		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	585							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207171142	207171142	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207171142C>A	uc002vbp.2	+	5	2140	c.1890C>A	c.(1888-1890)GTC>GTA	p.V630V		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	630							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210518129	210518129	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210518129C>T	uc002vde.1	+	4	483	c.235C>T	c.(235-237)CTG>TTG	p.L79L	MAP2_uc002vdc.1_Silent_p.L79L|MAP2_uc002vdd.1_Silent_p.L79L|MAP2_uc002vdf.1_Silent_p.L79L|MAP2_uc002vdg.1_Silent_p.L79L|MAP2_uc002vdh.1_Silent_p.L79L|MAP2_uc002vdi.1_Silent_p.L79L	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	79					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
ACADL	33	broad.mit.edu	37	2	211082788	211082788	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211082788T>C	uc002vdz.3	-	3	500	c.272A>G	c.(271-273)GAA>GGA	p.E91G	ACADL_uc010zjg.1_Missense_Mutation_p.E91G	NM_001608	NP_001599	P28330	ACADL_HUMAN	long-chain acyl-CoA dehydrogenase precursor	91					carnitine catabolic process|carnitine metabolic process, CoA-linked|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial matrix	long-chain-acyl-CoA dehydrogenase activity|palmitoyl-CoA oxidase activity				0		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)														---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212288922	212288922	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212288922G>A	uc002veg.1	-	23	2922	c.2824C>T	c.(2824-2826)CCT>TCT	p.P942S	ERBB4_uc002veh.1_Missense_Mutation_p.P942S|ERBB4_uc010zji.1_Missense_Mutation_p.P932S|ERBB4_uc010zjj.1_Missense_Mutation_p.P932S	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	942	Protein kinase.|Cytoplasmic (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212652859	212652859	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212652859T>C	uc002veg.1	-	4	545	c.447A>G	c.(445-447)GTA>GTG	p.V149V	ERBB4_uc002veh.1_Silent_p.V149V|ERBB4_uc010zji.1_Silent_p.V149V|ERBB4_uc010zjj.1_Silent_p.V149V|ERBB4_uc010fut.1_Silent_p.V149V	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	149	Extracellular (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
FN1	2335	broad.mit.edu	37	2	216253000	216253000	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216253000A>G	uc002vfa.2	-	27	4543	c.4277T>C	c.(4276-4278)GTA>GCA	p.V1426A	FN1_uc002vfb.2_Missense_Mutation_p.V1335A|FN1_uc002vfc.2_Missense_Mutation_p.V1335A|FN1_uc002vfd.2_Missense_Mutation_p.V1426A|FN1_uc002vfe.2_Missense_Mutation_p.V1335A|FN1_uc002vff.2_Missense_Mutation_p.V1335A|FN1_uc002vfg.2_Missense_Mutation_p.V1335A|FN1_uc002vfh.2_Missense_Mutation_p.V1335A|FN1_uc002vfi.2_Missense_Mutation_p.V1426A|FN1_uc002vfj.2_Missense_Mutation_p.V1426A|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Missense_Mutation_p.V53A	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1425	Fibronectin type-III 9.|Cell-attachment.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
RNF25	64320	broad.mit.edu	37	2	219530627	219530627	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219530627A>G	uc002vit.2	-						RNF25_uc010fvw.2_Intron	NM_022453	NP_071898			ring finger protein 25						positive regulation of NF-kappaB transcription factor activity	cytosol|nucleus	NF-kappaB binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
PRKAG3	53632	broad.mit.edu	37	2	219689020	219689020	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219689020T>C	uc002vjb.1	-	12	1297	c.1278A>G	c.(1276-1278)CTA>CTG	p.L426L		NM_017431	NP_059127	Q9UGI9	AAKG3_HUMAN	AMP-activated protein kinase, non-catalytic	426					cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|intracellular protein kinase cascade|regulation of fatty acid oxidation	cytosol	AMP-activated protein kinase activity|protein kinase binding			ovary(1)|lung(1)	2		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
STK16	8576	broad.mit.edu	37	2	220113164	220113164	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220113164G>T	uc002vko.2	+	8	958	c.801G>T	c.(799-801)CAG>CAT	p.Q267H	STK16_uc002vks.2_Missense_Mutation_p.Q149H|STK16_uc002vkp.2_Missense_Mutation_p.Q267H|STK16_uc002vkr.2_Missense_Mutation_p.Q200H|STK16_uc002vkq.2_Missense_Mutation_p.Q312H	NM_001008910	NP_001008910	O75716	STK16_HUMAN	serine/threonine kinase 16	267	Protein kinase.				protein complex assembly	membrane	ATP binding|protein binding|protein serine/threonine kinase activity			skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220333707	220333707	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220333707G>A	uc010fwg.2	+	12	3428	c.3428G>A	c.(3427-3429)GGC>GAC	p.G1143D		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1143	Ig-like 5.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220353849	220353849	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220353849C>T	uc010fwg.2	+	35	8223	c.8223C>T	c.(8221-8223)GGC>GGT	p.G2741G		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2741	Fibronectin type-III 2.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
FARSB	10056	broad.mit.edu	37	2	223478636	223478636	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223478636A>G	uc002vne.1	-	15	1391	c.1356T>C	c.(1354-1356)ACT>ACC	p.T452T	FARSB_uc010zlq.1_Silent_p.T472T|FARSB_uc002vnf.1_Silent_p.T353T	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	452					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)													---	---	---	---
CUL3	8452	broad.mit.edu	37	2	225376238	225376238	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225376238G>A	uc002vny.2	-	6	1100	c.716C>T	c.(715-717)GCT>GTT	p.A239V	CUL3_uc010zls.1_Missense_Mutation_p.A173V|CUL3_uc010fwy.1_Missense_Mutation_p.A245V	NM_003590	NP_003581	Q13618	CUL3_HUMAN	cullin 3	239					cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227892635	227892635	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227892635C>A	uc010zlt.1	-	42	4718	c.4064G>T	c.(4063-4065)GGG>GTG	p.G1355V		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1355	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
SP110	3431	broad.mit.edu	37	2	231042314	231042314	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231042314G>A	uc002vqh.3	-	14	1770	c.1530C>T	c.(1528-1530)AAC>AAT	p.N510N	SP110_uc002vqg.3_Silent_p.N510N|SP110_uc002vqi.3_Silent_p.N510N|SP110_uc010fxk.2_Silent_p.N508N|SP110_uc010fxj.2_Silent_p.N153N	NM_004509	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein isoform a	510	SAND.				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
ALPP	250	broad.mit.edu	37	2	233243931	233243931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233243931C>T	uc002vsq.2	+	3	380	c.215C>T	c.(214-216)ACA>ATA	p.T72I	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	72						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)														---	---	---	---
ALPP	250	broad.mit.edu	37	2	233245422	233245422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233245422C>T	uc002vsq.2	+	8	1120	c.955C>T	c.(955-957)CGC>TGC	p.R319C	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	319						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233671202	233671202	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233671202T>C	uc002vti.3	+	17	1978	c.1641T>C	c.(1639-1641)GGT>GGC	p.G547G	GIGYF2_uc010zmj.1_Silent_p.G547G|GIGYF2_uc002vtg.2_Silent_p.G541G|GIGYF2_uc002vtj.3_Silent_p.G568G|GIGYF2_uc002vtk.3_Silent_p.G547G|GIGYF2_uc002vth.3_Silent_p.G541G|GIGYF2_uc010zmk.1_RNA|GIGYF2_uc010zml.1_Silent_p.G378G	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b	547	GYF.|Required for GRB10-binding (By similarity).				cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238289897	238289897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238289897C>T	uc002vwl.2	-	5	1843	c.1558G>A	c.(1558-1560)GGC>AGC	p.G520S	COL6A3_uc002vwo.2_Missense_Mutation_p.G314S|COL6A3_uc010znj.1_Missense_Mutation_p.G113S|COL6A3_uc002vwq.2_Missense_Mutation_p.G314S|COL6A3_uc002vwr.2_Missense_Mutation_p.G113S|COL6A3_uc010znk.1_Missense_Mutation_p.G520S	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	520	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241496621	241496621	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241496621A>G	uc002vyz.1	-						ANKMY1_uc002vza.1_Silent_p.A44A|ANKMY1_uc010fzd.1_Silent_p.A44A|ANKMY1_uc002vzb.1_Silent_p.A44A|ANKMY1_uc002vzc.1_Silent_p.A44A|ANKMY1_uc002vzd.1_Silent_p.A44A|ANKMY1_uc010fze.1_Intron|ANKMY1_uc002vze.2_Intron|ANKMY1_uc002vzf.2_Intron|DUSP28_uc002vzg.2_5'Flank|DUSP28_uc002vzh.2_5'Flank	NM_016552	NP_057636			ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)												OREG0015353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RNPEPL1	57140	broad.mit.edu	37	2	241516115	241516115	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241516115C>T	uc002vzi.2	+	9	1574	c.981C>T	c.(979-981)TCC>TCT	p.S327S	RNPEPL1_uc010fzf.2_Silent_p.S233S|RNPEPL1_uc002vzj.2_5'UTR	NM_018226	NP_060696	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like	327					leukotriene biosynthetic process|proteolysis		aminopeptidase activity|metallopeptidase activity|zinc ion binding			large_intestine(1)|skin(1)	2		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)														---	---	---	---
AQP12B	653437	broad.mit.edu	37	2	241622123	241622123	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241622123C>T	uc010fzj.2	-	1	195	c.132G>A	c.(130-132)GCG>GCA	p.A44A	AQP12B_uc002vzt.2_Intron	NM_001102467	NP_001095937	A6NM10	AQ12B_HUMAN	aquaporin 12B	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane	transporter activity				0		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)														---	---	---	---
IL5RA	3568	broad.mit.edu	37	3	3118207	3118207	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3118207A>G	uc011ask.1	-						IL5RA_uc010hbq.2_Intron|IL5RA_uc010hbr.2_Intron|IL5RA_uc010hbs.2_Intron|IL5RA_uc011asl.1_Intron|IL5RA_uc010hbp.2_Intron	NM_000564	NP_000555			interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)														---	---	---	---
LRRN1	57633	broad.mit.edu	37	3	3886509	3886509	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3886509C>T	uc003bpt.3	+	2	945	c.184C>T	c.(184-186)CGC>TGC	p.R62C	SUMF1_uc003bps.1_Intron	NM_020873	NP_065924	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1 precursor	62	LRRNT.|Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)														---	---	---	---
EDEM1	9695	broad.mit.edu	37	3	5244713	5244713	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5244713T>C	uc003bqi.2	+	5	1053	c.921T>C	c.(919-921)GGT>GGC	p.G307G	EDEM1_uc011asz.1_Silent_p.G85G|EDEM1_uc003bqh.2_Silent_p.G307G	NM_014674	NP_055489	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like	307	Lumenal (Potential).				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			ovary(2)|breast(1)	3				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	6903265	6903265	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6903265G>A	uc003bqm.2	+	1	464	c.190G>A	c.(190-192)GGA>AGA	p.G64R	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Missense_Mutation_p.G64R|GRM7_uc003bql.2_Missense_Mutation_p.G64R	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	64	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
TADA3	10474	broad.mit.edu	37	3	9822157	9822157	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9822157A>C	uc003bsx.1	-	9	1731	c.1183T>G	c.(1183-1185)TTT>GTT	p.F395V	TADA3_uc010hcn.1_Missense_Mutation_p.F395V|TADA3_uc003bsw.1_Missense_Mutation_p.F224V	NM_006354	NP_006345	O75528	TADA3_HUMAN	transcriptional adaptor 3 isoform a	395	Potential.				estrogen receptor signaling pathway|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	ligand-dependent nuclear receptor binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SEC13	6396	broad.mit.edu	37	3	10346789	10346789	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10346789A>C	uc003bvn.2	-	7	755	c.636T>G	c.(634-636)AGT>AGG	p.S212R	SEC13_uc003bvl.2_Missense_Mutation_p.S144R|SEC13_uc003bvm.2_Missense_Mutation_p.S198R|SEC13_uc003bvp.2_Missense_Mutation_p.S215R|SEC13_uc003bvo.2_Missense_Mutation_p.S258R|SEC13_uc003bvq.1_Missense_Mutation_p.S198R|SEC13_uc003bvr.1_Missense_Mutation_p.S198R	NM_183352	NP_899195	P55735	SEC13_HUMAN	SEC13 protein isoform 1	212	WD 5.				COPII vesicle coating|intracellular protein transport|mitotic prometaphase|mRNA transport|post-translational protein modification|protein N-linked glycosylation via asparagine|transmembrane transport	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10382234	10382234	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10382234G>A	uc003bvt.2	-	20	3511	c.3072C>T	c.(3070-3072)GAC>GAT	p.D1024D	ATP2B2_uc003bvv.2_Silent_p.D979D|ATP2B2_uc003bvw.2_Silent_p.D979D|ATP2B2_uc010hdo.2_Silent_p.D729D	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	1024	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10387133	10387133	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10387133G>A	uc003bvt.2	-	18	3077	c.2638C>T	c.(2638-2640)CAG>TAG	p.Q880*	ATP2B2_uc003bvv.2_Nonsense_Mutation_p.Q835*|ATP2B2_uc003bvw.2_Nonsense_Mutation_p.Q835*|ATP2B2_uc010hdo.2_Nonsense_Mutation_p.Q585*	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	880	Helical; (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13371949	13371949	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13371949T>C	uc003bxv.1	-							NM_024923	NP_079199			nucleoporin 210 precursor						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13383334	13383334	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13383334C>T	uc003bxv.1	-	23	3225	c.3142G>A	c.(3142-3144)GGT>AGT	p.G1048S		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	1048	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
C3orf20	84077	broad.mit.edu	37	3	14744763	14744763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14744763G>A	uc003byy.2	+	6	1276	c.872G>A	c.(871-873)CGC>CAC	p.R291H	C3orf20_uc003byz.2_Missense_Mutation_p.R169H|C3orf20_uc003bza.2_Missense_Mutation_p.R169H|C3orf20_uc003byx.1_Missense_Mutation_p.R291H	NM_032137	NP_115513	Q8ND61	CC020_HUMAN	hypothetical protein LOC84077	291						cytoplasm|integral to membrane				ovary(3)|skin(1)	4																		---	---	---	---
FGD5	152273	broad.mit.edu	37	3	14939591	14939591	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14939591C>T	uc003bzc.2	+	6	3165	c.3055C>T	c.(3055-3057)CGT>TGT	p.R1019C	FGD5_uc011avk.1_Missense_Mutation_p.R1019C|FGD5_uc003bzd.2_Missense_Mutation_p.R97C	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1019	DH.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
RARB	5915	broad.mit.edu	37	3	25502773	25502773	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25502773G>A	uc011awl.1	+	2	334	c.268G>A	c.(268-270)GTC>ATC	p.V90I	RARB_uc003cdi.1_5'UTR|RARB_uc003cdh.2_Missense_Mutation_p.V83I	NM_016152	NP_057236	P10826	RARB_HUMAN	retinoic acid receptor, beta isoform 2	90	NR C4-type.|Nuclear receptor.		V -> I (in a colorectal cancer sample; somatic mutation).		embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	p.V83I(1)		ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)													---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25665821	25665821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25665821G>A	uc011awn.1	-	20	2505	c.2462C>T	c.(2461-2463)GCT>GTT	p.A821V	TOP2B_uc003cdj.2_Missense_Mutation_p.A816V	NM_001068	NP_001059	Q02880	TOP2B_HUMAN	DNA topoisomerase II, beta isozyme	821					DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
LRRC3B	116135	broad.mit.edu	37	3	26751789	26751789	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26751789C>T	uc003cdp.2	+	2	1215	c.626C>T	c.(625-627)ACC>ATC	p.T209I	LRRC3B_uc003cdq.2_Missense_Mutation_p.T209I	NM_052953	NP_443185	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B precursor	209	Helical; (Potential).					integral to membrane				pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27453218	27453218	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27453218A>G	uc003cdv.2	-	12	1725	c.1654T>C	c.(1654-1656)TTT>CTT	p.F552L	SLC4A7_uc011awu.1_RNA|SLC4A7_uc011awv.1_RNA|SLC4A7_uc003cdu.3_Missense_Mutation_p.F433L|SLC4A7_uc011aww.1_Missense_Mutation_p.F561L|SLC4A7_uc011awx.1_Missense_Mutation_p.F548L|SLC4A7_uc011awy.1_Missense_Mutation_p.F544L|SLC4A7_uc011awz.1_RNA|SLC4A7_uc011axa.1_Missense_Mutation_p.F433L|SLC4A7_uc011axb.1_Missense_Mutation_p.F548L|SLC4A7_uc010hfl.2_Missense_Mutation_p.F102L|SLC4A7_uc003cdw.2_Missense_Mutation_p.F428L	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	552	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27463207	27463207	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27463207C>T	uc003cdv.2	-	9	1374	c.1303G>A	c.(1303-1305)GAA>AAA	p.E435K	SLC4A7_uc011awu.1_RNA|SLC4A7_uc011awv.1_RNA|SLC4A7_uc003cdu.3_Missense_Mutation_p.E316K|SLC4A7_uc011aww.1_Missense_Mutation_p.E444K|SLC4A7_uc011awx.1_Missense_Mutation_p.E431K|SLC4A7_uc011awy.1_Missense_Mutation_p.E427K|SLC4A7_uc011awz.1_RNA|SLC4A7_uc011axa.1_Missense_Mutation_p.E316K|SLC4A7_uc011axb.1_Missense_Mutation_p.E431K|SLC4A7_uc010hfl.2_Intron|SLC4A7_uc003cdw.2_Missense_Mutation_p.E311K	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	435	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32769301	32769301	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32769301A>G	uc003cfc.1	+	10	1409	c.1154A>G	c.(1153-1155)TAT>TGT	p.Y385C	CNOT10_uc011axi.1_Missense_Mutation_p.Y157C|CNOT10_uc003cfd.1_Missense_Mutation_p.Y384C|CNOT10_uc003cfe.1_Missense_Mutation_p.Y385C|CNOT10_uc010hfv.1_RNA|CNOT10_uc011axj.1_Missense_Mutation_p.Y445C|CNOT10_uc010hfw.1_Missense_Mutation_p.Y80C	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10	385					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32800967	32800967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32800967G>A	uc003cfc.1	+	14	1868	c.1613G>A	c.(1612-1614)TGC>TAC	p.C538Y	CNOT10_uc011axi.1_Missense_Mutation_p.C310Y|CNOT10_uc003cfd.1_Missense_Mutation_p.C537Y|CNOT10_uc003cfe.1_Missense_Mutation_p.C511Y|CNOT10_uc010hfv.1_RNA|CNOT10_uc011axj.1_Missense_Mutation_p.C598Y|CNOT10_uc010hfw.1_Missense_Mutation_p.C233Y	NM_015442	NP_056257	Q9H9A5	CNOTA_HUMAN	CCR4-NOT transcription complex, subunit 10	538					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
TMPPE	643853	broad.mit.edu	37	3	33134737	33134737	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33134737A>G	uc003cfk.2	-	2	1142	c.951T>C	c.(949-951)GGT>GGC	p.G317G	GLB1_uc003cfh.1_Intron|GLB1_uc003cfi.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron|TMPPE_uc011axl.1_Silent_p.G180G	NM_001039770	NP_001034859	Q6ZT21	TMPPE_HUMAN	transmembrane protein with	317						integral to membrane	metal ion binding				0																		---	---	---	---
CRTAP	10491	broad.mit.edu	37	3	33165913	33165913	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33165913G>A	uc003cfl.3	+	3	755	c.635G>A	c.(634-636)CGA>CAA	p.R212Q	CRTAP_uc010hfz.2_Missense_Mutation_p.R212Q|CRTAP_uc003cfm.2_Missense_Mutation_p.R33Q|CRTAP_uc003cfn.2_Missense_Mutation_p.R33Q	NM_006371	NP_006362	O75718	CRTAP_HUMAN	cartilage associated protein precursor	212						proteinaceous extracellular matrix	binding				0																		---	---	---	---
SUSD5	26032	broad.mit.edu	37	3	33194480	33194480	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33194480C>T	uc003cfo.1	-	5	2062	c.1644G>A	c.(1642-1644)GGG>GGA	p.G548G		NM_015551	NP_056366	O60279	SUSD5_HUMAN	sushi domain containing 5 precursor	548	Extracellular (Potential).				cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STAC	6769	broad.mit.edu	37	3	36485023	36485023	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36485023G>A	uc003cgh.1	+	2	318	c.279G>A	c.(277-279)ACG>ACA	p.T93T	STAC_uc010hgd.1_RNA|STAC_uc011aya.1_Silent_p.T93T	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	93					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
TRANK1	9881	broad.mit.edu	37	3	36897095	36897095	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36897095T>G	uc003cgj.2	-	3	2638	c.2336A>C	c.(2335-2337)TAT>TCT	p.Y779S		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	1329					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
VILL	50853	broad.mit.edu	37	3	38037343	38037343	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38037343G>T	uc003chj.2	+						VILL_uc003chk.1_Intron|VILL_uc003chl.2_Intron|VILL_uc010hgu.2_Intron	NM_015873	NP_056957			villin-like protein						actin filament capping|cytoskeleton organization	actin cytoskeleton	actin binding|structural constituent of cytoskeleton				0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
ACVR2B	93	broad.mit.edu	37	3	38519934	38519934	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38519934T>C	uc003cif.2	+	5	615	c.591T>C	c.(589-591)GCT>GCC	p.A197A	ACVR2B_uc003cig.2_5'UTR	NM_001106	NP_001097	Q13705	AVR2B_HUMAN	activin A receptor, type IIB precursor	197	ATP (By similarity).|Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent	cell surface|cytoplasm|integral to plasma membrane	activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)														---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38802798	38802798	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38802798G>A	uc003ciq.2	-	6	768	c.768C>T	c.(766-768)TGC>TGT	p.C256C		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	256	Helical; Name=S5 of repeat I; (Potential).|I.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
HHATL	57467	broad.mit.edu	37	3	42734238	42734238	+	3'UTR	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42734238C>A	uc003clw.2	-	13					HHATL_uc003clx.2_3'UTR	NM_020707	NP_065758			hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)														---	---	---	---
SNRK	54861	broad.mit.edu	37	3	43389492	43389492	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43389492G>A	uc003cms.3	+	7	2073	c.1741G>A	c.(1741-1743)GGG>AGG	p.G581R	SNRK_uc003cmt.3_Missense_Mutation_p.G581R|SNRK_uc010hik.2_Missense_Mutation_p.G581R|SNRK_uc011azr.1_Missense_Mutation_p.G375R	NM_017719	NP_060189	Q9NRH2	SNRK_HUMAN	SNF related kinase	581					myeloid cell differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)														---	---	---	---
C3orf75	54859	broad.mit.edu	37	3	47537600	47537600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47537600C>T	uc003crk.2	-	7	879	c.760G>A	c.(760-762)GTG>ATG	p.V254M	C3orf75_uc003crj.2_Missense_Mutation_p.V181M|C3orf75_uc011bba.1_Missense_Mutation_p.V205M	NM_001031703	NP_001026873	Q0PNE2	CC075_HUMAN	transmembrane protein 103	254											0																		---	---	---	---
PLXNB1	5364	broad.mit.edu	37	3	48459755	48459755	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48459755A>G	uc003csw.2	-	15	3337	c.3067T>C	c.(3067-3069)TCC>CCC	p.S1023P	PLXNB1_uc003csu.2_Missense_Mutation_p.S840P|PLXNB1_uc003csx.2_Missense_Mutation_p.S1023P|PLXNB1_uc010hjx.1_RNA|PLXNB1_uc003csy.1_5'Flank	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1 precursor	1023	Extracellular (Potential).				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48628013	48628013	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48628013C>T	uc003ctz.2	-	14	1786	c.1785G>A	c.(1783-1785)CCG>CCA	p.P595P		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	595	Nonhelical region (NC1).				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48630677	48630677	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48630677A>G	uc003ctz.2	-	5	541	c.540T>C	c.(538-540)CCT>CCC	p.P180P		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	180	Nonhelical region (NC1).|VWFA 1.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
P4HTM	54681	broad.mit.edu	37	3	49038942	49038942	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49038942C>T	uc003cvg.2	+	3	857	c.508C>T	c.(508-510)CGC>TGC	p.R170C	P4HTM_uc003cvh.2_Missense_Mutation_p.R170C|P4HTM_uc010hkm.1_Missense_Mutation_p.R56C	NM_177939	NP_808808	Q9NXG6	P4HTM_HUMAN	hypoxia-inducible factor prolyl 4-hydroxylase	170	Lumenal (Potential).					endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)|pancreas(1)	2					Vitamin C(DB00126)													---	---	---	---
WDR6	11180	broad.mit.edu	37	3	49051263	49051263	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49051263G>A	uc003cvj.2	+	2	2524	c.2386G>A	c.(2386-2388)GCA>ACA	p.A796T	WDR6_uc011bbx.1_3'UTR|WDR6_uc011bby.1_Missense_Mutation_p.A244T|WDR6_uc010hkn.2_Missense_Mutation_p.A740T|WDR6_uc011bbz.1_Missense_Mutation_p.A715T	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	766	WD 12.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)												OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
QRICH1	54870	broad.mit.edu	37	3	49084020	49084020	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49084020G>A	uc010hkq.2	-						QRICH1_uc003cvu.2_Intron|QRICH1_uc003cvv.2_Intron	NM_198880	NP_942581			glutamine-rich 1											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49693858	49693858	+	Missense_Mutation	SNP	C	T	T	rs5848870		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49693858C>T	uc003cxe.3	+	5	6983	c.6869C>T	c.(6868-6870)GCC>GTC	p.A2290V		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	2290					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)														---	---	---	---
APEH	327	broad.mit.edu	37	3	49720100	49720100	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49720100G>T	uc003cxf.2	+	19	2214	c.1814G>T	c.(1813-1815)AGG>ATG	p.R605M	APEH_uc010hkw.1_Missense_Mutation_p.R605M	NM_001640	NP_001631	P13798	ACPH_HUMAN	N-acylaminoacyl-peptide hydrolase	605					proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
MST1	4485	broad.mit.edu	37	3	49721545	49721545	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49721545T>C	uc003cxg.2	-	18	2166	c.2094A>G	c.(2092-2094)GTA>GTG	p.V698V		NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	684	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
AMIGO3	386724	broad.mit.edu	37	3	49756812	49756812	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49756812A>G	uc003cxj.2	-	1	427	c.87T>C	c.(85-87)CGT>CGC	p.R29R	RNF123_uc003cxh.2_Intron|RNF123_uc003cxi.2_Intron	NM_198722	NP_942015	Q86WK7	AMGO3_HUMAN	adhesion molecule with Ig-like domain 3	29	Extracellular (Potential).|LRRNT.				heterophilic cell-cell adhesion	integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)												OREG0015572	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
BAP1	8314	broad.mit.edu	37	3	52443885	52443885	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52443885C>A	uc003ddx.2	-	1	125	c.10G>T	c.(10-12)GGC>TGC	p.G4C	PHF7_uc003ddy.2_5'Flank|PHF7_uc003ddz.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	4					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)				N|Mis|F|S|O		uveal melanoma|breast|NSCLC								---	---	---	---
SEMA3G	56920	broad.mit.edu	37	3	52472110	52472110	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52472110A>G	uc003dea.1	-	14	1615	c.1615T>C	c.(1615-1617)TAC>CAC	p.Y539H		NM_020163	NP_064548	Q9NS98	SEM3G_HUMAN	semaphorin sem2 precursor	539					multicellular organismal development	extracellular region|membrane	receptor activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)														---	---	---	---
NISCH	11188	broad.mit.edu	37	3	52491918	52491918	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52491918C>T	uc011beg.1	+	3	225	c.153C>T	c.(151-153)AGC>AGT	p.S51S	NISCH_uc003ded.3_Silent_p.S51S|NISCH_uc003dec.1_Silent_p.S51S	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	51	PX.|Necessary for binding to phosphoinositide-3-P; not sufficient for targeting to endosomes.				apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)														---	---	---	---
NISCH	11188	broad.mit.edu	37	3	52522418	52522418	+	Silent	SNP	C	T	T	rs61739223		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52522418C>T	uc011beg.1	+	17	2982	c.2910C>T	c.(2908-2910)CAC>CAT	p.H970H	NISCH_uc003ded.3_Silent_p.H970H|NISCH_uc003dee.3_Silent_p.H459H|NISCH_uc003deg.1_RNA|NISCH_uc003deh.3_5'Flank	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	970					apoptosis|cell communication	cytosol|early endosome|plasma membrane|recycling endosome	phosphatidylinositol binding|receptor activity			ovary(3)|central_nervous_system(1)	4				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)														---	---	---	---
DNASE1L3	1776	broad.mit.edu	37	3	58183580	58183580	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58183580C>T	uc003djo.1	-	6	769	c.672G>A	c.(670-672)ACG>ACA	p.T224T	DNASE1L3_uc011bfd.1_Silent_p.T194T|DNASE1L3_uc003djp.1_Silent_p.T224T|DNASE1L3_uc003djq.1_Silent_p.T224T	NM_004944	NP_004935	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3 precursor	224					apoptosis|DNA catabolic process	nucleus	calcium ion binding|DNA binding|endodeoxyribonuclease activity, producing 5'-phosphomonoesters			breast(2)|large_intestine(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)														---	---	---	---
ACOX2	8309	broad.mit.edu	37	3	58516206	58516206	+	Missense_Mutation	SNP	G	A	A	rs138459863		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58516206G>A	uc003dkl.2	-	8	1154	c.979C>T	c.(979-981)CGG>TGG	p.R327W		NM_003500	NP_003491	Q99424	ACOX2_HUMAN	acyl-Coenzyme A oxidase 2	327					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity|acyl-CoA dehydrogenase activity|pristanoyl-CoA oxidase activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)														---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67568743	67568743	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67568743A>G	uc003dna.3	-	6	616	c.588T>C	c.(586-588)TTT>TTC	p.F196F	SUCLG2_uc010hob.2_Silent_p.F77F	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit	196	ATP-grasp.				succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
LMOD3	56203	broad.mit.edu	37	3	69171388	69171388	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69171388C>A	uc003dns.2	-	1	359	c.150G>T	c.(148-150)GTG>GTT	p.V50V	LMOD3_uc003dnt.2_Silent_p.V50V	NM_198271	NP_938012	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	50						cytoplasm|cytoskeleton	tropomyosin binding			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)														---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73433392	73433392	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73433392G>A	uc003dpl.1	-	10	2421	c.2325C>T	c.(2323-2325)CCC>CCT	p.P775P	PDZRN3_uc011bgh.1_Silent_p.P432P|PDZRN3_uc010hoe.1_Silent_p.P473P|PDZRN3_uc011bgf.1_Silent_p.P492P|PDZRN3_uc011bgg.1_Silent_p.P495P	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	775							ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	78663931	78663931	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78663931C>T	uc003dqe.2	-	28	4510	c.4302G>A	c.(4300-4302)GCG>GCA	p.A1434A	ROBO1_uc003dqb.2_Silent_p.A1395A|ROBO1_uc003dqc.2_Silent_p.A1334A|ROBO1_uc003dqd.2_Silent_p.A1389A|ROBO1_uc010hoh.2_Silent_p.A626A|ROBO1_uc011bgl.1_Silent_p.A1006A	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	1434	Cytoplasmic (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
OR5K4	403278	broad.mit.edu	37	3	98073327	98073327	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98073327C>T	uc011bgv.1	+	1	630	c.630C>T	c.(628-630)ACC>ACT	p.T210T		NM_001005517	NP_001005517	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1																		---	---	---	---
OR5K3	403277	broad.mit.edu	37	3	98110293	98110293	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98110293G>A	uc011bgw.1	+	1	784	c.784G>A	c.(784-786)GCA>ACA	p.A262T		NM_001005516	NP_001005516	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K,	262	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98510829	98510829	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98510829A>T	uc003dsz.2	+	9	1137	c.901A>T	c.(901-903)ATG>TTG	p.M301L	ST3GAL6_uc003dsy.2_Missense_Mutation_p.M215L|ST3GAL6_uc003dta.2_Missense_Mutation_p.M183L|ST3GAL6_uc003dtb.2_Missense_Mutation_p.M157L|ST3GAL6_uc003dtc.2_Missense_Mutation_p.M301L|ST3GAL6_uc010hpd.2_Missense_Mutation_p.M354L	NM_006100	NP_006091	Q9Y274	SIA10_HUMAN	alpha2,3-sialyltransferase VI	301	Lumenal (Potential).				amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	100020962	100020962	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100020962G>A	uc003dtt.2	+	11	1321	c.1144G>A	c.(1144-1146)GCA>ACA	p.A382T	TBC1D23_uc003dts.2_Missense_Mutation_p.A382T	NM_018309	NP_060779	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	382	Rhodanese.					intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
ZBED2	79413	broad.mit.edu	37	3	111312782	111312782	+	Silent	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111312782A>C	uc003dxy.2	-	2	1152	c.267T>G	c.(265-267)CCT>CCG	p.P89P	CD96_uc003dxv.2_Intron|CD96_uc003dxw.2_Intron|CD96_uc003dxx.2_Intron|CD96_uc010hpy.1_Intron	NM_024508	NP_078784	Q9BTP6	ZBED2_HUMAN	zinc finger, BED domain containing 2	89	BED-type.						DNA binding|metal ion binding			skin(1)	1																		---	---	---	---
PLCXD2	257068	broad.mit.edu	37	3	111564673	111564673	+	3'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111564673C>T	uc003dya.2	+	5					PLCXD2_uc003dxz.2_Missense_Mutation_p.A291V|PHLDB2_uc003dyc.2_5'UTR	NM_001134478	NP_001127950			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1																		---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	111921157	111921157	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111921157T>C	uc003dyu.2	-	18	2484	c.2262A>G	c.(2260-2262)CAA>CAG	p.Q754Q	SLC9A10_uc011bhu.1_Silent_p.Q17Q|SLC9A10_uc010hqc.2_Silent_p.Q706Q	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	754					cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113376559	113376559	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113376559G>A	uc003eam.2	-	7	4381	c.3970C>T	c.(3970-3972)CGT>TGT	p.R1324C	KIAA2018_uc003eal.2_Missense_Mutation_p.R1268C	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1324					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3																		---	---	---	---
QTRTD1	79691	broad.mit.edu	37	3	113795686	113795686	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113795686G>T	uc003eay.2	+	7	873	c.643G>T	c.(643-645)GGT>TGT	p.G215C	QTRTD1_uc003eaz.2_Missense_Mutation_p.G227C|QTRTD1_uc011biq.1_Missense_Mutation_p.G92C|QTRTD1_uc011bir.1_Missense_Mutation_p.G109C|QTRTD1_uc003eba.2_Missense_Mutation_p.G92C	NM_024638	NP_078914	Q9H974	QTRD1_HUMAN	queuine tRNA-ribosyltransferase domain	215					queuosine biosynthetic process	mitochondrion	metal ion binding|queuine tRNA-ribosyltransferase activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
POLQ	10721	broad.mit.edu	37	3	121248525	121248525	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121248525G>A	uc003eee.3	-	7	1204	c.1075C>T	c.(1075-1077)CGA>TGA	p.R359*		NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	359	Helicase C-terminal.				DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)									DNA_polymerases_(catalytic_subunits)					---	---	---	---
DTX3L	151636	broad.mit.edu	37	3	122288531	122288531	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122288531G>A	uc003efk.2	+	3	1684	c.1595G>A	c.(1594-1596)AGC>AAC	p.S532N	DTX3L_uc010hrj.2_Intron	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like	532					histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)	4				GBM - Glioblastoma multiforme(114;0.0459)														---	---	---	---
DTX3L	151636	broad.mit.edu	37	3	122289427	122289427	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122289427T>C	uc003efk.2	+	4	2150	c.2061T>C	c.(2059-2061)TTT>TTC	p.F687F	DTX3L_uc010hrj.2_Silent_p.F175F	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN	deltex 3-like	687					histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)	4				GBM - Glioblastoma multiforme(114;0.0459)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124215203	124215203	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124215203A>G	uc003ehg.2	+	33	4999	c.4872A>G	c.(4870-4872)CAA>CAG	p.Q1624Q	KALRN_uc010hrv.1_Silent_p.Q1615Q|KALRN_uc003ehf.1_Silent_p.Q1624Q|KALRN_uc011bjy.1_Silent_p.Q1615Q	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1624					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
HEG1	57493	broad.mit.edu	37	3	124731892	124731892	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124731892G>A	uc003ehs.3	-	6	2599	c.2531C>T	c.(2530-2532)ACT>ATT	p.T844I	HEG1_uc011bke.1_Missense_Mutation_p.T944I	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	844	Extracellular (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	124953119	124953119	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124953119T>G	uc003ehx.3	-	8	1208	c.722A>C	c.(721-723)CAT>CCT	p.H241P	SLC12A8_uc003ehw.3_Intron|ZNF148_uc003ehz.3_Missense_Mutation_p.H241P|ZNF148_uc010hsa.2_Missense_Mutation_p.H241P|ZNF148_uc003eia.3_Missense_Mutation_p.H241P|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	241	C2H2-type 3.				cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ZXDC	79364	broad.mit.edu	37	3	126180390	126180390	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126180390G>A	uc003eiv.2	-	6	2169	c.2115C>T	c.(2113-2115)GGC>GGT	p.G705G	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Silent_p.G705G	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	705					positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126219539	126219539	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126219539T>A	uc003eiz.1	-	11	1176	c.1144A>T	c.(1144-1146)AGC>TGC	p.S382C	UROC1_uc010hsi.1_Missense_Mutation_p.S442C	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1	382					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126220661	126220661	+	Intron	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126220661A>C	uc003eiz.1	-						UROC1_uc010hsi.1_Missense_Mutation_p.F345V	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126226620	126226620	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126226620C>T	uc003eiz.1	-	6	599	c.567G>A	c.(565-567)ACG>ACA	p.T189T	UROC1_uc010hsi.1_Silent_p.T189T	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1	189					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126722168	126722168	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126722168C>A	uc003ejg.2	+							NM_032242	NP_115618			plexin A1						axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
RUVBL1	8607	broad.mit.edu	37	3	127806584	127806584	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127806584G>A	uc003ekh.2	-	9	1188	c.1084C>T	c.(1084-1086)CGG>TGG	p.R362W	RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Missense_Mutation_p.R302W|RUVBL1_uc010hss.2_Missense_Mutation_p.R362W	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1	362					cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)														---	---	---	---
CCDC48	79825	broad.mit.edu	37	3	128757721	128757721	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128757721C>T	uc011bkt.1	+	7	1638	c.1638C>T	c.(1636-1638)GAC>GAT	p.D546D		NM_024768	NP_079044	Q9HA90	CCD48_HUMAN	coiled-coil domain containing 48	546											0																		---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129233274	129233274	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129233274T>C	uc003emm.2	+	25	3236	c.3030T>C	c.(3028-3030)GGT>GGC	p.G1010G	IFT122_uc003eml.2_Silent_p.G1061G|IFT122_uc003emn.2_Silent_p.G951G|IFT122_uc003emo.2_Silent_p.G900G|IFT122_uc003emp.2_Silent_p.G860G|IFT122_uc010htc.2_Silent_p.G1003G|IFT122_uc011bky.1_Silent_p.G801G|IFT122_uc003emq.2_Silent_p.G850G|IFT122_uc003emr.2_Silent_p.G763G|IFT122_uc011bla.1_Silent_p.G784G|IFT122_uc010hte.2_Silent_p.G336G|IFT122_uc003ems.2_Silent_p.G392G	NM_052989	NP_443715	Q9HBG6	IF122_HUMAN	WD repeat domain 10 isoform 2	1010					camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
PLXND1	23129	broad.mit.edu	37	3	129281738	129281738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129281738G>A	uc003emx.2	-	27	4817	c.4717C>T	c.(4717-4719)CGG>TGG	p.R1573W	PLXND1_uc011blb.1_Missense_Mutation_p.R241W	NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	1573	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1																		---	---	---	---
PLXND1	23129	broad.mit.edu	37	3	129292568	129292568	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129292568C>T	uc003emx.2	-	13	2806	c.2706G>A	c.(2704-2706)CCG>CCA	p.P902P		NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	902	IPT/TIG 1.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1																		---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130187927	130187927	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130187927A>T	uc010htj.1	+	38	7573	c.7079A>T	c.(7078-7080)GAT>GTT	p.D2360V	COL29A1_uc010hti.1_RNA|COL29A1_uc010htk.1_Missense_Mutation_p.D399V	NM_153264	NP_694996	A8TX70	CO6A5_HUMAN	collagen, type XXIX, alpha 1	2360	VWFA 10.|Nonhelical region.				axon guidance|cell adhesion	collagen					0																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130292809	130292809	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130292809T>A	uc010htl.2	+	7	3018	c.2987T>A	c.(2986-2988)ATT>AAT	p.I996N		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	996	Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130307997	130307997	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130307997A>G	uc010htl.2	+	11	4220	c.4189A>G	c.(4189-4191)ATG>GTG	p.M1397V	COL6A6_uc003eni.3_5'UTR	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1397	Triple-helical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130345329	130345329	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130345329G>T	uc010htl.2	+	24	4910	c.4879G>T	c.(4879-4881)GGA>TGA	p.G1627*	COL6A6_uc003eni.3_Translation_Start_Site	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1627	Triple-helical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134851736	134851736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134851736C>T	uc003eqt.2	+	5	1362	c.1142C>T	c.(1141-1143)CCC>CTC	p.P381L	EPHB1_uc010htz.1_RNA|EPHB1_uc011bly.1_3'UTR|EPHB1_uc003equ.2_5'UTR	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	381	Extracellular (Potential).|Fibronectin type-III 1.					integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138417775	138417775	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138417775A>G	uc011bmq.1	-	11	1744	c.1744T>C	c.(1744-1746)TGG>CGG	p.W582R	PIK3CB_uc011bmn.1_Missense_Mutation_p.W94R|PIK3CB_uc011bmo.1_Missense_Mutation_p.W28R|PIK3CB_uc011bmp.1_Missense_Mutation_p.W169R	NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	582	PI3K helical.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
RNF7	9616	broad.mit.edu	37	3	141457324	141457324	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141457324C>T	uc003eud.2	+	1	274	c.141C>T	c.(139-141)TGC>TGT	p.C47C	RNF7_uc003euc.2_Silent_p.C47C|RNF7_uc003eue.2_RNA	NM_014245	NP_055060	Q9UBF6	RBX2_HUMAN	ring finger protein 7 isoform 1	47					anti-apoptosis|induction of apoptosis by oxidative stress|protein neddylation|response to redox state	cytoplasm|nucleus	copper ion binding|NEDD8 ligase activity|protein binding|zinc ion binding				0																OREG0015854	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CP	1356	broad.mit.edu	37	3	148897376	148897376	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148897376T>C	uc003ewy.3	-	15	2881	c.2628A>G	c.(2626-2628)CCA>CCG	p.P876P	CP_uc011bnr.1_RNA|CP_uc003eww.3_Silent_p.P28P|CP_uc003ewx.3_Silent_p.P657P|CP_uc003ewz.2_Silent_p.P876P	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	876	Plastocyanin-like 5.|F5/8 type A 3.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
FAM194A	131831	broad.mit.edu	37	3	150387183	150387183	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150387183T>C	uc003eyg.2	-	12	1456	c.1399A>G	c.(1399-1401)ACT>GCT	p.T467A	FAM194A_uc003eyh.2_Missense_Mutation_p.T321A	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	467										skin(2)|ovary(1)	3																		---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154011567	154011567	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154011567A>T	uc003ezy.3	-	14	1721	c.1640T>A	c.(1639-1641)ATA>AAA	p.I547K	DHX36_uc010hvq.2_Missense_Mutation_p.I533K|DHX36_uc003ezz.3_Missense_Mutation_p.I547K	NM_020865	NP_065916	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	547	Helicase C-terminal.					cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
MLF1	4291	broad.mit.edu	37	3	158310241	158310241	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158310241C>T	uc003fcb.2	+	2	203	c.66C>T	c.(64-66)CAC>CAT	p.H22H	MLF1_uc003fbz.2_5'UTR|MLF1_uc003fca.2_5'UTR|MLF1_uc003fbx.2_5'UTR|MLF1_uc003fcc.2_Silent_p.H38H|MLF1_uc003fby.2_5'UTR|MLF1_uc010hvx.2_5'UTR	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1	22					cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)					T	NPM1	AML								---	---	---	---
MLF1	4291	broad.mit.edu	37	3	158310320	158310320	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158310320G>T	uc003fcb.2	+	2	282	c.145G>T	c.(145-147)GGG>TGG	p.G49W	MLF1_uc003fbz.2_Missense_Mutation_p.G24W|MLF1_uc003fca.2_Missense_Mutation_p.G24W|MLF1_uc003fbx.2_Missense_Mutation_p.G24W|MLF1_uc003fcc.2_Missense_Mutation_p.G65W|MLF1_uc003fby.2_Translation_Start_Site|MLF1_uc010hvx.2_Missense_Mutation_p.G24W	NM_022443	NP_071888	P58340	MLF1_HUMAN	myeloid leukemia factor 1 isoform 1	49					cell cycle arrest|myeloid progenitor cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein domain specific binding				0		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)					T	NPM1	AML								---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167000016	167000016	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167000016A>G	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963			zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167250683	167250683	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167250683C>A	uc003fev.1	-	8	1287	c.981G>T	c.(979-981)TTG>TTT	p.L327F	WDR49_uc003feu.1_Missense_Mutation_p.L152F|WDR49_uc011bpd.1_Missense_Mutation_p.L391F|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	327										large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170727811	170727811	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170727811A>G	uc003fhe.1	-	4	741	c.432T>C	c.(430-432)TTT>TTC	p.F144F	SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Silent_p.F17F	NM_000340	NP_000331	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose	144	Helical; Name=3; (Potential).				carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)															---	---	---	---
ECT2	1894	broad.mit.edu	37	3	172486914	172486914	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172486914T>C	uc003fii.2	+	12	1454	c.1316T>C	c.(1315-1317)ATA>ACA	p.I439T	ECT2_uc010hwv.1_Missense_Mutation_p.I470T|ECT2_uc003fih.2_Missense_Mutation_p.I438T|ECT2_uc003fij.1_Missense_Mutation_p.I439T|ECT2_uc003fik.1_Missense_Mutation_p.I439T|ECT2_uc003fil.1_Missense_Mutation_p.I470T	NM_018098	NP_060568	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	439	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)															---	---	---	---
EHHADH	1962	broad.mit.edu	37	3	184910379	184910379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184910379A>G	uc003fpf.2	-	7	1834	c.1807T>C	c.(1807-1809)TAT>CAT	p.Y603H	EHHADH_uc011brs.1_Missense_Mutation_p.Y507H	NM_001966	NP_001957	Q08426	ECHP_HUMAN	enoyl-Coenzyme A, hydratase/3-hydroxyacyl	603						peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity			ovary(3)	3	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)													---	---	---	---
TRA2B	6434	broad.mit.edu	37	3	185636197	185636197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185636197C>T	uc003fpv.2	-	8	1088	c.812G>A	c.(811-813)CGT>CAT	p.R271H	TRA2B_uc003fpt.2_RNA|TRA2B_uc003fpu.2_RNA|TRA2B_uc010hym.2_Missense_Mutation_p.R171H|TRA2B_uc003fpw.2_Missense_Mutation_p.R251H	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10	271	Arg/Ser-rich (RS2 domain).				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2																		---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186953694	186953694	+	Intron	SNP	G	A	A	rs150583270		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186953694G>A	uc003frh.1	-						MASP1_uc003fri.2_Silent_p.G655G|MASP1_uc003frj.2_Silent_p.G624G	NM_001879	NP_001870			mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186974645	186974645	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186974645T>G	uc003frh.1	-	5	883	c.551A>C	c.(550-552)GAG>GCG	p.E184A	MASP1_uc003fri.2_Missense_Mutation_p.E184A|MASP1_uc003frj.2_Missense_Mutation_p.E153A|MASP1_uc003frk.1_Missense_Mutation_p.E184A|MASP1_uc011bse.1_Missense_Mutation_p.E158A	NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	184	Interaction with FCN2.|Interaction with MBL2.|Homodimerization (By similarity).				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
TP63	8626	broad.mit.edu	37	3	189526151	189526151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189526151G>A	uc003fry.2	+	4	504	c.415G>A	c.(415-417)GCG>ACG	p.A139T	TP63_uc003frx.2_Missense_Mutation_p.A139T|TP63_uc003frz.2_Missense_Mutation_p.A139T|TP63_uc010hzc.1_Missense_Mutation_p.A139T|TP63_uc003fsa.2_Missense_Mutation_p.A45T|TP63_uc003fsb.2_Missense_Mutation_p.A45T|TP63_uc003fsc.2_Missense_Mutation_p.A45T|TP63_uc003fsd.2_Missense_Mutation_p.A45T|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Missense_Mutation_p.A20T	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	139					anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
CLDN16	10686	broad.mit.edu	37	3	190127802	190127802	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190127802T>C	uc003fsi.2	+	5	963	c.895T>C	c.(895-897)TAT>CAT	p.Y299H	CLDN16_uc010hze.2_3'UTR	NM_006580	NP_006571	Q9Y5I7	CLD16_HUMAN	claudin 16	299	Cytoplasmic (Potential).				calcium-independent cell-cell adhesion|cellular metal ion homeostasis|excretion	integral to membrane|tight junction	identical protein binding|magnesium ion transmembrane transporter activity|structural molecule activity			ovary(1)	1	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;0.018)														---	---	---	---
IL1RAP	3556	broad.mit.edu	37	3	190326775	190326775	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190326775T>C	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173			interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)														---	---	---	---
C3orf34	84984	broad.mit.edu	37	3	196435397	196435397	+	Splice_Site	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196435397A>G	uc011btw.1	-	2	524	c.142_splice	c.e2+1	p.D48_splice		NM_032898	NP_116287			hypothetical protein LOC84984							centriole|spindle pole					0	all_cancers(143;1.48e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00301)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196867105	196867105	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196867105C>A	uc003fxo.3	-	9	908	c.718G>T	c.(718-720)GGA>TGA	p.G240*	DLG1_uc011bub.1_Nonsense_Mutation_p.G124*|DLG1_uc011buc.1_Nonsense_Mutation_p.G124*|DLG1_uc011bud.1_Translation_Start_Site|DLG1_uc003fxn.3_Nonsense_Mutation_p.G240*|DLG1_uc011bue.1_Nonsense_Mutation_p.G207*|DLG1_uc010ial.2_Nonsense_Mutation_p.G240*|DLG1_uc011buf.1_RNA|DLG1_uc003fxp.2_RNA|DLG1_uc010iam.1_Nonsense_Mutation_p.G207*|DLG1_uc010ian.2_Nonsense_Mutation_p.G107*	NM_001098424	NP_001091894	Q12959	DLG1_HUMAN	discs, large homolog 1 isoform 1	240	PDZ 1.				actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	628573	628573	+	Silent	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:628573A>C	uc003gap.2	+	2	629	c.576A>C	c.(574-576)GCA>GCC	p.A192A	PDE6B_uc003gao.3_Silent_p.A192A	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	192	GAF 1.				cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2339147	2339147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2339147C>T	uc003gex.1	-	5	917	c.598G>A	c.(598-600)GAG>AAG	p.E200K	ZFYVE28_uc011bvk.1_Missense_Mutation_p.E130K|ZFYVE28_uc011bvl.1_Missense_Mutation_p.E200K|ZFYVE28_uc003gey.3_Missense_Mutation_p.E130K|ZFYVE28_uc003gez.2_Missense_Mutation_p.E153K|ZFYVE28_uc003gew.1_Missense_Mutation_p.E86K	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	200					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																		---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3430399	3430399	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3430399A>G	uc003ggw.2	+	16	4430	c.3526A>G	c.(3526-3528)AAA>GAA	p.K1176E	RGS12_uc003ggv.2_Missense_Mutation_p.K1176E|RGS12_uc003ggy.1_Intron|RGS12_uc003ggz.2_Missense_Mutation_p.K528E|RGS12_uc011bvs.1_Intron|RGS12_uc003gha.2_Missense_Mutation_p.K518E|RGS12_uc010icv.2_Missense_Mutation_p.K375E	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	1176						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3494479	3494479	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3494479G>A	uc003ghd.2	+						DOK7_uc003ghe.2_Intron|DOK7_uc003ghf.2_Intron|DOK7_uc003ghg.1_5'Flank	NM_173660	NP_775931			downstream of tyrosine kinase 7 isoform 1						positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
EVC	2121	broad.mit.edu	37	4	5720985	5720985	+	Missense_Mutation	SNP	C	T	T	rs147280107		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5720985C>T	uc003gil.1	+	2	369	c.185C>T	c.(184-186)ACT>ATT	p.T62I	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	62					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6925544	6925544	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6925544C>A	uc011bwg.1	+	2	507	c.428C>A	c.(427-429)CCG>CAG	p.P143Q	TBC1D14_uc003gjs.3_Missense_Mutation_p.P143Q	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a	143						intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
GRPEL1	80273	broad.mit.edu	37	4	7064112	7064112	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7064112C>T	uc003gjy.1	-	3	348	c.307G>A	c.(307-309)GGC>AGC	p.G103S	GRPEL1_uc003gjz.1_Missense_Mutation_p.G103S	NM_025196	NP_079472	Q9HAV7	GRPE1_HUMAN	GrpE-like 1, mitochondrial precursor	103					protein folding|protein import into mitochondrial matrix	mitochondrial matrix	adenyl-nucleotide exchange factor activity|chaperone binding|protein homodimerization activity|unfolded protein binding				0																		---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26431567	26431567	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26431567C>T	uc003grx.1	+	10	1211	c.975C>T	c.(973-975)GGC>GGT	p.G325G	RBPJ_uc003gry.1_Silent_p.G310G|RBPJ_uc003grz.1_Silent_p.G325G|RBPJ_uc011bxt.1_Silent_p.G325G|RBPJ_uc003gsa.1_Silent_p.G311G|RBPJ_uc003gsb.1_Silent_p.G312G|RBPJ_uc003gsc.1_Silent_p.G311G	NM_005349	NP_005340	Q06330	SUH_HUMAN	recombining binding protein suppressor of	325					DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3		Breast(46;0.0503)																---	---	---	---
PHOX2B	8929	broad.mit.edu	37	4	41749473	41749473	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41749473C>A	uc003gwf.3	-	2	682	c.322G>T	c.(322-324)GCC>TCC	p.A108S		NM_003924	NP_003915	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	108	Homeobox.				positive regulation of transcription from RNA polymerase II promoter	nuclear chromatin	RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			autonomic_ganglia(7)|lung(2)|ovary(2)|central_nervous_system(1)	12								Mis|F		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42580304	42580304	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42580304T>C	uc003gwr.2	-	12	1333	c.1101A>G	c.(1099-1101)AAA>AAG	p.K367K	ATP8A1_uc003gws.2_Silent_p.K367K|ATP8A1_uc011byz.1_Silent_p.K367K	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	367	Cytoplasmic (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48545976	48545976	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48545976G>T	uc003gyh.1	-	44	6045	c.5440C>A	c.(5440-5442)CTG>ATG	p.L1814M	FRYL_uc003gyg.1_Missense_Mutation_p.L510M|FRYL_uc003gyi.1_Missense_Mutation_p.L702M|FRYL_uc003gyj.1_Missense_Mutation_p.L109M	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1814					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
USP46	64854	broad.mit.edu	37	4	53492381	53492381	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53492381T>C	uc003gzn.2	-	4	550	c.365A>G	c.(364-366)CAT>CGT	p.H122R	USP46_uc003gzm.3_Missense_Mutation_p.H115R|USP46_uc011bzr.1_Missense_Mutation_p.H99R|USP46_uc011bzs.1_Missense_Mutation_p.H6R	NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1	122					behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)															---	---	---	---
NMU	10874	broad.mit.edu	37	4	56471505	56471505	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56471505C>T	uc003hbc.2	-	7	478	c.372G>A	c.(370-372)GTG>GTA	p.V124V	NMU_uc003hbd.1_Intron|NMU_uc010igv.1_RNA|NMU_uc010igw.1_Silent_p.V39V|NMU_uc010igx.1_Intron	NM_006681	NP_006672	P48645	NMU_HUMAN	neuromedin U precursor	124					neuropeptide signaling pathway	extracellular region					0	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)														---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68492086	68492086	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68492086G>A	uc003hdg.3	-	28	2562	c.2510C>T	c.(2509-2511)GCC>GTC	p.A837V		NM_018227	NP_060697	A0AVT1	UBA6_HUMAN	ubiquitin-activating enzyme E1-like 2	837					protein ubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm	ATP binding|FAT10 activating enzyme activity|ligase activity|protein binding				0																		---	---	---	---
SULT1E1	6783	broad.mit.edu	37	4	70723269	70723269	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70723269C>T	uc003heo.2	-	2	207	c.94G>A	c.(94-96)GCG>ACG	p.A32T	SULT1E1_uc010ihv.1_Missense_Mutation_p.A32T	NM_005420	NP_005411	P49888	ST1E1_HUMAN	estrogen sulfotransferase	32					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol|nuclear membrane	estrone sulfotransferase activity|flavonol 3-sulfotransferase activity|steroid binding|steroid sulfotransferase activity			ovary(1)	1																		---	---	---	---
MUC7	4589	broad.mit.edu	37	4	71346558	71346558	+	Silent	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71346558A>C	uc011cat.1	+	4	385	c.97A>C	c.(97-99)AGG>CGG	p.R33R	MUC7_uc011cau.1_Silent_p.R33R|MUC7_uc003hfj.2_Silent_p.R33R|uc011cav.1_RNA	NM_001145006	NP_001138478	Q8TAX7	MUC7_HUMAN	mucin 7, secreted precursor	33						extracellular region	protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4			Lung(101;0.211)															---	---	---	---
PF4V1	5197	broad.mit.edu	37	4	74719777	74719777	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74719777A>T	uc003hhg.1	+	3	320	c.253A>T	c.(253-255)ATT>TTT	p.I85F		NM_002620	NP_002611	P10720	PF4V_HUMAN	platelet factor 4 variant 1	85					immune response	extracellular region	chemokine activity|heparin binding				0	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)															---	---	---	---
G3BP2	9908	broad.mit.edu	37	4	76570792	76570792	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76570792C>A	uc003hir.2	-	12	1436	c.1271G>T	c.(1270-1272)CGC>CTC	p.R424L	G3BP2_uc003his.2_Missense_Mutation_p.R424L|G3BP2_uc003hit.2_Missense_Mutation_p.R391L	NM_012297	NP_036429	Q9UN86	G3BP2_HUMAN	Ras-GTPase activating protein SH3 domain-binding	424	Gly-rich.				cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding			breast(2)|central_nervous_system(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
PPEF2	5470	broad.mit.edu	37	4	76797721	76797721	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76797721A>G	uc003hix.2	-	11	1396	c.1039T>C	c.(1039-1041)TTT>CTT	p.F347L	PPEF2_uc003hiy.2_RNA|PPEF2_uc003hiz.1_Missense_Mutation_p.F347L	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	347	Catalytic.				detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77637532	77637532	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77637532T>C	uc011cbx.1	+						SHROOM3_uc011cbz.1_Intron|SHROOM3_uc003hkf.1_Silent_p.L17L	NM_020859	NP_065910			shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95496980	95496980	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95496980G>A	uc003hti.2	+	5	656	c.505G>A	c.(505-507)GTC>ATC	p.V169I	PDLIM5_uc003htf.2_Intron|PDLIM5_uc003htg.2_Intron|PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_Missense_Mutation_p.V47I	NM_006457	NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5 isoform a	169					regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)														---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106746920	106746920	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106746920C>T	uc003hxz.3	+	8	1565	c.1493C>T	c.(1492-1494)GCA>GTA	p.A498V	GSTCD_uc003hxy.3_Missense_Mutation_p.A411V|GSTCD_uc011cfb.1_Missense_Mutation_p.A121V	NM_001031720	NP_001026890	Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain	498						cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107170076	107170076	+	Splice_Site	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107170076A>G	uc010ilv.2	-	8	1085	c.720_splice	c.e8+1	p.K240_splice	TBCK_uc003hyb.2_5'Flank|TBCK_uc003hye.2_Splice_Site_p.K201_splice|TBCK_uc003hyc.2_Splice_Site_p.K177_splice|TBCK_uc003hyd.2_Splice_Site_p.K68_splice|TBCK_uc003hyf.2_Splice_Site_p.K240_splice	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
CFI	3426	broad.mit.edu	37	4	110667573	110667573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110667573C>T	uc003hzr.3	-	11	1442	c.1234G>A	c.(1234-1236)GTG>ATG	p.V412M	CFI_uc003hzq.2_Missense_Mutation_p.V209M|CFI_uc011cft.1_Missense_Mutation_p.V420M|CFI_uc003hzs.3_Missense_Mutation_p.V405M	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein	412	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space|membrane	scavenger receptor activity|serine-type endopeptidase activity				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)														---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119689476	119689476	+	Intron	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119689476A>T	uc003ici.3	-						SEC24D_uc003ich.3_5'Flank|SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron|SEC24D_uc010imz.1_Intron	NM_014822	NP_055637			Sec24-related protein D						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
USP53	54532	broad.mit.edu	37	4	120177654	120177654	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120177654G>A	uc003ics.3	+	8	1611	c.545G>A	c.(544-546)CGG>CAG	p.R182Q	USP53_uc003icr.3_Missense_Mutation_p.R182Q|USP53_uc003icu.3_5'UTR	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53	182					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4																		---	---	---	---
PDE5A	8654	broad.mit.edu	37	4	120419827	120419827	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120419827A>G	uc003idh.2	-	21	2712	c.2557T>C	c.(2557-2559)TGG>CGG	p.W853R	uc003ide.3_Intron|PDE5A_uc003idf.2_Missense_Mutation_p.W811R|PDE5A_uc003idg.2_Missense_Mutation_p.W801R	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	853	Catalytic (By similarity).				platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)													---	---	---	---
PDE5A	8654	broad.mit.edu	37	4	120484020	120484020	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120484020A>G	uc003idh.2	-	6	1254	c.1099T>C	c.(1099-1101)TGC>CGC	p.C367R	PDE5A_uc003idf.2_Missense_Mutation_p.C325R|PDE5A_uc003idg.2_Missense_Mutation_p.C315R	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	367	GAF 2.				platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)													---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123227177	123227177	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123227177C>T	uc003ieh.2	+	55	9863	c.9818C>T	c.(9817-9819)GCA>GTA	p.A3273V	KIAA1109_uc003iel.1_Missense_Mutation_p.A1208V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	3273					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126373243	126373243	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126373243G>T	uc003ifj.3	+	9	11072	c.11072G>T	c.(11071-11073)AGC>ATC	p.S3691I	FAT4_uc011cgp.1_Missense_Mutation_p.S1989I|FAT4_uc003ifi.1_Missense_Mutation_p.S1169I	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3691	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
PCDH10	57575	broad.mit.edu	37	4	134071765	134071765	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134071765G>A	uc003iha.2	+	1	1296	c.470G>A	c.(469-471)CGC>CAC	p.R157H	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.R157H	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	157	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)														---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140811854	140811854	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140811854T>C	uc003ihz.1	-	2	1488	c.736A>G	c.(736-738)AAT>GAT	p.N246D	MAML3_uc011chd.1_Intron	NM_018717	NP_061187	Q96JK9	MAML3_HUMAN	mastermind-like 3	246					Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
RPS3A	6189	broad.mit.edu	37	4	152024153	152024153	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152024153G>A	uc003ilz.2	+	4	536	c.485G>A	c.(484-486)CGC>CAC	p.R162H	RPS3A_uc011cie.1_Missense_Mutation_p.R162H|SNORD73A_uc003ima.1_5'Flank	NM_001006	NP_000997	P61247	RS3A_HUMAN	ribosomal protein S3a	162					cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
PRSS48	345062	broad.mit.edu	37	4	152212409	152212409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152212409C>T	uc011cif.1	+	5	791	c.791C>T	c.(790-792)GCC>GTC	p.A264V	PRSS48_uc011cig.1_Missense_Mutation_p.A121V	NM_183375	NP_899231	Q7RTY5	PRS48_HUMAN	epidermis-specific serine protease-like protein	264	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			large_intestine(1)	1																		---	---	---	---
FGG	2266	broad.mit.edu	37	4	155530777	155530777	+	Intron	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155530777A>T	uc003ioj.2	-						FGG_uc003iog.2_Intron|FGG_uc003ioh.2_Intron|FGG_uc010ipx.2_Intron|FGG_uc010ipy.2_Intron|FGG_uc003ioi.2_Intron|FGG_uc003iok.2_Intron	NM_021870	NP_068656			fibrinogen, gamma chain isoform gamma-B						platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)													---	---	---	---
CTSO	1519	broad.mit.edu	37	4	156860511	156860511	+	Intron	SNP	G	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156860511G>C	uc003ipg.2	-							NM_001334	NP_001325			cathepsin O preproprotein						proteolysis	lysosome	cysteine-type endopeptidase activity				0	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)														---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159092437	159092437	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159092437G>A	uc003ipp.3	-	2	543	c.91C>T	c.(91-93)CGT>TGT	p.R31C	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.R31C|FAM198B_uc003ipr.3_Missense_Mutation_p.R31C|FAM198B_uc003ips.2_Missense_Mutation_p.R31C|uc003ipt.1_RNA	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	31	Cytoplasmic (Potential).					Golgi membrane|integral to membrane					0																		---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160274685	160274685	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160274685A>G	uc003iqg.3	+	22	3965	c.3655A>G	c.(3655-3657)ACA>GCA	p.T1219A		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1219					cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
ANP32C	23520	broad.mit.edu	37	4	165118603	165118603	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165118603C>T	uc011cjk.1	-	1	261	c.261G>A	c.(259-261)ACG>ACA	p.T87T	MARCH1_uc003iqs.1_Intron	NM_012403	NP_036535	O43423	AN32C_HUMAN	acidic nuclear phosphoprotein 32C	87	LRR 3.										0	all_hematologic(180;0.203)	Prostate(90;0.0138)|Melanoma(52;0.18)|all_neural(102;0.223)		KIRC - Kidney renal clear cell carcinoma(143;0.242)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169433418	169433418	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169433418C>T	uc011cjx.1	+	2	974	c.763C>T	c.(763-765)CGC>TGC	p.R255C	PALLD_uc003iru.2_Missense_Mutation_p.R255C	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2	255					cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
AADAT	51166	broad.mit.edu	37	4	171009703	171009703	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171009703C>T	uc003isr.2	-	2	422	c.80G>A	c.(79-81)AGC>AAC	p.S27N	AADAT_uc003iss.2_Missense_Mutation_p.S27N|AADAT_uc003ist.2_Missense_Mutation_p.S31N	NM_016228	NP_057312	Q8N5Z0	AADAT_HUMAN	kynurenine aminotransferase II	27					2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173942662	173942662	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173942662C>T	uc003isv.2	+	12	2260	c.1524C>T	c.(1522-1524)CCC>CCT	p.P508P		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	508	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	p.?(1)		breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
STOX2	56977	broad.mit.edu	37	4	184930482	184930482	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184930482T>A	uc003ivz.1	+	3	1926	c.491T>A	c.(490-492)ATA>AAA	p.I164K	STOX2_uc003iwa.1_5'UTR	NM_020225	NP_064610	Q9P2F5	STOX2_HUMAN	storkhead box 2	164					embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)														---	---	---	---
IRF2	3660	broad.mit.edu	37	4	185339859	185339859	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185339859T>G	uc003iwf.3	-	4	391	c.191A>C	c.(190-192)AAG>ACG	p.K64T		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	64	IRF tryptophan pentad repeat.				blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187540301	187540301	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187540301A>G	uc003izf.2	-	10	7627	c.7439T>C	c.(7438-7440)GTA>GCA	p.V2480A		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2480	Extracellular (Potential).|Cadherin 22.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
AHRR	57491	broad.mit.edu	37	5	434067	434067	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:434067G>A	uc003jav.2	+	12	1322	c.1278G>A	c.(1276-1278)GCG>GCA	p.A426A	AHRR_uc003jaw.2_Silent_p.A404A|AHRR_uc010isy.2_Silent_p.A254A|AHRR_uc010isz.2_Silent_p.A404A|AHRR_uc003jax.2_Silent_p.A167A|AHRR_uc003jay.2_Silent_p.A264A|AHRR_uc003jaz.2_Silent_p.A25A	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	408					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)															---	---	---	---
CEP72	55722	broad.mit.edu	37	5	637758	637758	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:637758C>T	uc003jbf.2	+	7	1103	c.1031C>T	c.(1030-1032)ACG>ATG	p.T344M	CEP72_uc011clz.1_RNA	NM_018140	NP_060610	Q9P209	CEP72_HUMAN	centrosomal protein 72 kDa	344					G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1081765	1081765	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1081765T>C	uc003jbu.2	-	9	1290	c.1224A>G	c.(1222-1224)GCA>GCG	p.A408A		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	408					potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)													---	---	---	---
CLPTM1L	81037	broad.mit.edu	37	5	1334411	1334411	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1334411G>A	uc003jch.2	-	7	930	c.884C>T	c.(883-885)GCG>GTG	p.A295V	CLPTM1L_uc003jcg.2_Missense_Mutation_p.A162V	NM_030782	NP_110409	Q96KA5	CLP1L_HUMAN	CLPTM1-like	295	Helical; (Potential).				apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)														---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5209338	5209338	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5209338C>T	uc003jdl.2	+	10	1722	c.1584C>T	c.(1582-1584)CTC>CTT	p.L528L	ADAMTS16_uc003jdk.1_Silent_p.L528L|ADAMTS16_uc003jdj.1_Silent_p.L528L	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	528	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
MTRR	4552	broad.mit.edu	37	5	7875484	7875484	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7875484G>A	uc003jed.2	+	4	508	c.478G>A	c.(478-480)GTA>ATA	p.V160I	MTRR_uc010itn.1_RNA|MTRR_uc003jee.3_Missense_Mutation_p.V133I|MTRR_uc003jef.3_RNA|MTRR_uc003jeg.3_RNA|MTRR_uc010ito.2_RNA	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2	160	Flavodoxin-like.				methionine biosynthetic process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)													---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9202323	9202323	+	Missense_Mutation	SNP	C	T	T	rs140433904	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9202323C>T	uc003jek.2	-	9	1388	c.676G>A	c.(676-678)GGA>AGA	p.G226R		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	226	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19473667	19473667	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19473667C>T	uc003jgc.2	-	12	2418	c.2041G>A	c.(2041-2043)GCT>ACT	p.A681T	CDH18_uc003jgd.2_Missense_Mutation_p.A681T|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	681	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21842333	21842333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21842333C>T	uc010iuc.2	-	5	1209	c.751G>A	c.(751-753)GGA>AGA	p.G251R	CDH12_uc011cno.1_Missense_Mutation_p.G211R|CDH12_uc003jgk.2_Missense_Mutation_p.G251R	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	251	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
GOLPH3	64083	broad.mit.edu	37	5	32126538	32126538	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32126538A>C	uc003jhp.1	-	4	962	c.677T>G	c.(676-678)GTG>GGG	p.V226G		NM_022130	NP_071413	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3	226					cell proliferation|positive regulation of TOR signaling cascade|regulation of mitochondrion organization	cytosol|endosome|Golgi cisterna membrane|mitochondrial intermembrane space|plasma membrane|trans-Golgi network	protein binding			ovary(1)	1																		---	---	---	---
SUB1	10923	broad.mit.edu	37	5	32599082	32599082	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32599082T>C	uc003jhs.2	+	4	339	c.211T>C	c.(211-213)TAC>CAC	p.Y71H	SUB1_uc003jht.2_RNA	NM_006713	NP_006704	P53999	TCP4_HUMAN	activated RNA polymerase II transcription	71					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus|transcription factor complex	protein binding|single-stranded DNA binding|transcription coactivator activity				0																		---	---	---	---
AMACR	23600	broad.mit.edu	37	5	34004719	34004719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34004719C>T	uc003jig.2	-	3	594	c.512G>A	c.(511-513)CGC>CAC	p.R171H	AMACR_uc003jih.2_Intron|AMACR_uc003jii.2_Missense_Mutation_p.R171H|AMACR_uc003jij.2_Missense_Mutation_p.R171H|AMACR_uc003jil.1_Missense_Mutation_p.R171H|AMACR_uc003jik.1_Intron	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1	171					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0																		---	---	---	---
DNAJC21	134218	broad.mit.edu	37	5	34954762	34954762	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34954762G>A	uc003jjc.2	+	12	1766	c.1539G>A	c.(1537-1539)TCG>TCA	p.S513S	DNAJC21_uc003jjb.2_Silent_p.S558S	NM_001012339	NP_001012339	Q5F1R6	DJC21_HUMAN	DnaJ homology subfamily A member 5 isoform 2	513					protein folding	ribosome	heat shock protein binding|nucleic acid binding|unfolded protein binding|zinc ion binding			breast(1)|skin(1)	2	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)															---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38370555	38370555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38370555C>T	uc003jlc.1	+	6	1027	c.703C>T	c.(703-705)CGG>TGG	p.R235W	EGFLAM_uc003jlb.1_Missense_Mutation_p.R235W	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G	235	Fibronectin type-III 2.					cell junction|proteinaceous extracellular matrix|synapse		p.R235W(1)		pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
DIMT1L	27292	broad.mit.edu	37	5	61686760	61686760	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61686760G>A	uc003jta.2	-	11	971	c.842C>T	c.(841-843)ACC>ATC	p.T281I		NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase	281				Missing (in Ref. 2; AAH02841).		nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)														---	---	---	---
DIMT1L	27292	broad.mit.edu	37	5	61686787	61686787	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61686787A>G	uc003jta.2	-	11	944	c.815T>C	c.(814-816)ATA>ACA	p.I272T		NM_014473	NP_055288	Q9UNQ2	DIMT1_HUMAN	dimethyladenosine transferase	272				IIPEDFSIADK -> VSAAVYPVKQI (in Ref. 2; AAH02841).		nucleolus	RNA binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			central_nervous_system(1)	1		Lung NSC(810;8.94e-06)|Prostate(74;0.0235)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.122)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64756033	64756033	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64756033G>A	uc003jtp.2	-	4	1409	c.595C>T	c.(595-597)CGA>TGA	p.R199*	ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_Translation_Start_Site	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	199					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66430464	66430464	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66430464C>T	uc003jut.1	+	17	1841	c.1773C>T	c.(1771-1773)TGC>TGT	p.C591C	MAST4_uc003juu.1_Silent_p.C601C|MAST4_uc011cra.1_Silent_p.C574C|MAST4_uc003juv.2_Silent_p.C586C|MAST4_uc003juw.2_Silent_p.C586C	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	783	Protein kinase.					cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
NAIP	4671	broad.mit.edu	37	5	70308328	70308328	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70308328C>T	uc003kar.1	-	4	1133	c.415G>A	c.(415-417)GAC>AAC	p.D139N	NAIP_uc003kat.1_Intron|NAIP_uc011crs.1_Missense_Mutation_p.D139N|NAIP_uc003kas.1_Intron	NM_004536	NP_004527	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein isoform	139					anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
UTP15	84135	broad.mit.edu	37	5	72868396	72868396	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72868396A>G	uc003kcw.1	+	7	979	c.756A>G	c.(754-756)ACA>ACG	p.T252T	UTP15_uc011cso.1_Silent_p.T233T|UTP15_uc011csp.1_Silent_p.T62T|UTP15_uc010ize.1_Silent_p.T252T	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,	252	WD 6.				rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)														---	---	---	---
ENC1	8507	broad.mit.edu	37	5	73931957	73931957	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73931957T>C	uc003kdc.3	-	2	1485	c.354A>G	c.(352-354)GAA>GAG	p.E118E	ENC1_uc011css.1_Silent_p.E45E	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	118				INEENAESLLEAGDMLEFQ -> HQLEGKCRNSLLGSLVTC WSFK (in Ref. 1).	nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)														---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75505643	75505643	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75505643C>T	uc003kei.1	+	4	978	c.844C>T	c.(844-846)CTC>TTC	p.L282F		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	282	Helical; (Potential).				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)														---	---	---	---
DMGDH	29958	broad.mit.edu	37	5	78328598	78328598	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78328598T>C	uc003kfs.2	-	9	1435	c.1429A>G	c.(1429-1431)AGG>GGG	p.R477G	DMGDH_uc011cte.1_Missense_Mutation_p.R327G|DMGDH_uc011ctf.1_Missense_Mutation_p.R276G|DMGDH_uc011ctg.1_Missense_Mutation_p.R97G	NM_013391	NP_037523	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase precursor	477					choline metabolic process|glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|dimethylglycine dehydrogenase activity|electron carrier activity			ovary(2)|liver(1)|skin(1)	4		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87498903	87498903	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87498903G>A	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron|TMEM161B_uc011ctx.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95099279	95099279	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95099279A>G	uc003klm.2	+	7	1653	c.1116A>G	c.(1114-1116)TCA>TCG	p.S372S		NM_014899	NP_055714	O94955	RHBT3_HUMAN	rho-related BTB domain containing 3	372					retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95116113	95116113	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95116113A>G	uc003klm.2	+	9	1977	c.1440A>G	c.(1438-1440)ACA>ACG	p.T480T		NM_014899	NP_055714	O94955	RHBT3_HUMAN	rho-related BTB domain containing 3	480	BTB 2.|Interaction with Rab9.				retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102487088	102487088	+	Intron	SNP	T	C	C	rs74430672	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102487088T>C	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron|PPIP5K2_uc010jbo.1_Intron	NM_015216	NP_056031			Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106763016	106763016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106763016G>A	uc003kol.2	-	2	602	c.320C>T	c.(319-321)TCT>TTT	p.S107F	EFNA5_uc010jbr.1_Missense_Mutation_p.S107F	NM_001962	NP_001953	P52803	EFNA5_HUMAN	ephrin-A5 precursor	107					cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111575375	111575375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111575375C>T	uc003kpv.1	-	11	1221	c.947G>A	c.(946-948)CGT>CAT	p.R316H		NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	316						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111576502	111576502	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111576502G>A	uc003kpv.1	-	10	1075	c.801C>T	c.(799-801)AAC>AAT	p.N267N		NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	267	FERM.					cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
KCNN2	3781	broad.mit.edu	37	5	113698843	113698843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113698843G>A	uc003kqo.2	+	1	828	c.371G>A	c.(370-372)CGG>CAG	p.R124Q		NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	124						integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)														---	---	---	---
TMED7-TICAM2	100302736	broad.mit.edu	37	5	114916761	114916761	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114916761C>T	uc003krd.2	-	4	1199	c.193G>A	c.(193-195)GTG>ATG	p.V65M	TMED7-TICAM2_uc003kre.2_Missense_Mutation_p.V234M|TICAM2_uc003krc.2_Missense_Mutation_p.V65M	NM_021649	NP_067681	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	65					I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	Golgi apparatus|intrinsic to membrane|plasma membrane	protein binding|transmembrane receptor activity				0																		---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118445967	118445967	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118445967T>C	uc003ksd.2	+	5	667	c.486T>C	c.(484-486)ATT>ATC	p.I162I	DMXL1_uc010jcl.1_Silent_p.I162I|DMXL1_uc003ksc.1_Silent_p.I162I	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	162										ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
HSD17B4	3295	broad.mit.edu	37	5	118792054	118792054	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118792054T>C	uc003ksj.2	+	2	226	c.103T>C	c.(103-105)TTA>CTA	p.L35L	HSD17B4_uc011cwg.1_5'UTR|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Missense_Mutation_p.V38A|HSD17B4_uc003ksk.3_5'UTR	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	35	NAD (By similarity).|(3R)-hydroxyacyl-CoA dehydrogenase.				bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)													---	---	---	---
LOX	4015	broad.mit.edu	37	5	121409818	121409818	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121409818C>T	uc003ksu.2	-	4	1300	c.925G>A	c.(925-927)GCC>ACC	p.A309T	LOX_uc010jcp.2_Missense_Mutation_p.A12T|LOX_uc010jcq.2_Missense_Mutation_p.A12T|LOX_uc011cwk.1_Missense_Mutation_p.A79T|LOX_uc010jcr.2_Missense_Mutation_p.A12T	NM_002317	NP_002308	P28300	LYOX_HUMAN	lysyl oxidase preproprotein	309	Lysyl-oxidase like.				protein modification process	extracellular space	copper ion binding|protein-lysine 6-oxidase activity			lung(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)														---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131972826	131972826	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131972826A>G	uc003kxi.2	+	22	3796	c.3409A>G	c.(3409-3411)AGT>GGT	p.S1137G	RAD50_uc003kxh.2_Missense_Mutation_p.S998G	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	1137					DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132232456	132232456	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132232456T>C	uc003kyd.2	-	11	2274	c.1866A>G	c.(1864-1866)CGA>CGG	p.R622R	AFF4_uc011cxk.1_Silent_p.R300R|AFF4_uc003kye.1_Silent_p.R622R	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	622					transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
SMAD5	4090	broad.mit.edu	37	5	135510101	135510101	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135510101C>T	uc003lbj.1	+	8	1478	c.1034C>T	c.(1033-1035)GCG>GTG	p.A345V	SMAD5_uc003lbk.1_Missense_Mutation_p.A345V|SMAD5_uc003lbl.1_Missense_Mutation_p.A345V	NM_001001419	NP_001001419	Q99717	SMAD5_HUMAN	SMAD family member 5	345	MH2.				BMP signaling pathway|embryonic pattern specification|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135692700	135692700	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135692700G>A	uc003lbn.1	-	1	376	c.373C>T	c.(373-375)CTC>TTC	p.L125F	TRPC7_uc010jef.1_Missense_Mutation_p.L117F|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.L117F|TRPC7_uc010jei.1_Missense_Mutation_p.L117F|TRPC7_uc010jej.1_5'UTR	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	126	Cytoplasmic (Potential).|ANK 3.				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137717276	137717276	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137717276C>T	uc003lcy.1	+	6	977	c.777C>T	c.(775-777)AGC>AGT	p.S259S	KDM3B_uc010jew.1_5'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	259					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
TMCO6	55374	broad.mit.edu	37	5	140024251	140024251	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140024251C>T	uc003lgl.2	+	11	1395	c.1294C>T	c.(1294-1296)CTA>TTA	p.L432L	TMCO6_uc003lgm.2_Silent_p.L438L|TMCO6_uc010jft.2_Silent_p.L192L|TMCO6_uc003lgn.2_Silent_p.L323L|TMCO6_uc003lgo.2_Silent_p.L192L	NM_018502	NP_060972	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	432					protein import into nucleus	cytoplasm|nuclear pore	binding|protein transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HARS2	23438	broad.mit.edu	37	5	140077206	140077206	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140077206C>A	uc003lgx.2	+	11	1466	c.1250C>A	c.(1249-1251)CCA>CAA	p.P417Q	HARS2_uc011czr.1_Missense_Mutation_p.P392Q|HARS2_uc011czs.1_Missense_Mutation_p.P273Q|HARS2_uc011czt.1_Missense_Mutation_p.P245Q|HARS2_uc011czu.1_Missense_Mutation_p.P243Q|ZMAT2_uc003lgy.1_5'Flank	NM_012208	NP_036340	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2 precursor	417					histidyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|histidine-tRNA ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140165915	140165915	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140165915C>A	uc003lhb.2	+	1	40	c.40C>A	c.(40-42)CTG>ATG	p.L14M	PCDHA1_uc003lha.2_Missense_Mutation_p.L14M|PCDHA1_uc003lgz.2_Missense_Mutation_p.L14M	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	14					homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140181913	140181913	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140181913C>T	uc003lhf.2	+	1	1131	c.1131C>T	c.(1129-1131)CGC>CGT	p.R377R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.R377R	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	377	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188818	140188818	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188818G>A	uc003lhi.2	+	1	2147	c.2046G>A	c.(2044-2046)GCG>GCA	p.A682A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.A682A|PCDHA4_uc011daa.1_Silent_p.A682A	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	682	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA7	56141	broad.mit.edu	37	5	140215781	140215781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215781G>A	uc003lhq.2	+	1	1813	c.1813G>A	c.(1813-1815)GCG>ACG	p.A605T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.A605T	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	605	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140229616	140229616	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140229616G>A	uc003lhu.2	+	1	2260	c.1536G>A	c.(1534-1536)GCG>GCA	p.A512A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Silent_p.A512A	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	512	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA10	56139	broad.mit.edu	37	5	140236079	140236079	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140236079C>A	uc003lhx.2	+	1	446	c.446C>A	c.(445-447)TCT>TAT	p.S149Y	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Missense_Mutation_p.S149Y|PCDHA10_uc011dad.1_Missense_Mutation_p.S149Y	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	149	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA11	56138	broad.mit.edu	37	5	140249397	140249397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140249397G>A	uc003lia.2	+	1	1567	c.709G>A	c.(709-711)GAC>AAC	p.D237N	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Missense_Mutation_p.D237N	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	237	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140262322	140262322	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140262322G>A	uc003lif.2	+	1	469	c.469G>A	c.(469-471)GCA>ACA	p.A157T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Missense_Mutation_p.A157T|PCDHA13_uc003lid.2_Missense_Mutation_p.A157T	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	157	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB5	26167	broad.mit.edu	37	5	140516378	140516378	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140516378C>A	uc003liq.2	+	1	1579	c.1362C>A	c.(1360-1362)TCC>TCA	p.S454S		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	454	Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB6	56130	broad.mit.edu	37	5	140530649	140530649	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140530649G>T	uc003lir.2	+	1	811	c.811G>T	c.(811-813)GGA>TGA	p.G271*	PCDHB6_uc011dah.1_Nonsense_Mutation_p.G135*	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	271	Cadherin 3.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140581504	140581504	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140581504G>A	uc003liy.2	+	1	2157	c.2157G>A	c.(2155-2157)GCG>GCA	p.A719A	PCDHB11_uc011daj.1_Silent_p.A354A	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	719	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626516	140626516	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626516C>T	uc003lje.2	+	1	1370	c.1370C>T	c.(1369-1371)ACC>ATC	p.T457I		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	457	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA4	56111	broad.mit.edu	37	5	140735488	140735488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140735488G>A	uc003ljq.1	+	1	721	c.721G>A	c.(721-723)GTG>ATG	p.V241M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljp.1_Missense_Mutation_p.V241M	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	241	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA10	56106	broad.mit.edu	37	5	140794590	140794590	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140794590C>T	uc003lkl.1	+	1	1848	c.1848C>T	c.(1846-1848)AGC>AGT	p.S616S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc011day.1_Silent_p.S616S|PCDHGB7_uc003lkm.2_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1	616	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA10	56106	broad.mit.edu	37	5	140794641	140794641	+	Silent	SNP	G	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140794641G>C	uc003lkl.1	+	1	1899	c.1899G>C	c.(1897-1899)GCG>GCC	p.A633A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc011day.1_Silent_p.A633A|PCDHGB7_uc003lkm.2_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10 isoform 1	633	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA11	56105	broad.mit.edu	37	5	140801363	140801363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140801363C>T	uc003lkq.1	+	1	827	c.569C>T	c.(568-570)GCC>GTC	p.A190V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lko.1_Missense_Mutation_p.A190V|PCDHGA11_uc003lkp.1_Missense_Mutation_p.A190V	NM_018914	NP_061737	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11 isoform 1	190	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGC3	5098	broad.mit.edu	37	5	140856231	140856231	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140856231G>A	uc003lkv.1	+	1	663	c.548G>A	c.(547-549)CGC>CAC	p.R183H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Missense_Mutation_p.R183H|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3 isoform 1	183	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140896555	140896555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140896555C>T	uc003llb.3	-	29	3823	c.3682G>A	c.(3682-3684)GCA>ACA	p.A1228T	DIAPH1_uc011dbd.1_Silent_p.V139V|DIAPH1_uc003llc.3_Missense_Mutation_p.A1219T	NM_005219	NP_005210	O60610	DIAP1_HUMAN	diaphanous 1 isoform 1	1228					regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDH12	51294	broad.mit.edu	37	5	141336022	141336022	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141336022A>G	uc003llx.2	-	1	2606	c.1395T>C	c.(1393-1395)TAT>TAC	p.Y465Y		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	465	Extracellular (Potential).|Cadherin 5.				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
GNPDA1	10007	broad.mit.edu	37	5	141384619	141384619	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141384619G>A	uc003lmf.3	-	4	1231	c.472C>T	c.(472-474)CGT>TGT	p.R158C	GNPDA1_uc003lmg.3_Missense_Mutation_p.R158C|GNPDA1_uc010jgh.2_Missense_Mutation_p.R158C|GNPDA1_uc003lmh.3_Missense_Mutation_p.R124C	NM_005471	NP_005462	P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	158					generation of precursor metabolites and energy|glucosamine catabolic process|N-acetylglucosamine metabolic process|single fertilization	cytoplasm	glucosamine-6-phosphate deaminase activity|hydrolase activity				0		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ADRB2	154	broad.mit.edu	37	5	148207339	148207339	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148207339C>T	uc003lpr.1	+	1	1184	c.945C>T	c.(943-945)GGC>GGT	p.G315G	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	315	Agonist and antagonist binding.|Helical; Name=7.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)													---	---	---	---
AFAP1L1	134265	broad.mit.edu	37	5	148699169	148699169	+	Missense_Mutation	SNP	C	T	T	rs143811672	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148699169C>T	uc003lqh.2	+	13	1635	c.1504C>T	c.(1504-1506)CGC>TGC	p.R502C	AFAP1L1_uc010jgy.2_Missense_Mutation_p.R502C|AFAP1L1_uc003lqi.1_Missense_Mutation_p.R117C	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	502	PH 2.						protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
TIGD6	81789	broad.mit.edu	37	5	149375760	149375760	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149375760C>T	uc003lri.2	-	2	914	c.152G>A	c.(151-153)CGC>CAC	p.R51H	TIGD6_uc003lrj.2_Missense_Mutation_p.R51H	NM_030953	NP_112215	Q17RP2	TIGD6_HUMAN	hypothetical protein LOC81789	51	HTH psq-type.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
SYNPO	11346	broad.mit.edu	37	5	150029539	150029539	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150029539C>T	uc003lsn.2	+	3	2808	c.2434C>T	c.(2434-2436)CGC>TGC	p.R812C	SYNPO_uc003lso.3_Missense_Mutation_p.R568C|SYNPO_uc003lsp.2_Missense_Mutation_p.R568C	NM_001109974	NP_001103444	Q8N3V7	SYNPO_HUMAN	synaptopodin isoform B	812	Pro-rich.				positive regulation of actin filament bundle assembly|regulation of stress fiber assembly	actin cytoskeleton|cytoplasm|dendritic spine|perikaryon|postsynaptic density|postsynaptic membrane|tight junction	actin binding|protein binding			large_intestine(1)	1		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
RBM22	55696	broad.mit.edu	37	5	150075217	150075217	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150075217T>C	uc003lst.2	-	7	719	c.597A>G	c.(595-597)AAA>AAG	p.K199K		NM_018047	NP_060517	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	199					protein import into nucleus, translocation	catalytic step 2 spliceosome|cytoplasm	calcium-dependent protein binding|nucleotide binding|RNA binding|zinc ion binding				0		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150932868	150932868	+	Silent	SNP	C	T	T	rs150507279		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150932868C>T	uc003lue.3	-	5	4039	c.4026G>A	c.(4024-4026)CCG>CCA	p.P1342P	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1342	Extracellular (Potential).|Cadherin 11.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161576143	161576143	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161576143C>A	uc003lyz.3	+	8	1310	c.952C>A	c.(952-954)CTC>ATC	p.L318I	GABRG2_uc010jjc.2_Missense_Mutation_p.L358I|GABRG2_uc003lyy.3_Missense_Mutation_p.L318I|GABRG2_uc011dej.1_Missense_Mutation_p.L223I	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	318	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169477279	169477279	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169477279G>A	uc003maf.2	+	41	4171	c.4091G>A	c.(4090-4092)CGC>CAC	p.R1364H	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Missense_Mutation_p.R856H	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1364	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
HRH2	3274	broad.mit.edu	37	5	175110585	175110585	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175110585T>C	uc003mdd.2	+	1	2122	c.349T>C	c.(349-351)TAC>CAC	p.Y117H	HRH2_uc003mdc.3_Missense_Mutation_p.Y117H	NM_022304	NP_071640	P25021	HRH2_HUMAN	histamine receptor H2 isoform 2	117	Cytoplasmic (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|immune response	integral to plasma membrane	histamine receptor activity			ovary(1)	1	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Nizatidine(DB00585)|Ranitidine(DB00863)													---	---	---	---
EIF4E1B	253314	broad.mit.edu	37	5	176072487	176072487	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176072487C>T	uc010jkf.1	+	8	1168	c.584C>T	c.(583-585)GCG>GTG	p.A195V	TSPAN17_uc003mes.3_5'Flank|TSPAN17_uc003met.2_5'Flank|TSPAN17_uc003meu.2_5'Flank|TSPAN17_uc003mev.2_5'Flank|TSPAN17_uc003mew.2_5'Flank	NM_001099408	NP_001092878	A6NMX2	I4E1B_HUMAN	eukaryotic translation initiation factor 4E	195					regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
HK3	3101	broad.mit.edu	37	5	176308391	176308391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176308391C>T	uc003mfa.2	-	18	2631	c.2539G>A	c.(2539-2541)GTG>ATG	p.V847M	HK3_uc003mez.2_Missense_Mutation_p.V403M	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	847	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	7	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
FGFR4	2264	broad.mit.edu	37	5	176520703	176520703	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176520703A>G	uc003mfl.2	+	11	1613	c.1446A>G	c.(1444-1446)GTA>GTG	p.V482V	FGFR4_uc003mfm.2_Silent_p.V482V|FGFR4_uc011dfu.1_Silent_p.V414V|FGFR4_uc003mfo.2_Silent_p.V442V	NM_002011	NP_002002	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4 isoform 1	482	Protein kinase.|Cytoplasmic (Potential).				insulin receptor signaling pathway|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity			lung(11)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|prostate(1)	16	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	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)		Palifermin(DB00039)										TSP Lung(9;0.080)			---	---	---	---
DDX41	51428	broad.mit.edu	37	5	176939513	176939513	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176939513C>A	uc003mho.2	-	14	1554	c.1533G>T	c.(1531-1533)GAG>GAT	p.E511D	DOK3_uc003mhi.3_5'Flank|DOK3_uc003mhj.3_5'Flank|DOK3_uc003mhk.2_5'Flank|DOK3_uc003mhl.2_5'Flank|DDX41_uc003mhm.2_Missense_Mutation_p.E291D|DDX41_uc003mhn.2_Missense_Mutation_p.E380D|DDX41_uc003mhp.2_Missense_Mutation_p.E380D	NM_016222	NP_057306	Q9UJV9	DDX41_HUMAN	DEAD-box protein abstrakt	511	Helicase C-terminal.				apoptosis|multicellular organismal development	catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|zinc ion binding				0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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;0.191)															---	---	---	---
ZFP2	80108	broad.mit.edu	37	5	178359697	178359697	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178359697G>A	uc003mjn.1	+	5	1892	c.1383G>A	c.(1381-1383)ACG>ACA	p.T461T	ZFP2_uc010jky.2_Silent_p.T461T|ZFP2_uc010jkx.1_Silent_p.T461T	NM_030613	NP_085116	Q6ZN57	ZFP2_HUMAN	zinc finger protein 2 homolog	461					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)														---	---	---	---
MGAT4B	11282	broad.mit.edu	37	5	179227025	179227025	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179227025A>G	uc003mks.2	-	8	1208	c.839T>C	c.(838-840)ATG>ACG	p.M280T	MGAT4B_uc003mkp.2_Missense_Mutation_p.M135T|MGAT4B_uc003mkq.2_Missense_Mutation_p.M135T|MGAT4B_uc003mkr.2_Missense_Mutation_p.M295T|MIR1229_hsa-mir-1229|MI0006319_5'Flank	NM_014275	NP_055090	Q9UQ53	MGT4B_HUMAN	alpha-1,3-mannosyl-glycoprotein	280	Lumenal (Potential).				N-glycan processing|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				0	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
TRIM7	81786	broad.mit.edu	37	5	180622608	180622608	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180622608C>T	uc003mmz.1	-	7	1161	c.1094G>A	c.(1093-1095)CGC>CAC	p.R365H	TRIM7_uc003mmv.1_Missense_Mutation_p.R183H|TRIM7_uc003mmw.1_Missense_Mutation_p.R157H|TRIM7_uc003mmx.1_Missense_Mutation_p.R157H|TRIM7_uc003mmy.1_Missense_Mutation_p.R157H	NM_203293	NP_976038	Q9C029	TRIM7_HUMAN	tripartite motif-containing 7 isoform 1	365	B30.2/SPRY.					cytoplasm|nucleus	zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)														---	---	---	---
TRIM41	90933	broad.mit.edu	37	5	180651518	180651518	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180651518G>A	uc003mne.1	+	1	1213	c.519G>A	c.(517-519)CCG>CCA	p.P173P	uc003mnb.1_3'UTR|TRIM41_uc003mnc.1_Silent_p.P173P|TRIM41_uc003mnd.1_Silent_p.P173P|TRIM41_uc003mnf.1_RNA	NM_033549	NP_291027	Q8WV44	TRI41_HUMAN	tripartite motif-containing 41 isoform 1	173						cytoplasm|nucleus	ligase activity|protein binding|zinc ion binding				0	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CDYL	9425	broad.mit.edu	37	6	4892607	4892607	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4892607G>T	uc003mwi.2	+	4	978	c.847G>T	c.(847-849)GGG>TGG	p.G283W	CDYL_uc003mwj.2_Missense_Mutation_p.G229W|CDYL_uc003mwk.2_Intron|CDYL_uc011dhx.1_Missense_Mutation_p.G97W|CDYL_uc011dhy.1_Missense_Mutation_p.G97W	NM_001143971	NP_001137443	Q9Y232	CDYL1_HUMAN	chromodomain protein, Y chromosome-like isoform	283					regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	histone acetyltransferase activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)														---	---	---	---
GCM2	9247	broad.mit.edu	37	6	10874821	10874821	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10874821G>A	uc003mzn.3	-	5	1000	c.928C>T	c.(928-930)CTA>TTA	p.L310L	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	310					cellular calcium ion homeostasis|cellular phosphate ion homeostasis|parathyroid gland development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)																---	---	---	---
C6orf105	84830	broad.mit.edu	37	6	11778881	11778881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11778881C>T	uc003nab.2	-	1	400	c.112G>A	c.(112-114)GCA>ACA	p.A38T	C6orf105_uc011dip.1_Missense_Mutation_p.A38T	NM_032744	NP_116133	Q96IZ2	CF105_HUMAN	hypothetical protein LOC84830 isoform 2	38						integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)															---	---	---	---
EDN1	1906	broad.mit.edu	37	6	12296244	12296244	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12296244C>T	uc003nae.3	+	5	917	c.583C>T	c.(583-585)CTG>TTG	p.L195L	EDN1_uc003nad.2_3'UTR|EDN1_uc003naf.3_Silent_p.L194L	NM_001955	NP_001946	P05305	EDN1_HUMAN	endothelin 1 precursor	195					artery smooth muscle contraction|calcium-mediated signaling|leukocyte activation|negative regulation of blood coagulation|negative regulation of cellular protein metabolic process|negative regulation of nitric-oxide synthase biosynthetic process|negative regulation of transcription from RNA polymerase II promoter|nitric oxide transport|peptide hormone secretion|phosphatidylinositol 3-kinase cascade|positive regulation of cardiac muscle hypertrophy|positive regulation of cell size|positive regulation of endothelial cell migration|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of JUN kinase activity|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of sarcomere organization|positive regulation of smooth muscle cell proliferation|prostaglandin biosynthetic process|protein kinase C deactivation|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	cytoplasm|extracellular space	cytokine activity|endothelin A receptor binding|endothelin B receptor binding|hormone activity			skin(1)	1	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15501269	15501269	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15501269C>T	uc003nbj.2	+	8	2321	c.2077C>T	c.(2077-2079)CGG>TGG	p.R693W	JARID2_uc011div.1_Missense_Mutation_p.R521W|JARID2_uc011diw.1_Missense_Mutation_p.R655W	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	693	ARID.				central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15507634	15507634	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15507634C>T	uc003nbj.2	+	11	2962	c.2718C>T	c.(2716-2718)CTC>CTT	p.L906L	JARID2_uc011div.1_Silent_p.L734L|JARID2_uc011diw.1_Silent_p.L868L	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	906	JmjC.				central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15520429	15520429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15520429C>T	uc003nbj.2	+	18	3932	c.3688C>T	c.(3688-3690)CCC>TCC	p.P1230S	JARID2_uc011div.1_Missense_Mutation_p.P1058S	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	1230					central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
NUP153	9972	broad.mit.edu	37	6	17629339	17629339	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17629339A>C	uc003ncd.1	-	18	3291	c.3091T>G	c.(3091-3093)TCC>GCC	p.S1031A	NUP153_uc011dje.1_Missense_Mutation_p.S1062A|NUP153_uc010jpl.1_Missense_Mutation_p.S989A	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	1031					carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(4)|ovary(2)|breast(2)|skin(1)	9	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)															---	---	---	---
HIST1H4F	8361	broad.mit.edu	37	6	26240942	26240942	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26240942A>G	uc003nhe.1	+	1	289	c.289A>G	c.(289-291)ACT>GCT	p.T97A		NM_003540	NP_003531	P62805	H4_HUMAN	histone cluster 1, H4f	97					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)																---	---	---	---
BTN2A2	10385	broad.mit.edu	37	6	26384103	26384103	+	Silent	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26384103C>G	uc003nhq.2	+	2	140	c.54C>G	c.(52-54)CTC>CTG	p.L18L	BTN2A2_uc011dkf.1_Silent_p.L18L|BTN2A2_uc011dkg.1_Silent_p.L18L|BTN2A2_uc003nhr.2_Silent_p.L18L|BTN2A2_uc011dkh.1_Silent_p.L18L|BTN2A2_uc003nhs.2_Silent_p.L18L|BTN2A2_uc003nht.2_Silent_p.L18L	NM_006995	NP_008926	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2 isoform a	18					negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion	integral to membrane					0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26423300	26423300	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26423300A>G	uc011dkl.1	+	2	249	c.219A>G	c.(217-219)GCA>GCG	p.A73A	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26423392	26423392	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26423392G>A	uc011dkl.1	+	2	341	c.311G>A	c.(310-312)GGC>GAC	p.G104D	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26423427	26423427	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26423427G>A	uc011dkl.1	+	2	376	c.346G>A	c.(346-348)GAG>AAG	p.E116K	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN3A3	10384	broad.mit.edu	37	6	26452045	26452045	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26452045T>C	uc003nhz.2	+	11	1341	c.1161T>C	c.(1159-1161)TGT>TGC	p.C387C	BTN3A3_uc003nia.2_Silent_p.C345C|BTN3A3_uc011dkn.1_Silent_p.C338C	NM_006994	NP_008925	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3 isoform a	387	B30.2/SPRY.|Cytoplasmic (Potential).					integral to membrane					0																		---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29797196	29797196	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29797196C>T	uc003nnw.2	+	5	799	c.621C>T	c.(619-621)GAC>GAT	p.D207D	HLA-G_uc011dmb.1_Silent_p.D179D|HLA-G_uc003raj.3_Silent_p.D212D|HLA-G_uc003nnz.3_Silent_p.N115N|HLA-G_uc010jrn.2_Intron|HLA-G_uc003nny.3_RNA|HLA-G_uc003ran.1_5'Flank	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	207	Extracellular (Potential).|Alpha-3.				antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
TRIM26	7726	broad.mit.edu	37	6	30154088	30154088	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30154088C>T	uc003npr.2	-	9	1394	c.1185G>A	c.(1183-1185)GAG>GAA	p.E395E	TRIM26_uc003nps.2_Silent_p.E395E|TRIM26_uc010jry.2_Silent_p.E125E|TRIM26_uc003npt.2_Silent_p.E395E	NM_003449	NP_003440	Q12899	TRI26_HUMAN	tripartite motif-containing 26	395	B30.2/SPRY.|Poly-Glu.						DNA binding|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
PPP1R10	5514	broad.mit.edu	37	6	30574361	30574361	+	Missense_Mutation	SNP	C	T	T	rs16897725		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30574361C>T	uc003nqn.1	-	8	1070	c.518G>A	c.(517-519)CGA>CAA	p.R173Q	PPP1R10_uc010jsc.1_5'UTR	NM_002714	NP_002705	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	173	Interaction with TOX4 (By similarity).				protein import into nucleus|transcription, DNA-dependent	PTW/PP1 phosphatase complex	DNA binding|protein phosphatase inhibitor activity|RNA binding|zinc ion binding			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
DHX16	8449	broad.mit.edu	37	6	30632714	30632714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30632714G>A	uc003nqz.2	-	7	1393	c.1181C>T	c.(1180-1182)GCC>GTC	p.A394V	DHX16_uc003nqy.2_5'Flank|DHX16_uc011dmo.1_Missense_Mutation_p.A334V	NM_003587	NP_003578	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	394					mRNA processing|RNA splicing	nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(2)|kidney(2)	4																		---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30672220	30672220	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30672220A>G	uc003nrg.3	-	10	5180	c.4740T>C	c.(4738-4740)CCT>CCC	p.P1580P	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Silent_p.P1187P	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1580	Interaction with the PRKDC complex.				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4													Other_conserved_DNA_damage_response_genes					---	---	---	---
SKIV2L	6499	broad.mit.edu	37	6	31931826	31931826	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31931826C>T	uc003nyn.1	+	16	2173	c.1784C>T	c.(1783-1785)TCG>TTG	p.S595L	SKIV2L_uc011dou.1_Missense_Mutation_p.S437L|SKIV2L_uc011dov.1_Missense_Mutation_p.S402L	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	595	Helicase C-terminal.					nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33411085	33411085	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33411085A>G	uc011dri.1	+	15	2951	c.2756A>G	c.(2755-2757)CAG>CGG	p.Q919R	SYNGAP1_uc010juy.2_Missense_Mutation_p.Q890R|SYNGAP1_uc010juz.2_Missense_Mutation_p.Q631R	NM_006772	NP_006763	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	919					negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34008491	34008491	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34008491C>T	uc003oir.3	-	6	1373	c.1203G>A	c.(1201-1203)GAG>GAA	p.E401E	GRM4_uc011dsn.1_Silent_p.E354E|GRM4_uc010jvh.2_Silent_p.E401E|GRM4_uc010jvi.2_Silent_p.E93E|GRM4_uc003oio.2_Silent_p.E93E|GRM4_uc003oip.2_RNA|GRM4_uc011dsl.1_Silent_p.E261E|GRM4_uc003oiq.2_Silent_p.E268E|GRM4_uc011dsm.1_Silent_p.E232E	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	401	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	34937854	34937854	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34937854C>A	uc003ojx.3	+	3	488	c.346C>A	c.(346-348)CCT>ACT	p.P116T	ANKS1A_uc011dss.1_Missense_Mutation_p.P116T|ANKS1A_uc011dst.1_5'UTR|ANKS1A_uc010jvp.1_5'UTR|ANKS1A_uc010jvq.1_RNA|ANKS1A_uc010jvr.1_5'Flank	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain	116	ANK 2.					cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
ZNF76	7629	broad.mit.edu	37	6	35260699	35260699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35260699C>T	uc003oki.1	+	11	1412	c.1207C>T	c.(1207-1209)CGG>TGG	p.R403W	ZNF76_uc003okj.1_Missense_Mutation_p.R403W	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)	403					regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TULP1	7287	broad.mit.edu	37	6	35478786	35478786	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35478786C>A	uc003okv.3	-	5	363	c.351G>T	c.(349-351)GAG>GAT	p.E117D	TULP1_uc003okw.3_Missense_Mutation_p.E64D	NM_003322	NP_003313	O00294	TULP1_HUMAN	tubby like protein 1	117	Poly-Glu.				dendrite development|eye photoreceptor cell development|phagocytosis|photoreceptor cell maintenance|positive regulation of phagocytosis	cell junction|cytoplasm|extracellular region|photoreceptor inner segment|photoreceptor outer segment|synapse	actin filament binding|phosphatidylinositol-4,5-bisphosphate binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
PI16	221476	broad.mit.edu	37	6	36930862	36930862	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36930862C>A	uc003ona.2	+	5	1072	c.744C>A	c.(742-744)GTC>GTA	p.V248V	PI16_uc003omz.1_Intron|PI16_uc003onb.2_Intron|PI16_uc011dts.1_Silent_p.V19V	NM_153370	NP_699201	Q6UXB8	PI16_HUMAN	protease inhibitor 16 precursor	248	Extracellular (Potential).					extracellular region|integral to membrane	peptidase inhibitor activity				0																		---	---	---	---
FTSJD2	23070	broad.mit.edu	37	6	37430630	37430630	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37430630G>A	uc003ons.2	+	13	1604	c.1351G>A	c.(1351-1353)GTG>ATG	p.V451M		NM_015050	NP_055865	Q8N1G2	MTR1_HUMAN	FtsJ methyltransferase domain containing 2	451					mRNA capping	cytoplasm|nucleus	mRNA (nucleoside-2'-O-)-methyltransferase activity|nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38560444	38560444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38560444G>A	uc003ooa.3	-	5	1298	c.722C>T	c.(721-723)CCT>CTT	p.P241L	BTBD9_uc003ony.3_Missense_Mutation_p.P173L|BTBD9_uc010jwv.2_Missense_Mutation_p.P173L|BTBD9_uc010jww.2_RNA|BTBD9_uc010jwx.2_Missense_Mutation_p.P241L	NM_052893	NP_443125	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9 isoform a	241					cell adhesion						0																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38863896	38863896	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38863896T>C	uc003ooe.1	+	58	8784	c.8184T>C	c.(8182-8184)TGT>TGC	p.C2728C		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																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40399588	40399588	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40399588G>A	uc003oph.1	-	2	1730	c.1265C>T	c.(1264-1266)CCG>CTG	p.P422L		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	422	Fibronectin type-III.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42637820	42637820	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42637820T>C	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
CNPY3	10695	broad.mit.edu	37	6	42903362	42903362	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42903362A>C	uc003ota.3	+	3	775	c.326A>C	c.(325-327)GAT>GCT	p.D109A	CNPY3_uc003osy.2_RNA|CNPY3_uc003osz.2_Missense_Mutation_p.D109A|CNPY3_uc003otc.3_5'UTR|CNPY3_uc003otb.3_Missense_Mutation_p.D20A	NM_006586	NP_006577	Q9BT09	CNPY3_HUMAN	trinucleotide repeat containing 5 precursor	109	Saposin B-type.				innate immune response	endoplasmic reticulum				ovary(1)	1	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)															---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42936059	42936059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42936059G>A	uc003otf.2	-	7	1750	c.1657C>T	c.(1657-1659)CAC>TAC	p.H553Y	PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	553					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
MRPL2	51069	broad.mit.edu	37	6	43023827	43023827	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43023827C>T	uc003ots.1	-	4	635	c.512G>A	c.(511-513)CGA>CAA	p.R171Q	CUL7_uc011dvb.1_5'Flank|CUL7_uc003otq.2_5'Flank|CUL7_uc010jyh.2_5'Flank|KLC4_uc003otr.1_Intron|MRPL2_uc011dvc.1_Missense_Mutation_p.R171Q	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor	171					translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)														---	---	---	---
TMEM63B	55362	broad.mit.edu	37	6	44120388	44120388	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44120388C>T	uc003owr.2	+	20	1959	c.1895C>T	c.(1894-1896)ACG>ATG	p.T632M	TMEM63B_uc003ows.2_Missense_Mutation_p.T535M|TMEM63B_uc010jyz.2_RNA	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B	632	Helical; (Potential).					integral to membrane	nucleotide binding|protein binding			pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)													OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TDRD6	221400	broad.mit.edu	37	6	46661387	46661387	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46661387C>T	uc003oyj.2	+	1	5522	c.5522C>T	c.(5521-5523)CCT>CTT	p.P1841L	TDRD6_uc010jze.2_Missense_Mutation_p.P1835L	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	1841					cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)															---	---	---	---
CD2AP	23607	broad.mit.edu	37	6	47471097	47471097	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47471097T>C	uc003oyw.2	+	2	542	c.86T>C	c.(85-87)GTG>GCG	p.V29A		NM_012120	NP_036252	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	29	Interaction with ANLN and localization to the midbody.|SH3 1; truncated.				cell division|mitosis|protein complex assembly|signal transduction|substrate-dependent cell migration, cell extension	cytoplasm|filamentous actin|nucleolus|plasma membrane|ruffle	SH3 domain binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)															---	---	---	---
OPN5	221391	broad.mit.edu	37	6	47759639	47759639	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47759639T>C	uc003ozc.2	+	3	357	c.352T>C	c.(352-354)TGT>CGT	p.C118R	OPN5_uc003ozd.2_5'UTR	NM_181744	NP_859528	Q6U736	OPN5_HUMAN	opsin 5 isoform 1	118	Helical; Name=3; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1																		---	---	---	---
PGK2	5232	broad.mit.edu	37	6	49754751	49754751	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49754751G>A	uc003ozu.2	-	1	257	c.150C>T	c.(148-150)TGC>TGT	p.C50C		NM_138733	NP_620061	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	50					glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			ovary(1)	1	Lung NSC(77;0.0402)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51882291	51882291	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51882291A>G	uc003pah.1	-	34	5793	c.5517T>C	c.(5515-5517)ATT>ATC	p.I1839I	PKHD1_uc003pai.2_Silent_p.I1839I	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1839	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53706924	53706924	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53706924T>C	uc003pcd.1	+	2	453	c.176T>C	c.(175-177)GTC>GCC	p.V59A		NM_018214	NP_060684	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	59						cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
TINAG	27283	broad.mit.edu	37	6	54212213	54212213	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54212213C>T	uc003pcj.2	+	6	943	c.797C>T	c.(796-798)GCC>GTC	p.A266V	TINAG_uc010jzt.2_Intron	NM_014464	NP_055279	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	266					cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis	basement membrane	cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity			ovary(3)|central_nervous_system(1)	4	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57398247	57398247	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57398247G>T	uc003pdx.2	+	10	1037	c.950G>T	c.(949-951)GGT>GTT	p.G317V		NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	317					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)														---	---	---	---
BAI3	577	broad.mit.edu	37	6	70098693	70098693	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70098693G>T	uc003pev.3	+	32	4927	c.4479G>T	c.(4477-4479)AAG>AAT	p.K1493N	BAI3_uc010kak.2_Missense_Mutation_p.K1493N|BAI3_uc011dxx.1_Missense_Mutation_p.K699N	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1493	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70423622	70423622	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70423622C>T	uc003pfa.2	-	9	945	c.830G>A	c.(829-831)CGA>CAA	p.R277Q	LMBRD1_uc003pey.2_Missense_Mutation_p.R73Q|LMBRD1_uc003pez.2_Missense_Mutation_p.R204Q|LMBRD1_uc010kal.2_Missense_Mutation_p.R204Q|LMBRD1_uc003pfb.2_RNA	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein	277	Cytoplasmic (Potential).				interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72889303	72889303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72889303G>A	uc003pga.2	+	5	574	c.497G>A	c.(496-498)CGA>CAA	p.R166Q	RIMS1_uc011dyb.1_5'Flank|RIMS1_uc003pgc.2_5'Flank|RIMS1_uc003pgb.3_5'Flank	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	166	RabBD.|FYVE-type.				calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73902309	73902309	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73902309A>G	uc003pgk.2	+	13	2078	c.1731A>G	c.(1729-1731)AAA>AAG	p.K577K	KCNQ5_uc011dyh.1_Silent_p.K596K|KCNQ5_uc011dyi.1_Silent_p.K587K|KCNQ5_uc010kat.2_Silent_p.K568K|KCNQ5_uc011dyj.1_Silent_p.K467K|KCNQ5_uc011dyk.1_Silent_p.K327K	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	577					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73904255	73904255	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73904255C>T	uc003pgk.2	+	14	2264	c.1917C>T	c.(1915-1917)CTC>CTT	p.L639L	KCNQ5_uc011dyh.1_Silent_p.L658L|KCNQ5_uc011dyi.1_Silent_p.L649L|KCNQ5_uc010kat.2_Silent_p.L630L|KCNQ5_uc011dyj.1_Silent_p.L529L|KCNQ5_uc011dyk.1_Silent_p.L389L	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	639					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74150030	74150030	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74150030C>T	uc003pgx.1	-	3	1155	c.1016G>A	c.(1015-1017)CGC>CAC	p.R339H		NM_138441	NP_612450	Q8N884	M21D1_HUMAN	hypothetical protein LOC115004	339											0																		---	---	---	---
SLC35A1	10559	broad.mit.edu	37	6	88187198	88187198	+	Silent	SNP	C	A	A	rs3173204		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88187198C>A	uc011dzj.1	+	2	214	c.135C>A	c.(133-135)ACC>ACA	p.T45T	SLC35A1_uc003plx.2_RNA|SLC35A1_uc010kbw.2_5'UTR|SLC35A1_uc003plz.2_RNA|SLC35A1_uc011dzi.1_5'UTR|SLC35A1_uc003ply.2_RNA|SLC35A1_uc010kbx.2_Silent_p.T45T|SLC35A1_uc010kby.2_RNA|C6orf165_uc010kbv.1_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid	45	Lumenal (Potential).				carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90354754	90354754	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90354754A>G	uc003pnn.1	-	101	16698	c.16582T>C	c.(16582-16584)TTG>CTG	p.L5528L		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	5528	VWFA.				protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90513053	90513053	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90513053A>G	uc003pnn.1	-	2	439	c.323T>C	c.(322-324)GTC>GCC	p.V108A	MDN1_uc003pnp.1_Missense_Mutation_p.V108A	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	108					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
FBXL4	26235	broad.mit.edu	37	6	99374804	99374804	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99374804G>A	uc003ppf.1	-	3	419	c.61C>T	c.(61-63)CGC>TGC	p.R21C	FBXL4_uc003ppg.1_Missense_Mutation_p.R21C|FBXL4_uc003pph.1_5'UTR	NM_012160	NP_036292	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	21					ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)														---	---	---	---
C6orf168	84553	broad.mit.edu	37	6	99739692	99739692	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99739692A>T	uc003ppj.3	-	5	1111	c.828T>A	c.(826-828)GAT>GAA	p.D276E	C6orf168_uc003ppi.3_5'UTR	NM_032511	NP_115900	Q5TGI0	CF168_HUMAN	hypothetical protein LOC84553	276										ovary(2)|central_nervous_system(1)	3		all_cancers(76;1.63e-06)|Acute lymphoblastic leukemia(125;5.12e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00898)|Colorectal(196;0.0699)|Lung NSC(302;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.073)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100896434	100896434	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100896434C>T	uc003pqj.3	-	6	871	c.664G>A	c.(664-666)GTC>ATC	p.V222I	SIM1_uc010kcu.2_Missense_Mutation_p.V222I	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	222	PAS 2.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)														---	---	---	---
BEND3	57673	broad.mit.edu	37	6	107391922	107391922	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107391922T>G	uc003prs.2	-	5	1123	c.473A>C	c.(472-474)AAG>ACG	p.K158T		NM_001080450	NP_001073919	Q5T5X7	BEND3_HUMAN	BEN domain containing 3	158										ovary(3)	3																		---	---	---	---
FOXO3	2309	broad.mit.edu	37	6	108984784	108984784	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108984784C>T	uc003psk.2	+	3	1064	c.748C>T	c.(748-750)CGG>TGG	p.R250W	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Missense_Mutation_p.R250W|FOXO3_uc011ean.1_Missense_Mutation_p.R30W|FOXO3_uc010kdj.1_Missense_Mutation_p.R30W	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	250	Fork-head.|Nuclear localization signal.				antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|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			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)														---	---	---	---
RPF2	84154	broad.mit.edu	37	6	111320954	111320954	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111320954A>G	uc003pun.2	+	6	376	c.357A>G	c.(355-357)TTA>TTG	p.L119L	RPF2_uc003puo.2_Silent_p.L56L	NM_032194	NP_115570	Q9H7B2	RPF2_HUMAN	brix domain containing 1	119	Brix.					nucleolus	protein binding			ovary(2)	2																		---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111654524	111654524	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111654524T>A	uc003puy.3	-	23	8050	c.7727A>T	c.(7726-7728)TAT>TTT	p.Y2576F	REV3L_uc003pux.3_Missense_Mutation_p.Y2498F|REV3L_uc003puz.3_Missense_Mutation_p.Y2498F|REV3L_uc003pva.1_RNA	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	2576					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111695100	111695100	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111695100A>G	uc003puy.3	-	13	4781	c.4458T>C	c.(4456-4458)TTT>TTC	p.F1486F	REV3L_uc003pux.3_Silent_p.F1408F|REV3L_uc003puz.3_Silent_p.F1408F	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	1486					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
TRAF3IP2	10758	broad.mit.edu	37	6	111912543	111912543	+	Silent	SNP	C	T	T	rs141106401		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111912543C>T	uc011ebc.1	-	3	1362	c.747G>A	c.(745-747)CAG>CAA	p.Q249Q	TRAF3IP2_uc003pvg.2_Silent_p.Q249Q|TRAF3IP2_uc003pvf.2_Silent_p.Q249Q|TRAF3IP2_uc010kdw.2_Silent_p.Q249Q|TRAF3IP2_uc010kdx.2_Silent_p.Q249Q	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	258					intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)														---	---	---	---
KPNA5	3841	broad.mit.edu	37	6	117037453	117037453	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117037453G>A	uc003pxh.2	+	8	859	c.728G>A	c.(727-729)GGC>GAC	p.G243D		NM_002269	NP_002260	O15131	IMA5_HUMAN	karyopherin alpha 5	240	ARM 4.				NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)														---	---	---	---
VGLL2	245806	broad.mit.edu	37	6	117586919	117586919	+	5'UTR	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117586919G>A	uc003pxn.2	+	1					VGLL2_uc003pxo.2_5'UTR	NM_182645	NP_872586			vestigial-like 2 isoform 1						transcription, DNA-dependent	nucleus				central_nervous_system(1)	1				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)														---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117650526	117650526	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117650526C>A	uc003pxp.1	-	32	5531	c.5332G>T	c.(5332-5334)GGA>TGA	p.G1778*	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	1778	Fibronectin type-III 9.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
DCBLD1	285761	broad.mit.edu	37	6	117864339	117864339	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117864339G>A	uc003pxs.2	+	12	1535	c.1410G>A	c.(1408-1410)GTG>GTA	p.V470V	GOPC_uc003pxq.1_Intron|DCBLD1_uc003pxr.1_Silent_p.V470V|DCBLD1_uc003pxt.1_Silent_p.V125V	NM_173674	NP_775945	Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1	470	Helical; (Potential).				cell adhesion	integral to membrane				ovary(1)	1		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119281303	119281303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119281303G>A	uc003pyj.2	-	18	3736	c.3388C>T	c.(3388-3390)CGC>TGC	p.R1130C	FAM184A_uc003pyk.3_Missense_Mutation_p.R961C|FAM184A_uc003pyl.3_Missense_Mutation_p.R926C|FAM184A_uc003pyi.2_RNA	NM_024581	NP_078857	Q8NB25	F184A_HUMAN	hypothetical protein LOC79632 isoform 1	1130										ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
CLVS2	134829	broad.mit.edu	37	6	123318992	123318992	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123318992C>A	uc003pzi.1	+	2	939	c.70C>A	c.(70-72)CCA>ACA	p.P24T		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	24					lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128388769	128388769	+	Silent	SNP	C	T	T	rs146089088	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128388769C>T	uc003qbk.2	-	12	2419	c.2052G>A	c.(2050-2052)CCG>CCA	p.P684P	PTPRK_uc003qbj.2_Silent_p.P684P|PTPRK_uc010kfc.2_Silent_p.P684P|PTPRK_uc011ebu.1_Silent_p.P684P|PTPRK_uc003qbl.1_Silent_p.P554P|PTPRK_uc011ebv.1_Silent_p.P684P	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	684	Extracellular (Potential).				cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128561240	128561240	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128561240G>A	uc003qbk.2	-	5	1000	c.633C>T	c.(631-633)AAC>AAT	p.N211N	PTPRK_uc003qbj.2_Silent_p.N211N|PTPRK_uc010kfc.2_Silent_p.N211N|PTPRK_uc011ebu.1_Silent_p.N211N|PTPRK_uc003qbl.1_Silent_p.N81N|PTPRK_uc011ebv.1_Silent_p.N211N	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	211	Extracellular (Potential).|Ig-like C2-type.				cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129775324	129775324	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129775324C>T	uc003qbn.2	+	46	6703	c.6598C>T	c.(6598-6600)CGT>TGT	p.R2200C	LAMA2_uc003qbo.2_Missense_Mutation_p.R2200C	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2200	Laminin G-like 1.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131191139	131191139	+	Missense_Mutation	SNP	C	T	T	rs150621192	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131191139C>T	uc003qch.2	-	15	2353	c.2171G>A	c.(2170-2172)CGT>CAT	p.R724H	EPB41L2_uc003qce.1_Missense_Mutation_p.R102H|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Missense_Mutation_p.R654H|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Missense_Mutation_p.R654H|EPB41L2_uc003qcd.1_5'Flank|EPB41L2_uc003qcj.1_Missense_Mutation_p.R121H	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	724					cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
CTGF	1490	broad.mit.edu	37	6	132270619	132270619	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132270619A>G	uc003qcz.2	-	5	1041	c.835T>C	c.(835-837)TAC>CAC	p.Y279H		NM_001901	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor precursor	279	CTCK.|Heparin-binding.				cellular lipid metabolic process|DNA replication|epidermis development|regulation of cell growth|response to wounding	plasma membrane|proteinaceous extracellular matrix	heparin binding|insulin-like growth factor binding				0	Breast(56;0.0602)			GBM - Glioblastoma multiforme(226;0.015)|OV - Ovarian serous cystadenocarcinoma(155;0.0169)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	137018441	137018441	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137018441T>C	uc003qhc.2	-	5	1252	c.891A>G	c.(889-891)GCA>GCG	p.A297A	MAP3K5_uc011edk.1_Silent_p.A142A|MAP3K5_uc010kgw.1_Silent_p.A297A	NM_005923	NP_005914	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase	297					activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137193328	137193328	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137193328T>C	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279			peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143093783	143093783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143093783C>T	uc003qjd.2	-	5	2836	c.2093G>A	c.(2092-2094)CGG>CAG	p.R698Q		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	698					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144724272	144724272	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144724272C>T	uc003qkt.2	+	2	185	c.93C>T	c.(91-93)GAC>GAT	p.D31D	UTRN_uc010khq.1_Silent_p.D31D	NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	31	CH 1.|Actin-binding.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147705840	147705840	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147705840C>T	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron|uc003qmb.2_5'Flank	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
UST	10090	broad.mit.edu	37	6	149342520	149342520	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149342520C>T	uc003qmg.2	+	7	1136	c.840C>T	c.(838-840)CTC>CTT	p.L280L		NM_005715	NP_005706	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	280	Lumenal (Potential).				protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
RAET1E	135250	broad.mit.edu	37	6	150210620	150210620	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150210620A>G	uc003qnl.1	-	3	546	c.486T>C	c.(484-486)CAT>CAC	p.H162H	uc003qni.1_Intron|RAET1E_uc003qnj.2_Silent_p.H162H|RAET1E_uc003qnk.1_Silent_p.H126H|RAET1E_uc010kih.1_RNA	NM_139165	NP_631904	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E precursor	162	Extracellular (Potential).|MHC class I alpha-2 like.				antigen processing and presentation|immune response|regulation of immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152129084	152129084	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152129084G>A	uc003qom.3	+	3	407	c.37G>A	c.(37-39)GCC>ACC	p.A13T	ESR1_uc010kin.2_Missense_Mutation_p.A13T|ESR1_uc010kio.2_Missense_Mutation_p.A13T|ESR1_uc010kip.2_Missense_Mutation_p.A13T|ESR1_uc003qon.3_Missense_Mutation_p.A13T|ESR1_uc003qoo.3_Missense_Mutation_p.A13T|ESR1_uc010kiq.2_5'UTR|ESR1_uc010kir.2_Missense_Mutation_p.A13T	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4	13	Modulating; mediates interaction with MACROD1.				positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152711422	152711422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152711422C>T	uc010kiw.2	-	53	8772	c.8170G>A	c.(8170-8172)GCT>ACT	p.A2724T	SYNE1_uc003qot.3_Missense_Mutation_p.A2731T|SYNE1_uc003qou.3_Missense_Mutation_p.A2724T|SYNE1_uc010kjb.1_Missense_Mutation_p.A2707T	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2724	Cytoplasmic (Potential).|HAT 5.				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154489165	154489165	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154489165G>A	uc003qpx.2	-	11	1147	c.991C>T	c.(991-993)CGA>TGA	p.R331*	OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_Nonsense_Mutation_p.R202*|IPCEF1_uc003qpw.2_Nonsense_Mutation_p.R332*|IPCEF1_uc010kjh.2_Nonsense_Mutation_p.R332*	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform	331					response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
NOX3	50508	broad.mit.edu	37	6	155761270	155761270	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761270T>C	uc003qqm.2	-	6	591	c.488A>G	c.(487-489)AAC>AGC	p.N163S		NM_015718	NP_056533	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	163	Ferric oxidoreductase.|Extracellular (Potential).						electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162622151	162622151	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162622151G>A	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162683713	162683713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162683713C>T	uc003qtx.3	-	3	390	c.256G>A	c.(256-258)GAC>AAC	p.D86N	PARK2_uc003qtv.3_RNA|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_5'UTR|PARK2_uc003qty.3_Missense_Mutation_p.D86N|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Missense_Mutation_p.D86N	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	86					aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
T	6862	broad.mit.edu	37	6	166580961	166580961	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166580961C>T	uc003quu.1	-	2	612	c.119G>A	c.(118-120)CGC>CAC	p.R40H	T_uc003qut.1_Missense_Mutation_p.R40H|T_uc003quv.1_Missense_Mutation_p.R40H	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	40					anterior/posterior axis specification, embryo|mesoderm development|primitive streak formation	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)										Chordoma_Familial_Clustering_of				---	---	---	---
TTLL2	83887	broad.mit.edu	37	6	167754476	167754476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167754476C>T	uc003qvs.1	+	3	1176	c.1088C>T	c.(1087-1089)GCT>GTT	p.A363V	TTLL2_uc011egr.1_RNA	NM_031949	NP_114155	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	363	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168319469	168319469	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168319469C>T	uc003qwd.2	+	20	2882	c.2740C>T	c.(2740-2742)CGC>TGC	p.R914C	MLLT4_uc003qwb.1_Missense_Mutation_p.R899C|MLLT4_uc003qwc.1_Missense_Mutation_p.R915C|MLLT4_uc003qwg.1_Missense_Mutation_p.R224C	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	915					adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169648977	169648977	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169648977G>A	uc003qwt.2	-	4	392	c.144C>T	c.(142-144)CCC>CCT	p.P48P		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	48	TSP N-terminal.|Heparin-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
SUN1	23353	broad.mit.edu	37	7	888201	888201	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:888201T>C	uc011jvp.1	+						SUN1_uc003sje.1_Missense_Mutation_p.S269P|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron|SUN1_uc003sjg.2_Missense_Mutation_p.S80P|SUN1_uc011jvr.1_Missense_Mutation_p.S17P|SUN1_uc003sji.2_5'Flank	NM_001130965	NP_001124437			unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
MICALL2	79778	broad.mit.edu	37	7	1478512	1478512	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1478512C>T	uc003skj.3	-	10	2233	c.2086G>A	c.(2086-2088)GAG>AAG	p.E696K	MICALL2_uc003skh.3_5'UTR|MICALL2_uc003ski.3_Missense_Mutation_p.E183K	NM_182924	NP_891554	Q8IY33	MILK2_HUMAN	MICAL-like 2 isoform 1	696						cytoplasm|cytoskeleton	zinc ion binding			central_nervous_system(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)														---	---	---	---
SLC29A4	222962	broad.mit.edu	37	7	5340174	5340174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5340174G>A	uc003sod.2	+	10	1492	c.1331G>A	c.(1330-1332)CGT>CAT	p.R444H	SLC29A4_uc003soc.2_Missense_Mutation_p.R444H|SLC29A4_uc003soe.2_Missense_Mutation_p.R430H|SLC29A4_uc010ksw.2_Intron	NM_153247	NP_694979	Q7RTT9	S29A4_HUMAN	solute carrier family 29 (nucleoside	444	Extracellular (Potential).				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			liver(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5662498	5662498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5662498C>T	uc003soy.1	-	17	2784	c.2594G>A	c.(2593-2595)CGC>CAC	p.R865H	RNF216_uc010ksz.1_Missense_Mutation_p.R487H|RNF216_uc010kta.1_Missense_Mutation_p.R487H|RNF216_uc011jwj.1_Missense_Mutation_p.R487H|RNF216_uc003sox.1_Missense_Mutation_p.R922H	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	865					apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6155062	6155062	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6155062G>A	uc011jwo.1	+	3	473	c.350G>A	c.(349-351)GGC>GAC	p.G117D	USP42_uc011jwn.1_5'UTR|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Missense_Mutation_p.G117D|USP42_uc011jwq.1_5'UTR|USP42_uc011jwr.1_5'Flank	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	117					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8125841	8125841	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8125841G>A	uc003srk.2	+	8	1876	c.1317G>A	c.(1315-1317)TCG>TCA	p.S439S		NM_138426	NP_612435	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	439											0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11022051	11022051	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11022051A>C	uc003sry.1	+	3	600	c.165A>C	c.(163-165)GAA>GAC	p.E55D	PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Missense_Mutation_p.E55D|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	55							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12683795	12683795	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12683795C>T	uc003ssn.3	+	12	1824	c.1614C>T	c.(1612-1614)AAC>AAT	p.N538N	SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Silent_p.N291N	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1	538	Ca(2+)-dependent actin binding.|Gelsolin-like 5.				actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)														---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18630000	18630000	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18630000C>A	uc003suh.2	+	3	338	c.297C>A	c.(295-297)CTC>CTA	p.L99L	HDAC9_uc003sue.2_Silent_p.L99L|HDAC9_uc011jyd.1_Silent_p.L99L|HDAC9_uc003sui.2_Silent_p.L102L|HDAC9_uc003suj.2_Silent_p.L102L|HDAC9_uc011jya.1_Silent_p.L140L|HDAC9_uc003sua.1_Silent_p.L121L|HDAC9_uc011jyb.1_Silent_p.L99L|HDAC9_uc003sud.1_Silent_p.L99L|HDAC9_uc011jyc.1_Silent_p.L102L|HDAC9_uc003suf.1_Silent_p.L130L|HDAC9_uc010kud.1_Silent_p.L102L|HDAC9_uc011jye.1_Silent_p.L71L|HDAC9_uc011jyf.1_Silent_p.L68L|HDAC9_uc010kue.1_5'UTR	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1	99				L -> I (in Ref. 8; AAF04254).	B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18875107	18875107	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18875107C>T	uc003suh.2	+	19	2516	c.2475C>T	c.(2473-2475)AAC>AAT	p.N825N	HDAC9_uc003sue.2_Silent_p.N825N|HDAC9_uc011jyd.1_Silent_p.N825N|HDAC9_uc003sui.2_Silent_p.N828N|HDAC9_uc003suj.2_Silent_p.N784N|HDAC9_uc003suk.2_Silent_p.N73N	NM_058176	NP_478056	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 1	825	Histone deacetylase.				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
CDCA7L	55536	broad.mit.edu	37	7	21942601	21942601	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21942601C>T	uc010kuk.2	-	9	1449	c.1329G>A	c.(1327-1329)CTG>CTA	p.L443L	CDCA7L_uc003sve.3_Silent_p.L409L|CDCA7L_uc010kul.2_Silent_p.L397L|CDCA7L_uc003svf.3_Silent_p.L442L	NM_018719	NP_061189	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like isoform 1	443					positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22206738	22206738	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22206738C>T	uc011jym.1	-	2	398	c.324G>A	c.(322-324)ACG>ACA	p.T108T	RAPGEF5_uc003svg.2_Silent_p.T258T			Q92565	RPGF5_HUMAN	Synthetic construct DNA, clone: pF1KSDA0277, Homo sapiens RAPGEF5 gene for Rap guanine nucleotide exchange factor 5, complete cds, without stop codon, in Flexi system.	108	N-terminal Ras-GEF.				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																		---	---	---	---
HOXA2	3199	broad.mit.edu	37	7	27140675	27140675	+	Silent	SNP	G	A	A	rs140022054		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27140675G>A	uc003syh.2	-	2	1076	c.801C>T	c.(799-801)GGC>GGT	p.G267G		NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2	267						nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
HOXA5	3202	broad.mit.edu	37	7	27181672	27181672	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27181672G>A	uc003syn.1	-	2	656	c.595C>T	c.(595-597)CGG>TGG	p.R199W		NM_019102	NP_061975	P20719	HXA5_HUMAN	homeobox A5	199	Homeobox.				negative regulation of angiogenesis|negative regulation of erythrocyte differentiation|positive regulation of apoptosis|positive regulation of myeloid cell differentiation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																OREG0017911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WIPF3	644150	broad.mit.edu	37	7	29918676	29918676	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29918676C>T	uc003taj.1	+	3	275	c.275C>T	c.(274-276)GCG>GTG	p.A92V		NM_001080529	NP_001073998	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	92										ovary(1)	1																		---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31692254	31692254	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31692254G>T	uc003tcj.1	+	14	3939	c.2946G>T	c.(2944-2946)AGG>AGT	p.R982S	CCDC129_uc011kad.1_Missense_Mutation_p.R992S|CCDC129_uc003tci.1_Missense_Mutation_p.R833S|CCDC129_uc011kae.1_Missense_Mutation_p.R1008S|CCDC129_uc003tck.1_Missense_Mutation_p.R890S	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	982											0																		---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31692285	31692285	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31692285G>A	uc003tcj.1	+	14	3970	c.2977G>A	c.(2977-2979)GCT>ACT	p.A993T	CCDC129_uc011kad.1_Missense_Mutation_p.A1003T|CCDC129_uc003tci.1_Missense_Mutation_p.A844T|CCDC129_uc011kae.1_Missense_Mutation_p.A1019T|CCDC129_uc003tck.1_Missense_Mutation_p.A901T	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	993											0																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35029564	35029564	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35029564A>G	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43477677	43477677	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43477677A>G	uc003tid.1	+	9	1482	c.877A>G	c.(877-879)ATC>GTC	p.I293V	HECW1_uc011kbi.1_Missense_Mutation_p.I293V|HECW1_uc003tie.1_Missense_Mutation_p.I325V	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	293	C2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
URGCP	55665	broad.mit.edu	37	7	43918266	43918266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43918266C>T	uc003tiw.2	-	6	853	c.796G>A	c.(796-798)GTG>ATG	p.V266M	URGCP_uc003tiu.2_Missense_Mutation_p.V223M|URGCP_uc003tiv.2_Missense_Mutation_p.V191M|URGCP_uc003tix.2_Missense_Mutation_p.V257M|URGCP_uc003tiy.2_Missense_Mutation_p.V223M|URGCP_uc003tiz.2_Missense_Mutation_p.V223M|URGCP_uc011kbj.1_Missense_Mutation_p.V223M	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	266					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45753312	45753312	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45753312G>A	uc003tne.3	+	20	3096	c.3078G>A	c.(3076-3078)CGG>CGA	p.R1026R		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	1026	Cytoplasmic (Potential).|Interaction with calmodulin (By similarity).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
ZNF107	51427	broad.mit.edu	37	7	64168629	64168629	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64168629A>G	uc003ttd.2	+	7	2733	c.1947A>G	c.(1945-1947)TCA>TCG	p.S649S	ZNF107_uc003tte.2_Silent_p.S649S	NM_016220	NP_057304	Q9UII5	ZN107_HUMAN	zinc finger protein 107	649	C2H2-type 21.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.00948)|all_lung(88;0.0249)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71252835	71252835	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71252835G>A	uc003twa.3	-	6	1112	c.585C>T	c.(583-585)TGC>TGT	p.C195C	CALN1_uc003twb.3_Silent_p.C237C|CALN1_uc003twc.3_Silent_p.C195C	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 2	195	Helical; Anchor for type IV membrane protein; (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77567104	77567104	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77567104T>C	uc003ugs.3	+	12	1542	c.1416T>C	c.(1414-1416)TGT>TGC	p.C472C	PHTF2_uc003ugp.2_Silent_p.C434C|PHTF2_uc003ugq.3_Silent_p.C434C|PHTF2_uc010ldv.2_Silent_p.C434C|PHTF2_uc003ugt.3_Silent_p.C438C|PHTF2_uc003ugu.3_Silent_p.C434C|PHTF2_uc003ugv.2_Silent_p.C297C|PHTF2_uc010ldw.1_Intron	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	472					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78636481	78636481	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78636481G>A	uc003ugx.2	-	2	597	c.343C>T	c.(343-345)CGA>TGA	p.R115*	MAGI2_uc003ugy.2_Nonsense_Mutation_p.R115*	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	115	Guanylate kinase-like.					cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
GNAT3	346562	broad.mit.edu	37	7	80108232	80108232	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80108232C>T	uc011kgu.1	-	4	386	c.386G>A	c.(385-387)CGG>CAG	p.R129Q	CD36_uc003uhc.2_Intron	NM_001102386	NP_001095856	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha	129					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|rhodopsin mediated phototransduction|sensory perception of sweet taste|sensory perception of umami taste	cytoplasm|heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82544741	82544741	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82544741C>T	uc003uhx.2	-	7	12850	c.12561G>A	c.(12559-12561)AAG>AAA	p.K4187K	PCLO_uc003uhv.2_Silent_p.K4187K|PCLO_uc010lec.2_Silent_p.K1152K	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4118					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88963180	88963180	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88963180C>A	uc011khi.1	+	4	1422	c.884C>A	c.(883-885)ACC>AAC	p.T295N		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	295						intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
STEAP1	26872	broad.mit.edu	37	7	89790622	89790622	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89790622A>G	uc003ujx.2	+	3	788	c.588A>G	c.(586-588)GCA>GCG	p.A196A	STEAP1_uc010lem.2_Silent_p.A196A	NM_012449	NP_036581	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the	196	Ferric oxidoreductase.				electron transport chain|ion transport|iron ion homeostasis	cell-cell junction|endosome membrane|integral to plasma membrane	channel activity|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	all_hematologic(106;0.112)																	---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91632476	91632476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91632476C>T	uc003ulg.2	+	8	3470	c.3245C>T	c.(3244-3246)TCA>TTA	p.S1082L	AKAP9_uc003ule.2_Missense_Mutation_p.S1094L|AKAP9_uc003ulf.2_Missense_Mutation_p.S1082L|AKAP9_uc003uli.2_Missense_Mutation_p.S707L	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1094					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94168365	94168365	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94168365T>C	uc003uni.3	+	10	1580	c.1353T>C	c.(1351-1353)AGT>AGC	p.S451S	CASD1_uc003unj.3_Silent_p.S451S	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	451	Helical; (Potential).					integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
DLX5	1749	broad.mit.edu	37	7	96651485	96651485	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96651485C>T	uc003uon.2	-						DLX5_uc011kim.1_Silent_p.A184A	NM_005221	NP_005212			distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97935802	97935802	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97935802G>A	uc003upj.2	-	11	1453	c.1190C>T	c.(1189-1191)ACG>ATG	p.T397M	uc003upk.1_5'Flank	NM_018842	NP_061330	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	397	SH3.				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)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98534814	98534814	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98534814A>G	uc003upp.2	+	29	4356	c.4147A>G	c.(4147-4149)AGG>GGG	p.R1383G	TRRAP_uc011kis.1_Missense_Mutation_p.R1383G|TRRAP_uc003upr.2_Missense_Mutation_p.R1075G	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	1383					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98580976	98580976	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98580976C>T	uc003upp.2	+	59	9104	c.8895C>T	c.(8893-8895)CAC>CAT	p.H2965H	TRRAP_uc011kis.1_Silent_p.H2947H|TRRAP_uc003upr.2_Silent_p.H2664H	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2965	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
LRCH4	4034	broad.mit.edu	37	7	100175014	100175014	+	Splice_Site	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100175014T>C	uc003uvj.2	-	11	1232	c.1179_splice	c.e11-1	p.R393_splice	LRCH4_uc010lgz.2_Splice_Site|LRCH4_uc003uvi.2_Splice_Site|LRCH4_uc011kjw.1_Splice_Site|LRCH4_uc011kjx.1_Splice_Site	NM_002319	NP_002310			leucine-rich repeats and calponin homology (CH)						nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
MOSPD3	64598	broad.mit.edu	37	7	100212539	100212539	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100212539G>T	uc003uvq.2	+	5	763	c.561G>T	c.(559-561)ACG>ACT	p.T187T	MOSPD3_uc003uvr.2_Silent_p.T187T|MOSPD3_uc003uvs.2_Silent_p.T187T|MOSPD3_uc003uvt.2_Silent_p.T177T	NM_001040097	NP_001035186	O75425	MSPD3_HUMAN	motile sperm domain containing 3 isoform a	187	Helical; (Potential).					integral to membrane	structural molecule activity			ovary(2)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100551663	100551663	+	RNA	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100551663G>A	uc003uxk.1	+	1		c.914G>A			uc003uxl.1_Silent_p.T38T					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104742433	104742433	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104742433A>G	uc003vcm.2	+	17	2522	c.1988A>G	c.(1987-1989)CAG>CGG	p.Q663R	MLL5_uc010ljc.2_Missense_Mutation_p.Q663R|MLL5_uc010lje.1_RNA	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	663					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104748331	104748331	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104748331G>A	uc003vcm.2	+	22	3961	c.3427G>A	c.(3427-3429)GAC>AAC	p.D1143N	MLL5_uc010ljc.2_Missense_Mutation_p.D1143N|MLL5_uc010lje.1_RNA|MLL5_uc010ljf.1_RNA|MLL5_uc010ljg.2_5'UTR|MLL5_uc010ljh.1_5'Flank	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1143					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
PIK3CG	5294	broad.mit.edu	37	7	106522568	106522568	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106522568C>A	uc003vdv.3	+	7	2630	c.2545C>A	c.(2545-2547)CGA>AGA	p.R849R	PIK3CG_uc003vdu.2_Silent_p.R849R|PIK3CG_uc003vdw.2_Silent_p.R849R	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	849	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38																		---	---	---	---
TMEM168	64418	broad.mit.edu	37	7	112407372	112407372	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112407372G>A	uc003vgn.2	-	5	2366	c.1974C>T	c.(1972-1974)TGC>TGT	p.C658C	TMEM168_uc010lju.2_Silent_p.C658C|TMEM168_uc011kmr.1_Silent_p.C274C	NM_022484	NP_071929	Q9H0V1	TM168_HUMAN	transmembrane protein 168	658	Helical; (Potential).					integral to membrane|transport vesicle				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114299690	114299690	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114299690A>G	uc003vhb.2	+	13	1983	c.1609A>G	c.(1609-1611)ACA>GCA	p.T537A	FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Missense_Mutation_p.T562A|FOXP2_uc003vha.2_Missense_Mutation_p.T445A|FOXP2_uc011kmu.1_Missense_Mutation_p.T554A|FOXP2_uc011kmv.1_Missense_Mutation_p.T536A|FOXP2_uc010ljz.1_Missense_Mutation_p.T352A|FOXP2_uc003vhe.1_Missense_Mutation_p.T107A	NM_014491	NP_055306	O15409	FOXP2_HUMAN	forkhead box P2 isoform I	537	Fork-head.				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
RNF148	378925	broad.mit.edu	37	7	122341990	122341990	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122341990C>T	uc003vkk.1	-	1	1032	c.815G>A	c.(814-816)CGC>CAC	p.R272H	CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron|RNF133_uc003vkj.1_5'Flank|RNF148_uc010lkr.1_3'UTR	NM_198085	NP_932351	Q8N7C7	RN148_HUMAN	ring finger protein 148 precursor	272	RING-type; atypical.					integral to membrane	zinc ion binding				0																		---	---	---	---
LRRC4	64101	broad.mit.edu	37	7	127669218	127669218	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127669218C>T	uc003vmk.2	-	2	1613	c.1476G>A	c.(1474-1476)ACG>ACA	p.T492T	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	492	Thr-rich.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)														---	---	---	---
IMPDH1	3614	broad.mit.edu	37	7	128038480	128038480	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128038480G>A	uc011kol.1	-	7	913	c.807C>T	c.(805-807)GAC>GAT	p.D269D	IMPDH1_uc011kom.1_Silent_p.D264D|IMPDH1_uc003vmt.2_Silent_p.D244D|IMPDH1_uc003vmu.2_Silent_p.D354D|IMPDH1_uc003vmw.2_Silent_p.D344D|IMPDH1_uc011kon.1_Silent_p.D321D|IMPDH1_uc003vmv.2_Silent_p.D318D|IMPDH1_uc003vmx.2_Silent_p.D277D|IMPDH1_uc003vmy.2_Silent_p.D285D	NM_001142573	NP_001136045	P20839	IMDH1_HUMAN	inosine monophosphate dehydrogenase 1 isoform e	269	NAD (By similarity).				GMP biosynthetic process|purine base metabolic process	cytosol|nucleus	DNA binding|IMP dehydrogenase activity|metal ion binding			skin(2)|lung(1)|central_nervous_system(1)	4					Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|NADH(DB00157)|Ribavirin(DB00811)|Thioguanine(DB00352)											OREG0018292	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129098623	129098623	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129098623G>A	uc011koy.1	+						FAM40B_uc003vow.2_Intron|FAM40B_uc011koz.1_Intron	NM_020704	NP_065755			hypothetical protein LOC57464 isoform a												0																		---	---	---	---
CPA4	51200	broad.mit.edu	37	7	129950820	129950820	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129950820G>T	uc003vpr.2	+	9	1034	c.987G>T	c.(985-987)GAG>GAT	p.E329D	CPA4_uc011kpd.1_Missense_Mutation_p.E296D|CPA4_uc011kpe.1_Missense_Mutation_p.E225D	NM_016352	NP_057436	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4 preproprotein	329					histone acetylation|proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137263010	137263010	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137263010A>G	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138832998	138832998	+	Silent	SNP	T	C	C	rs144351469		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138832998T>C	uc003vus.2	+	7	706	c.592T>C	c.(592-594)TTG>CTG	p.L198L	TTC26_uc003vuq.2_Silent_p.L198L|TTC26_uc011kqm.1_Intron|TTC26_uc003vur.3_Silent_p.L198L|TTC26_uc011kqn.1_Silent_p.L198L|TTC26_uc011kqo.1_Silent_p.L167L|TTC26_uc011kqp.1_Silent_p.L93L|TTC26_uc003vut.2_Silent_p.L58L|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202	A0AVF1	TTC26_HUMAN	tetratricopeptide repeat domain 26 isoform 1	198							binding			ovary(1)	1																		---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140051864	140051864	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140051864A>T	uc003vvo.2	-	8	867	c.701T>A	c.(700-702)ATT>AAT	p.I234N	SLC37A3_uc003vvp.2_Missense_Mutation_p.I234N|SLC37A3_uc010lnh.2_Missense_Mutation_p.I234N|SLC37A3_uc011kqz.1_RNA|SLC37A3_uc011kra.1_Missense_Mutation_p.I234N|SLC37A3_uc011krb.1_Missense_Mutation_p.I206N	NM_207113	NP_996996	Q8NCC5	SPX3_HUMAN	solute carrier family 37 (glycerol-3-phosphate	234					carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
CASP2	835	broad.mit.edu	37	7	142997069	142997069	+	Silent	SNP	G	A	A	rs114290247	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142997069G>A	uc003wco.2	+	7	948	c.801G>A	c.(799-801)ACG>ACA	p.T267T	CASP2_uc003wcp.2_3'UTR|CASP2_uc011kta.1_Silent_p.T151T|CASP2_uc003wcq.2_RNA|CASP2_uc011ktb.1_Silent_p.T17T	NM_032982	NP_116764	P42575	CASP2_HUMAN	caspase 2 isoform 1 preproprotein	267					apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein maturation by peptide bond cleavage	cytosol	cysteine-type endopeptidase activity|enzyme binding|protein binding|protein domain specific binding			lung(2)|ovary(1)	3	Melanoma(164;0.059)															OREG0018400	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM115A	9747	broad.mit.edu	37	7	143573696	143573696	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143573696C>T	uc003wdo.1	-	2	139	c.6G>A	c.(4-6)GCG>GCA	p.A2A	FAM115A_uc011ktu.1_Intron|FAM115A_uc003wdp.1_Silent_p.A2A	NM_014719	NP_055534	Q9Y4C2	F115A_HUMAN	hypothetical protein LOC9747	2											0	Melanoma(164;0.0903)																	---	---	---	---
OR2A14	135941	broad.mit.edu	37	7	143827119	143827119	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143827119G>T	uc011kua.1	+	1	914	c.914G>T	c.(913-915)AGG>ATG	p.R305M		NM_001001659	NP_001001659	Q96R47	O2A14_HUMAN	olfactory receptor, family 2, subfamily A,	305	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)																	---	---	---	---
NOBOX	135935	broad.mit.edu	37	7	144096957	144096957	+	Splice_Site	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144096957C>A	uc011kue.1	-	6	1048	c.1048_splice	c.e6-1	p.V350_splice		NM_001080413	NP_001073882			NOBOX oogenesis homeobox						cell differentiation|oogenesis	nucleus	sequence-specific DNA binding			ovary(1)	1	Melanoma(164;0.14)																	---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	147926877	147926877	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147926877C>T	uc003weu.1	+							NM_014141	NP_054860			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)												HNSCC(39;0.1)			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148485685	148485685	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148485685C>A	uc010lpg.2	+	14	2042	c.1516C>A	c.(1516-1518)CGC>AGC	p.R506S	CUL1_uc003wey.2_Missense_Mutation_p.R506S|CUL1_uc003wez.2_Missense_Mutation_p.R396S|CUL1_uc003wfa.2_Missense_Mutation_p.R167S	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	506					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148496368	148496368	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148496368C>T	uc010lpg.2	+	21	2664	c.2138C>T	c.(2137-2139)GCG>GTG	p.A713V	CUL1_uc003wey.2_Missense_Mutation_p.A713V|CUL1_uc003wez.2_Missense_Mutation_p.A603V|CUL1_uc003wfa.2_Missense_Mutation_p.A374V	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	713					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
ZNF425	155054	broad.mit.edu	37	7	148801590	148801590	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148801590C>T	uc003wfj.2	-	4	1446	c.1373G>A	c.(1372-1374)CGC>CAC	p.R458H		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	458	C2H2-type 9.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)															---	---	---	---
ZNF777	27153	broad.mit.edu	37	7	149129573	149129573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149129573C>T	uc003wfv.2	-	6	1953	c.1790G>A	c.(1789-1791)CGC>CAC	p.R597H		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	597					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149522359	149522359	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149522359G>A	uc010lpk.2	+						SSPO_uc010lpm.1_Intron|SSPO_uc003wgg.2_Intron|SSPO_uc003wgh.2_Intron|SSPO_uc003wgi.1_Intron	NM_198455	NP_940857			SCO-spondin precursor						cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
KCNH2	3757	broad.mit.edu	37	7	150656686	150656686	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150656686C>G	uc003wic.2	-	3	459	c.446G>C	c.(445-447)GGC>GCC	p.G149A	KCNH2_uc011kux.1_Missense_Mutation_p.G53A|KCNH2_uc003wie.2_Missense_Mutation_p.G149A	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,	149	Cytoplasmic (Potential).				blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)													---	---	---	---
ACCN3	9311	broad.mit.edu	37	7	150747697	150747697	+	Splice_Site	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150747697T>C	uc003win.2	+	3	1181	c.813_splice	c.e3+2	p.Q271_splice	ACCN3_uc003wio.2_Splice_Site_p.Q271_splice|ACCN3_uc003wip.2_Splice_Site_p.Q271_splice|ACCN3_uc003wiq.2_Splice_Site	NM_004769	NP_004760			amiloride-sensitive cation channel 3 isoform a						sensory perception|signal transduction	cytoplasm|integral to plasma membrane	ligand-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
AGAP3	116988	broad.mit.edu	37	7	150815665	150815665	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150815665G>A	uc003wjg.1	+	7	918	c.915G>A	c.(913-915)TCG>TCA	p.S305S	AGAP3_uc003wje.1_Silent_p.S77S|AGAP3_uc003wjf.1_Silent_p.S305S|AGAP3_uc010lpy.1_Silent_p.S305S|AGAP3_uc003wjh.1_Silent_p.S485S|AGAP3_uc003wji.1_5'Flank	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	269	Small GTPase-like.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151802408	151802408	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151802408G>A	uc010lqg.1	+	5	895	c.665G>A	c.(664-666)CGT>CAT	p.R222H	GALNT11_uc011kvm.1_Missense_Mutation_p.R141H|GALNT11_uc003wku.2_Missense_Mutation_p.R222H|GALNT11_uc011kvn.1_RNA|GALNT11_uc003wkw.1_5'Flank	NM_022087	NP_071370	Q8NCW6	GLT11_HUMAN	N-acetylgalactosaminyltransferase 11	222	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151878749	151878749	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151878749G>A	uc003wla.2	-	36	6415	c.6196C>T	c.(6196-6198)CGA>TGA	p.R2066*	MLL3_uc003wkz.2_Nonsense_Mutation_p.R1127*	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	2066	Pro-rich.				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)				N		medulloblastoma								---	---	---	---
PAXIP1	22976	broad.mit.edu	37	7	154739611	154739611	+	Splice_Site	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154739611A>G	uc003wlp.2	-	17	2965	c.2922_splice	c.e17+1	p.K974_splice	LOC100132707_uc003wlo.2_RNA|PAXIP1_uc003wlq.1_Splice_Site_p.K940_splice|PAXIP1_uc011kvs.1_Splice_Site_p.K938_splice	NM_007349	NP_031375			PAX interacting protein 1						DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent	histone methyltransferase complex|nuclear matrix				lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)														---	---	---	---
ZNF596	169270	broad.mit.edu	37	8	196042	196042	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:196042G>T	uc003wot.2	+	6	1483	c.1195G>T	c.(1195-1197)GCC>TCC	p.A399S	ZNF596_uc003wou.2_Missense_Mutation_p.A298S|ZNF596_uc003wov.2_Missense_Mutation_p.A399S|ZNF596_uc003wow.2_Missense_Mutation_p.A399S	NM_173539	NP_775810	Q8TC21	ZN596_HUMAN	zinc finger protein 596	399	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3019715	3019715	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3019715A>G	uc011kwk.1	-	38	6203	c.5813T>C	c.(5812-5814)CTC>CCC	p.L1938P	CSMD1_uc011kwj.1_Missense_Mutation_p.L1330P|CSMD1_uc003wqe.2_Missense_Mutation_p.L1094P|CSMD1_uc010lrg.2_Missense_Mutation_p.L6P	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	1938	Sushi 11.|Extracellular (Potential).					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)														---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8185550	8185550	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8185550G>A	uc003wsh.3	-	4	2742	c.2742C>T	c.(2740-2742)CCC>CCT	p.P914P		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	914							ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8748408	8748408	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8748408C>T	uc003wsj.1	-	1	2724	c.2161G>A	c.(2161-2163)GCT>ACT	p.A721T		NM_004225	NP_004216	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified	721											0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
ERI1	90459	broad.mit.edu	37	8	8869198	8869198	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8869198C>T	uc011kwu.1	+	3	694	c.434C>T	c.(433-435)CCT>CTT	p.P145L	ERI1_uc003wsk.2_Missense_Mutation_p.P145L	NM_153332	NP_699163	Q8IV48	ERI1_HUMAN	three prime histone mRNA exonuclease 1	145	Exonuclease.				gene silencing by RNA|rRNA 3'-end processing	cytoplasm|histone pre-mRNA 3'end processing complex|nucleolus	3'-5' exonuclease activity|histone pre-mRNA stem-loop binding|metal ion binding|ribosome binding|rRNA binding				0					Adenosine monophosphate(DB00131)													---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9634228	9634228	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9634228C>T	uc003wss.2	+	27	3971	c.3966C>T	c.(3964-3966)GCC>GCT	p.A1322A	TNKS_uc011kww.1_Silent_p.A1085A	NM_003747	NP_003738	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1322					mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
MSRA	4482	broad.mit.edu	37	8	10159084	10159084	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10159084G>T	uc003wsx.2	+	4	569	c.372G>T	c.(370-372)CAG>CAT	p.Q124H	MSRA_uc011kwx.1_Missense_Mutation_p.Q84H|MSRA_uc011kwy.1_Missense_Mutation_p.Q81H|MSRA_uc003wsz.2_Missense_Mutation_p.Q81H|MSRA_uc003wsy.2_Missense_Mutation_p.Q58H	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a	124					methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10468221	10468221	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10468221C>T	uc003wtc.2	-	4	3616	c.3387G>A	c.(3385-3387)GAG>GAA	p.E1129E		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1129					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11615818	11615818	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11615818C>T	uc003wuc.2	+	7	1717	c.1163C>T	c.(1162-1164)GCG>GTG	p.A388V	GATA4_uc003wub.1_Missense_Mutation_p.A182V|GATA4_uc011kxc.1_Missense_Mutation_p.A389V|uc003wud.1_5'Flank	NM_002052	NP_002043	P43694	GATA4_HUMAN	GATA binding protein 4	388					atrial septum primum morphogenesis|atrial septum secundum morphogenesis|blood coagulation|cardiac right ventricle morphogenesis|cell-cell signaling|embryonic foregut morphogenesis|embryonic heart tube anterior/posterior pattern formation|endocardial cushion development|endoderm development|heart looping|intestinal epithelial cell differentiation|male gonad development|positive regulation of angiogenesis|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|response to drug|transcription from RNA polymerase II promoter|ventricular septum development	nucleoplasm	activating transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)														---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13357399	13357399	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13357399A>G	uc003wwm.2	-	2	626	c.182T>C	c.(181-183)CTA>CCA	p.L61P	DLC1_uc003wwn.2_Missense_Mutation_p.L61P|DLC1_uc011kxy.1_Missense_Mutation_p.L61P	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	61					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17401110	17401110	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17401110G>A	uc011kyc.1	+	2	431	c.262G>A	c.(262-264)GAA>AAA	p.E88K	SLC7A2_uc011kyd.1_Missense_Mutation_p.E128K|SLC7A2_uc011kye.1_Missense_Mutation_p.E128K|SLC7A2_uc011kyf.1_Missense_Mutation_p.E88K	NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2	88	Cytoplasmic (Potential).				cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19263582	19263582	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19263582T>C	uc011kyn.1	-						CSGALNACT1_uc011kyo.1_Intron|CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron	NM_001130518	NP_001123990			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22471699	22471699	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22471699T>G	uc003xch.2	+	9	936	c.799T>G	c.(799-801)TTC>GTC	p.F267V	KIAA1967_uc003xci.2_Missense_Mutation_p.F267V|KIAA1967_uc003xcj.1_5'UTR	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	267					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22473240	22473240	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22473240G>A	uc003xch.2	+	13	1560	c.1423G>A	c.(1423-1425)GCA>ACA	p.A475T	KIAA1967_uc003xci.2_Missense_Mutation_p.A475T|KIAA1967_uc003xcj.1_Missense_Mutation_p.A144T	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	475					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
EGR3	1960	broad.mit.edu	37	8	22548748	22548748	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22548748C>A	uc003xcm.1	-	2	760	c.402G>T	c.(400-402)CAG>CAT	p.Q134H	EGR3_uc011kzn.1_Missense_Mutation_p.Q96H|EGR3_uc011kzo.1_Missense_Mutation_p.Q80H	NM_004430	NP_004421	Q06889	EGR3_HUMAN	early growth response 3	134					circadian rhythm|muscle organ development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)														---	---	---	---
RHOBTB2	23221	broad.mit.edu	37	8	22868168	22868168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22868168C>T	uc003xcq.2	+	7	2275	c.1738C>T	c.(1738-1740)CGC>TGC	p.R580C	RHOBTB2_uc003xcp.2_Missense_Mutation_p.R602C|RHOBTB2_uc011kzp.1_Missense_Mutation_p.R587C|uc003xcr.2_Intron	NM_015178	NP_055993	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2 isoform 3	580					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			ovary(1)|lung(1)	2		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
LOXL2	4017	broad.mit.edu	37	8	23191084	23191084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23191084T>C	uc003xdh.1	-	5	1135	c.796A>G	c.(796-798)ACC>GCC	p.T266A	uc003xdj.2_5'Flank|uc003xdi.2_5'Flank	NM_002318	NP_002309	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2 precursor	266	SRCR 2.				aging|cell adhesion|protein modification process	extracellular space|membrane	copper ion binding|electron carrier activity|oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor|scavenger receptor activity			breast(2)|ovary(1)	3		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)														---	---	---	---
NEFL	4747	broad.mit.edu	37	8	24813138	24813138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24813138C>T	uc003xee.2	-	1	994	c.892G>A	c.(892-894)GTG>ATG	p.V298M		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	298	Rod.|Coil 2B.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
ADRA1A	148	broad.mit.edu	37	8	26721708	26721708	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26721708C>A	uc003xfh.1	-	1	1215	c.779G>T	c.(778-780)AGG>ATG	p.R260M	ADRA1A_uc003xfc.1_Missense_Mutation_p.R260M|ADRA1A_uc010lul.1_Missense_Mutation_p.R260M|ADRA1A_uc003xfd.1_RNA|ADRA1A_uc003xfe.1_Missense_Mutation_p.R260M|ADRA1A_uc010lum.1_Missense_Mutation_p.R260M|ADRA1A_uc003xff.1_RNA|ADRA1A_uc003xfg.1_Missense_Mutation_p.R260M	NM_000680	NP_000671	P35348	ADA1A_HUMAN	alpha-1A-adrenergic receptor isoform 1	260	Cytoplasmic (By similarity).				activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)													---	---	---	---
STMN4	81551	broad.mit.edu	37	8	27101235	27101235	+	Silent	SNP	G	T	T	rs138378493	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27101235G>T	uc003xfk.2	-	2	120	c.6C>A	c.(4-6)ACC>ACA	p.T2T	STMN4_uc003xfj.2_Silent_p.T2T|STMN4_uc011lai.1_Silent_p.T2T|STMN4_uc011laj.1_Intron|STMN4_uc011lak.1_Silent_p.T2T|STMN4_uc010luo.2_Silent_p.T2T			Q9H169	STMN4_HUMAN	RecName: Full=Stathmin-4; AltName: Full=Stathmin-like protein B3;          Short=RB3;	2					intracellular signal transduction					large_intestine(1)|pancreas(1)	2		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27296915	27296915	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27296915G>A	uc003xfn.1	+	25	2642	c.1834G>A	c.(1834-1836)GCC>ACC	p.A612T	PTK2B_uc003xfo.1_Missense_Mutation_p.A612T|PTK2B_uc003xfp.1_Missense_Mutation_p.A612T|PTK2B_uc003xfq.1_Missense_Mutation_p.A612T|PTK2B_uc003xfr.1_Missense_Mutation_p.A358T	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	612	Protein kinase.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27922180	27922180	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27922180G>A	uc003xgm.3	-	7	923	c.780C>T	c.(778-780)GCC>GCT	p.A260A		NM_001010906	NP_001010906	Q68CJ6	SLIP_HUMAN	speckled-like pattern in the germinal center	260						nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)														---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27925085	27925085	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27925085C>T	uc003xgm.3	-	6	800	c.657G>A	c.(655-657)GCG>GCA	p.A219A		NM_001010906	NP_001010906	Q68CJ6	SLIP_HUMAN	speckled-like pattern in the germinal center	219						nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29025013	29025013	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29025013C>T	uc003xhh.3	-	11	1094	c.1035G>A	c.(1033-1035)CGG>CGA	p.R345R	KIF13B_uc003xhj.2_Silent_p.R242R|KIF13B_uc010lvf.1_Silent_p.R281R	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	345					microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32472059	32472059	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32472059C>T	uc003xiv.2	+	4	945	c.428C>T	c.(427-429)ACT>ATT	p.T143I	NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Missense_Mutation_p.T143I|NRG1_uc010lvl.2_Missense_Mutation_p.T143I|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Missense_Mutation_p.T143I|NRG1_uc011lbf.1_Missense_Mutation_p.T143I|NRG1_uc010lvo.2_Missense_Mutation_p.T143I|NRG1_uc003xiu.2_Missense_Mutation_p.T143I|NRG1_uc003xiw.2_Missense_Mutation_p.T143I|NRG1_uc003xit.2_Missense_Mutation_p.T143I|NRG1_uc010lvr.2_5'UTR|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Missense_Mutation_p.T109I|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Missense_Mutation_p.T33I	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	143	Extracellular (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
PROSC	11212	broad.mit.edu	37	8	37632909	37632909	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37632909C>T	uc003xkh.2	+	6	584	c.507C>T	c.(505-507)AAC>AAT	p.N169N		NM_007198	NP_009129	O94903	PROSC_HUMAN	proline synthetase co-transcribed homolog	169							pyridoxal phosphate binding			central_nervous_system(1)	1		Lung NSC(58;0.174)	BRCA - Breast invasive adenocarcinoma(5;6.14e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)		L-Proline(DB00172)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38912036	38912036	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38912036T>C	uc003xmr.2	+	13	1417	c.1339T>C	c.(1339-1341)TGT>CGT	p.C447R	ADAM9_uc011lcf.1_RNA|ADAM9_uc011lcg.1_RNA|ADAM9_uc010lwr.2_RNA|ADAM9_uc003xms.2_5'Flank	NM_003816	NP_003807	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9 isoform 1	447	Extracellular (Potential).|Disintegrin.				activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39872860	39872860	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39872860C>T	uc010lwy.1	+	11	1244	c.1002C>T	c.(1000-1002)ATC>ATT	p.I334I	IDO2_uc003xno.1_RNA|IDO2_uc010lwz.1_Silent_p.I75I|IDO2_uc003xnp.1_Silent_p.I75I	NM_194294	NP_919270	Q6ZQW0	I23O2_HUMAN	indoleamine-pyrrole 2,3 dioxygenase-like 1	321					tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2																		---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41798536	41798536	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41798536G>T	uc010lxb.2	-	16	3407	c.2863C>A	c.(2863-2865)CCT>ACT	p.P955T	MYST3_uc010lxc.2_Missense_Mutation_p.P955T|MYST3_uc003xon.3_Missense_Mutation_p.P955T	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	955					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
POTEA	340441	broad.mit.edu	37	8	43173622	43173622	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43173622T>C	uc003xpz.1	+	9	1087	c.1044T>C	c.(1042-1044)CAT>CAC	p.H348H	POTEA_uc003xqa.1_Silent_p.H302H	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	348										ovary(1)	1																		---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48809839	48809839	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48809839G>A	uc003xqi.2	-	30	3537	c.3480C>T	c.(3478-3480)TCC>TCT	p.S1160S	PRKDC_uc003xqj.2_Silent_p.S1160S|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	1160					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)											NHEJ					---	---	---	---
MCM4	4173	broad.mit.edu	37	8	48888298	48888298	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48888298C>T	uc003xqk.1	+	16	2484	c.2389C>T	c.(2389-2391)CGG>TGG	p.R797W	MCM4_uc003xql.1_Missense_Mutation_p.R797W|MCM4_uc011ldi.1_Missense_Mutation_p.R784W	NM_182746	NP_877423	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	797					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(2)|skin(2)	4		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53055565	53055565	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53055565T>A	uc003xqz.2	-	12	2249	c.2093A>T	c.(2092-2094)AAG>ATG	p.K698M	ST18_uc011ldq.1_Missense_Mutation_p.K345M|ST18_uc011ldr.1_Missense_Mutation_p.K663M|ST18_uc011lds.1_Missense_Mutation_p.K603M|ST18_uc003xra.2_Missense_Mutation_p.K698M	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	698						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
NPBWR1	2831	broad.mit.edu	37	8	53853346	53853346	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53853346C>A	uc011ldu.1	+	1	879	c.879C>A	c.(877-879)ACC>ACA	p.T293T		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	293	Helical; Name=7; (Potential).				synaptic transmission	plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)																---	---	---	---
FAM110B	90362	broad.mit.edu	37	8	59059757	59059757	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59059757A>G	uc003xtj.1	+	5	1848	c.968A>G	c.(967-969)GAC>GGC	p.D323G		NM_147189	NP_671722	Q8TC76	F110B_HUMAN	hypothetical protein LOC90362	323						microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)																---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68189648	68189648	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68189648T>C	uc003xxo.1	-	8	1462	c.1072A>G	c.(1072-1074)ATT>GTT	p.I358V		NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	358					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70744031	70744031	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70744031A>G	uc003xyl.2	-	2	1585	c.878T>C	c.(877-879)GTC>GCC	p.V293A	SLCO5A1_uc010lzb.2_Missense_Mutation_p.V293A|SLCO5A1_uc011lfa.1_RNA|SLCO5A1_uc003xyk.2_Missense_Mutation_p.V293A|SLCO5A1_uc010lzc.2_Missense_Mutation_p.V293A	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	293	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77617605	77617605	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77617605T>C	uc003yav.2	+	2	1669	c.1282T>C	c.(1282-1284)TCA>CCA	p.S428P	ZFHX4_uc003yat.1_Missense_Mutation_p.S428P|ZFHX4_uc003yau.1_Missense_Mutation_p.S428P|ZFHX4_uc003yaw.1_Missense_Mutation_p.S428P	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	428						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
FAM164A	51101	broad.mit.edu	37	8	79590866	79590866	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79590866G>T	uc003ybd.2	+	3	264	c.162G>T	c.(160-162)CAG>CAT	p.Q54H		NM_016010	NP_057094	Q96GY0	F164A_HUMAN	hypothetical protein LOC51101	54										ovary(1)	1																		---	---	---	---
PAG1	55824	broad.mit.edu	37	8	81897170	81897170	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81897170A>G	uc003ybz.2	-	7	1428	c.717T>C	c.(715-717)AGT>AGC	p.S239S		NM_018440	NP_060910	Q9NWQ8	PAG1_HUMAN	phosphoprotein associated with glycosphingolipid	239	Cytoplasmic (Potential).				epidermal growth factor receptor signaling pathway|intracellular signal transduction|T cell receptor signaling pathway	integral to membrane|intracellular|membrane raft|plasma membrane	SH2 domain binding|SH3/SH2 adaptor activity				0	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)															---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95680236	95680236	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95680236C>T	uc003ygq.3	+	10	1174	c.991C>T	c.(991-993)CGG>TGG	p.R331W	ESRP1_uc003ygr.3_Missense_Mutation_p.R331W|ESRP1_uc003ygs.3_Missense_Mutation_p.R331W|ESRP1_uc003ygt.3_Missense_Mutation_p.R331W|ESRP1_uc003ygu.3_Missense_Mutation_p.R331W|ESRP1_uc003ygv.2_Missense_Mutation_p.R171W|ESRP1_uc003ygw.2_Missense_Mutation_p.R171W	NM_017697	NP_060167	Q6NXG1	ESRP1_HUMAN	RNA binding motif protein 35A isoform 1	331	RRM 2.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus|plasma membrane	mRNA binding|nucleotide binding		ESRP1/RAF1(4)	prostate(4)	4																		---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98827611	98827611	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98827611T>C	uc003yia.2	+	3	696	c.540T>C	c.(538-540)GCT>GCC	p.A180A	LAPTM4B_uc010mbg.2_Intron	NM_018407	NP_060877	Q86VI4	LAP4B_HUMAN	lysosomal associated transmembrane protein 4	233	Helical; (Potential).				transport	endomembrane system|integral to membrane	protein binding			skin(1)	1	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98943434	98943434	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98943434G>A	uc003yic.2	+	3	627	c.396G>A	c.(394-396)ACG>ACA	p.T132T	MATN2_uc003yib.1_Silent_p.T132T|MATN2_uc010mbh.1_Silent_p.T132T|MATN2_uc003yid.2_Silent_p.T132T|MATN2_uc003yie.1_Silent_p.T132T|MATN2_uc010mbi.1_Silent_p.T6T	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	132	VWFA 1.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100844800	100844800	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100844800A>G	uc003yiv.2	+	52	9720	c.9609A>G	c.(9607-9609)CCA>CCG	p.P3203P	VPS13B_uc003yiw.2_Silent_p.P3178P	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3203					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
SPAG1	6674	broad.mit.edu	37	8	101243518	101243518	+	Splice_Site	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101243518C>T	uc003yjh.1	+	15	2074	c.1988_splice	c.e15+2	p.R663_splice	SPAG1_uc003yji.1_Splice_Site_p.R663_splice	NM_172218	NP_757367			sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103297968	103297968	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103297968G>A	uc003ykr.1	-	39	5290	c.5257C>T	c.(5257-5259)CGC>TGC	p.R1753C	UBR5_uc003yks.1_Missense_Mutation_p.R1753C	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1753					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
NUDCD1	84955	broad.mit.edu	37	8	110255326	110255326	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110255326G>T	uc003ynb.3	-	10	1775	c.1664C>A	c.(1663-1665)CCT>CAT	p.P555H	NUDCD1_uc003yna.2_Missense_Mutation_p.P526H|NUDCD1_uc010mcl.2_Missense_Mutation_p.P468H	NM_032869	NP_116258	Q96RS6	NUDC1_HUMAN	NudC domain containing 1 isoform 1	555										ovary(1)|breast(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)															---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113326150	113326150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113326150G>A	uc003ynu.2	-	49	7840	c.7681C>T	c.(7681-7683)CGG>TGG	p.R2561W	CSMD3_uc003yns.2_Missense_Mutation_p.R1763W|CSMD3_uc003ynt.2_Missense_Mutation_p.R2521W|CSMD3_uc011lhx.1_Missense_Mutation_p.R2457W|CSMD3_uc003ynw.1_Missense_Mutation_p.R272W	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2561	CUB 14.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113988066	113988066	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113988066C>T	uc003ynu.2	-	7	1501	c.1342G>A	c.(1342-1344)GTG>ATG	p.V448M	CSMD3_uc003ynt.2_Missense_Mutation_p.V408M|CSMD3_uc011lhx.1_Intron	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	448	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114448937	114448937	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114448937G>A	uc003ynu.2	-	1	306	c.147C>T	c.(145-147)CTC>CTT	p.L49L	CSMD3_uc011lhx.1_Silent_p.L49L|CSMD3_uc010mcx.1_Silent_p.L49L|CSMD3_uc003ynx.3_Silent_p.L49L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	49	Helical; (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118819559	118819559	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118819559C>T	uc003yok.1	-	9	2553	c.1780G>A	c.(1780-1782)GCG>ACG	p.A594T		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	594	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120596014	120596014	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120596014T>C	uc003yot.1	-	17	1572	c.1486A>G	c.(1486-1488)AAG>GAG	p.K496E	ENPP2_uc011lic.1_Missense_Mutation_p.K13E|ENPP2_uc003yor.1_Missense_Mutation_p.K135E|ENPP2_uc003yos.1_Missense_Mutation_p.K548E|ENPP2_uc010mdd.1_Missense_Mutation_p.K496E	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	496					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DSCC1	79075	broad.mit.edu	37	8	120854138	120854138	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120854138G>A	uc003yov.2	-	7	955	c.820C>T	c.(820-822)CGA>TGA	p.R274*		NM_024094	NP_076999	Q9BVC3	DCC1_HUMAN	defective in sister chromatid cohesion 1	274					DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121282285	121282285	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121282285G>A	uc003yox.2	+	26	3350	c.3085G>A	c.(3085-3087)GCC>ACC	p.A1029T	COL14A1_uc003yoz.2_5'UTR	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	1029					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)															---	---	---	---
ZHX1	11244	broad.mit.edu	37	8	124267220	124267220	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124267220A>G	uc003yqe.2	-	3	1397	c.967T>C	c.(967-969)TAT>CAT	p.Y323H	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Missense_Mutation_p.Y323H|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Missense_Mutation_p.Y323H	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	323	Required for dimerization.|Homeobox 1.|Required for interaction with NFYA.				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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124383982	124383982	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124383982C>T	uc003yqh.3	-	4	572	c.464G>A	c.(463-465)CGT>CAT	p.R155H	ATAD2_uc011lii.1_5'UTR|ATAD2_uc003yqi.3_RNA|ATAD2_uc003yqj.2_Missense_Mutation_p.R155H	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	155					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
NDUFB9	4715	broad.mit.edu	37	8	125559294	125559294	+	Silent	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125559294T>G	uc003yrg.3	+	3	433	c.348T>G	c.(346-348)CCT>CCG	p.P116P	NDUFB9_uc011lim.1_Silent_p.P116P	NM_005005	NP_004996	Q9Y6M9	NDUB9_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta	116					mitochondrial electron transport, NADH to ubiquinone|sensory perception of sound|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)|skin(1)	2	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)		NADH(DB00157)													---	---	---	---
KIAA0196	9897	broad.mit.edu	37	8	126062902	126062902	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126062902A>G	uc003yrt.2	-	18	2432	c.2103T>C	c.(2101-2103)GAT>GAC	p.D701D	KIAA0196_uc011lir.1_Silent_p.D553D|KIAA0196_uc003yru.1_Silent_p.D275D	NM_014846	NP_055661	Q12768	STRUM_HUMAN	strumpellin	701					cell death	WASH complex				ovary(2)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)															---	---	---	---
FAM49B	51571	broad.mit.edu	37	8	130863080	130863080	+	Splice_Site	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130863080C>T	uc003yss.2	-	12	1262	c.713_splice	c.e12+1	p.P238_splice	FAM49B_uc003yst.2_Splice_Site_p.P238_splice|FAM49B_uc003ysu.2_Splice_Site_p.P238_splice|FAM49B_uc003ysv.2_Splice_Site_p.P92_splice|FAM49B_uc003ysw.2_Splice_Site_p.P238_splice|FAM49B_uc003ysx.2_Splice_Site_p.P238_splice|FAM49B_uc003ysy.1_Splice_Site_p.P238_splice	NM_016623	NP_057707			hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)															---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133807030	133807030	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133807030T>C	uc003ytt.2	+	4	632	c.307T>C	c.(307-309)TAC>CAC	p.Y103H	PHF20L1_uc003ytr.2_Missense_Mutation_p.Y103H|PHF20L1_uc010mdv.2_Missense_Mutation_p.Y103H|PHF20L1_uc003yts.2_Missense_Mutation_p.Y103H|PHF20L1_uc011lja.1_Missense_Mutation_p.Y103H|PHF20L1_uc003ytu.1_RNA|PHF20L1_uc003ytq.2_Missense_Mutation_p.Y103H	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	103	Tudor 2.						nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133913652	133913652	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133913652C>A	uc003ytw.2	+	16	3529	c.3488C>A	c.(3487-3489)CCA>CAA	p.P1163Q	TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1163	Thyroglobulin type-1 10.				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)														---	---	---	---
TG	7038	broad.mit.edu	37	8	133913747	133913747	+	Missense_Mutation	SNP	G	A	A	rs138469414	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133913747G>A	uc003ytw.2	+	16	3624	c.3583G>A	c.(3583-3585)GGA>AGA	p.G1195R	TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1195	Thyroglobulin type-1 10.				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)														---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134488056	134488056	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134488056G>A	uc003yuk.2	-	5	1041	c.212C>T	c.(211-213)TCG>TTG	p.S71L	ST3GAL1_uc003yum.2_Missense_Mutation_p.S71L	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	71	Lumenal (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)															---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135614560	135614560	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135614560C>T	uc003yup.2	-	6	1577	c.1402G>A	c.(1402-1404)GTC>ATC	p.V468I	ZFAT_uc003yun.2_Missense_Mutation_p.V456I|ZFAT_uc003yuo.2_Missense_Mutation_p.V456I|ZFAT_uc010meh.2_Missense_Mutation_p.V456I|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Missense_Mutation_p.V456I|ZFAT_uc010mej.2_Missense_Mutation_p.V406I|ZFAT_uc003yur.2_Missense_Mutation_p.V456I	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	468	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140715158	140715158	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140715158G>A	uc003yvf.1	-	1	142	c.78C>T	c.(76-78)TTC>TTT	p.F26F	KCNK9_uc003yvg.1_Silent_p.F26F	NM_016601	NP_057685	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	26	Helical; (Potential).					integral to membrane|membrane fraction	potassium channel activity|voltage-gated ion channel activity			ovary(2)|lung(1)	3	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)															---	---	---	---
PTP4A3	11156	broad.mit.edu	37	8	142441050	142441050	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142441050G>A	uc003ywg.1	+	5	762	c.428G>A	c.(427-429)AGC>AAC	p.S143N	PTP4A3_uc003ywh.1_Missense_Mutation_p.S118N|PTP4A3_uc010met.1_Missense_Mutation_p.A57T	NM_032611	NP_116000	O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	143	Tyrosine-protein phosphatase.					early endosome|plasma membrane	identical protein binding|prenylated protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)															---	---	---	---
ZC3H3	23144	broad.mit.edu	37	8	144547949	144547949	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144547949C>T	uc003yyd.2	-	9	2274	c.2245G>A	c.(2245-2247)GTG>ATG	p.V749M		NM_015117	NP_055932	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	749	C3H1-type 3.				mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)															---	---	---	---
ZNF707	286075	broad.mit.edu	37	8	144776046	144776046	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144776046G>A	uc003yze.3	+	7	777	c.462G>A	c.(460-462)ACG>ACA	p.T154T	ZNF707_uc010mfh.2_Silent_p.T154T|ZNF707_uc010mfi.2_Silent_p.T154T|ZNF707_uc003yzf.3_Silent_p.T154T|ZNF707_uc003yzh.3_Silent_p.T81T|ZNF707_uc011lkq.1_RNA	NM_173831	NP_776192	Q96C28	ZN707_HUMAN	zinc finger protein 707	154					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)	1	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;5.6e-41)|Epithelial(56;1.02e-39)|all cancers(56;9.65e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
MAPK15	225689	broad.mit.edu	37	8	144803569	144803569	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144803569C>A	uc003yzj.2	+	11	1233	c.1192C>A	c.(1192-1194)CCT>ACT	p.P398T		NM_139021	NP_620590	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	398					protein autophosphorylation	extracellular region	ATP binding|MAP kinase activity|SH3 domain binding			lung(2)	2	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145101719	145101719	+	Silent	SNP	C	T	T	rs149191984	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145101719C>T	uc011lkw.1	+	5	1740	c.1638C>T	c.(1636-1638)GGC>GGT	p.G546G	SPATC1_uc011lkx.1_3'UTR	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	546										ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
FBXL6	26233	broad.mit.edu	37	8	145580725	145580725	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145580725A>G	uc003zcb.2	-	4	721	c.696T>C	c.(694-696)GGT>GGC	p.G232G	C8ORFK29_uc011llb.1_5'Flank|C8ORFK29_uc010mfw.2_5'Flank|C8ORFK29_uc003zby.3_5'Flank|FBXL6_uc003zbz.2_5'UTR|FBXL6_uc003zca.2_Silent_p.G226G|FBXL6_uc010mfx.2_5'UTR|GPR172A_uc003zcc.1_5'Flank|GPR172A_uc003zcd.1_5'Flank|GPR172A_uc003zce.1_5'Flank|GPR172A_uc010mfy.1_5'Flank|GPR172A_uc003zcf.1_5'Flank|GPR172A_uc011llc.1_5'Flank	NM_012162	NP_036294	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6 isoform	232	LRR 3.				proteolysis		ubiquitin-protein ligase activity			ovary(1)|lung(1)	2	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;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
GPR172A	79581	broad.mit.edu	37	8	145583729	145583729	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145583729G>A	uc003zcc.1	+	3	734	c.577G>A	c.(577-579)GCC>ACC	p.A193T	FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_5'Flank|FBXL6_uc003zcb.2_5'Flank|FBXL6_uc010mfx.2_5'Flank|GPR172A_uc003zcd.1_Missense_Mutation_p.A193T|GPR172A_uc003zce.1_Missense_Mutation_p.A193T|GPR172A_uc010mfy.1_Missense_Mutation_p.A193T|GPR172A_uc003zcf.1_Missense_Mutation_p.A193T|GPR172A_uc011llc.1_Missense_Mutation_p.A105T	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	193						integral to plasma membrane	receptor activity|riboflavin transporter activity				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;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
SLC39A4	55630	broad.mit.edu	37	8	145638280	145638280	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145638280G>A	uc003zcq.2	-	11	1778	c.1678C>T	c.(1678-1680)CTG>TTG	p.L560L	SLC39A4_uc003zcm.1_Silent_p.L62L|SLC39A4_uc003zcn.2_Silent_p.L62L|SLC39A4_uc003zco.2_Silent_p.L284L|SLC39A4_uc003zcp.2_Silent_p.L535L	NM_130849	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter),	560	Helical; Name=4; (Potential).					cytoplasmic membrane-bounded vesicle|integral to membrane|recycling endosome membrane	zinc ion transmembrane transporter activity				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;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)															---	---	---	---
CYHR1	50626	broad.mit.edu	37	8	145689776	145689776	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145689776C>T	uc003zcv.2	-						CYHR1_uc003zcw.2_Missense_Mutation_p.G105S|CYHR1_uc003zcx.2_Missense_Mutation_p.G105S|CYHR1_uc003zcy.2_Missense_Mutation_p.G105S|KIFC2_uc003zcz.2_5'Flank	NM_138496	NP_612505			cysteine/histidine-rich 1 isoform 1							perinuclear region of cytoplasm	zinc ion binding				0	all_cancers(97;4.61e-11)|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)															---	---	---	---
RECQL4	9401	broad.mit.edu	37	8	145741187	145741187	+	Missense_Mutation	SNP	C	T	T	rs117670586	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145741187C>T	uc003zdj.2	-	6	1251	c.1219G>A	c.(1219-1221)GAG>AAG	p.E407K	LRRC14_uc003zdk.1_5'Flank|LRRC14_uc003zdl.1_5'Flank	NM_004260	NP_004251	O94761	RECQ4_HUMAN	RecQ protein-like 4	407					DNA duplex unwinding|DNA recombination|DNA repair	cytoplasm|nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|DNA strand annealing activity|zinc ion binding			breast(2)|lung(1)|skin(1)	4	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)					N|F|S			osteosarcoma|skin basal and sqamous cell		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	RAPADILINO_syndrome|Rothmund-Thomson_syndrome|Baller-Gerold_syndrome				---	---	---	---
KANK1	23189	broad.mit.edu	37	9	732477	732477	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:732477G>A	uc003zgl.1	+	10	3754	c.3105G>A	c.(3103-3105)GAG>GAA	p.E1035E	KANK1_uc003zgm.2_3'UTR|KANK1_uc003zgn.1_Silent_p.E1035E|KANK1_uc003zgs.1_Silent_p.E877E|KANK1_uc010mgx.1_5'UTR|KANK1_uc010mgy.1_5'UTR|KANK1_uc003zgt.1_5'Flank	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	1035					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)														---	---	---	---
DMRT3	58524	broad.mit.edu	37	9	990546	990546	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:990546C>A	uc003zgw.1	+	2	998	c.960C>A	c.(958-960)TCC>TCA	p.S320S		NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor	320					cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)														---	---	---	---
KCNV2	169522	broad.mit.edu	37	9	2718833	2718833	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2718833C>T	uc003zho.1	+	1	1308	c.1094C>T	c.(1093-1095)ACG>ATG	p.T365M		NM_133497	NP_598004	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	365	Extracellular (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(50;0.0257)														---	---	---	---
UHRF2	115426	broad.mit.edu	37	9	6475403	6475403	+	Silent	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6475403A>T	uc003zjy.2	+	5	1216	c.876A>T	c.(874-876)GGA>GGT	p.G292G	UHRF2_uc003zjz.2_RNA|UHRF2_uc003zka.1_Silent_p.G69G	NM_152896	NP_690856	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains	292					cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)														---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7015920	7015920	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7015920G>A	uc003zkh.2	+	15	2830	c.2250G>A	c.(2248-2250)GCG>GCA	p.A750A	KDM4C_uc010mhu.2_Silent_p.A772A|KDM4C_uc011lmi.1_Silent_p.A750A|KDM4C_uc011lmj.1_RNA|KDM4C_uc003zkg.2_Silent_p.A750A|KDM4C_uc011lmk.1_Silent_p.A495A|KDM4C_uc011lml.1_Silent_p.A437A	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	750					positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
TYRP1	7306	broad.mit.edu	37	9	12694013	12694013	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12694013T>A	uc003zkv.3	+	2	195	c.17T>A	c.(16-18)CTC>CAC	p.L6H		NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor	6					melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)										Oculocutaneous_Albinism				---	---	---	---
PSIP1	11168	broad.mit.edu	37	9	15474206	15474206	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15474206T>C	uc003zlv.3	-	9	989	c.659A>G	c.(658-660)AAG>AGG	p.K220R	PSIP1_uc003zlw.3_Missense_Mutation_p.K220R|PSIP1_uc003zlz.3_Missense_Mutation_p.K220R|PSIP1_uc003zma.3_Missense_Mutation_p.K211R|PSIP1_uc003zly.2_Missense_Mutation_p.K220R	NM_033222	NP_150091	O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1 isoform 2	220					initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19360238	19360238	+	Intron	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19360238T>A	uc003znq.2	+						DENND4C_uc011lnc.1_Intron|DENND4C_uc011lnd.1_Intron|DENND4C_uc003znr.2_Intron|DENND4C_uc003zns.2_Intron	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
IFNA10	3446	broad.mit.edu	37	9	21206750	21206750	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21206750A>G	uc003zoq.1	-	1	393	c.347T>C	c.(346-348)CTG>CCG	p.L116P	IFNA14_uc003zoo.1_Intron	NM_002171	NP_002162	P01566	IFN10_HUMAN	interferon, alpha 10 precursor	116					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)														---	---	---	---
OR13J1	392309	broad.mit.edu	37	9	35869831	35869831	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35869831C>T	uc011lph.1	-	1	568	c.568G>A	c.(568-570)GGC>AGC	p.G190S		NM_001004487	NP_001004487	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J,	190	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71827497	71827497	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71827497T>C	uc004ahe.2	+	2	294	c.94T>C	c.(94-96)TAC>CAC	p.Y32H	TJP2_uc011lrs.1_Missense_Mutation_p.Y9H|TJP2_uc004ahb.1_Missense_Mutation_p.Y9H|TJP2_uc011lrt.1_Missense_Mutation_p.Y9H|TJP2_uc004ahd.2_Missense_Mutation_p.Y32H|TJP2_uc004ahf.2_Missense_Mutation_p.Y32H|TJP2_uc011lru.1_Missense_Mutation_p.Y36H|TJP2_uc011lrv.1_Missense_Mutation_p.Y54H	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	32					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72965075	72965075	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72965075A>G	uc004ahr.2	+	23	3052	c.2935A>G	c.(2935-2937)AGT>GGT	p.S979G	SMC5_uc011lry.1_Missense_Mutation_p.S124G	NM_015110	NP_055925	Q8IY18	SMC5_HUMAN	SMC5 protein	979					DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84607323	84607323	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607323C>T	uc004amn.2	+	4	1985	c.1938C>T	c.(1936-1938)TCC>TCT	p.S646S		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	646						integral to membrane					0																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88940282	88940282	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88940282T>C	uc004aoq.2	-	12	1971	c.1756A>G	c.(1756-1758)AAG>GAG	p.K586E	ZCCHC6_uc011ltf.1_RNA|ZCCHC6_uc004aor.2_RNA|ZCCHC6_uc004aos.2_RNA|ZCCHC6_uc004aot.2_Missense_Mutation_p.K463E|ZCCHC6_uc004aou.2_Missense_Mutation_p.K586E	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	586	PAP-associated 1.				RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SPTLC1	10558	broad.mit.edu	37	9	94809515	94809515	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94809515C>T	uc004arl.1	-	11	1058	c.1020G>A	c.(1018-1020)TCG>TCA	p.S340S	SPTLC1_uc011ltv.1_Silent_p.S340S	NM_006415	NP_006406	O15269	SPTC1_HUMAN	serine palmitoyltransferase subunit 1 isoform a	340	Cytoplasmic (Potential).					integral to membrane|SPOTS complex	protein binding|pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			ovary(1)|breast(1)	2					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101340346	101340346	+	Silent	SNP	G	A	A	rs139594158	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101340346G>A	uc004ays.2	-	2	486	c.330C>T	c.(328-330)AAC>AAT	p.N110N		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	110	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112166777	112166777	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112166777G>A	uc004bed.2	-	19	2016	c.1904C>T	c.(1903-1905)GCA>GTA	p.A635V	PTPN3_uc004beb.2_Missense_Mutation_p.A504V|PTPN3_uc004bec.2_Missense_Mutation_p.A459V|PTPN3_uc010mtu.2_RNA|PTPN3_uc011lwg.1_Missense_Mutation_p.A590V|PTPN3_uc011lwh.1_Missense_Mutation_p.A481V|PTPN3_uc011lwd.1_Missense_Mutation_p.A103V|PTPN3_uc011lwe.1_Missense_Mutation_p.A348V|PTPN3_uc011lwf.1_Missense_Mutation_p.A303V	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type	635					negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113261516	113261516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113261516G>A	uc010mtz.2	-	7	1823	c.1486C>T	c.(1486-1488)CGC>TGC	p.R496C	SVEP1_uc010mua.1_Missense_Mutation_p.R496C|SVEP1_uc004beu.2_Missense_Mutation_p.R496C	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	496	Sushi 3.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
DNAJC25-GNG10	552891	broad.mit.edu	37	9	114429191	114429191	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114429191C>T	uc004bfn.2	+	2	455	c.433C>T	c.(433-435)CGG>TGG	p.R145W	GNG10_uc011lws.1_RNA|GNG10_uc004bfp.2_Missense_Mutation_p.R60W	NM_004125	NP_004116	Q9H1X3	DJC25_HUMAN	DNAJC25-GNG10 protein	Error:Variant_position_missing_in_Q9H1X3_after_alignment					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
WDR31	114987	broad.mit.edu	37	9	116082681	116082681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116082681T>C	uc004bhe.2	-	9	988	c.736A>G	c.(736-738)ATC>GTC	p.I246V	WDR31_uc004bhc.2_Missense_Mutation_p.I245V|WDR31_uc004bhd.2_Missense_Mutation_p.I121V|WDR31_uc004bhf.2_RNA	NM_001012361	NP_001012361	Q8NA23	WDR31_HUMAN	WD repeat domain 31 isoform 1	246											0																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	118164388	118164388	+	Intron	SNP	G	A	A	rs72359055		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118164388G>A	uc004bjk.1	+						DEC1_uc004bjl.1_Intron	NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124089468	124089468	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124089468C>T	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124532969	124532969	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124532969C>T	uc004bln.2	+	11	2029	c.1960C>T	c.(1960-1962)CTG>TTG	p.L654L	DAB2IP_uc004blo.2_Silent_p.L558L|DAB2IP_uc004blp.2_Silent_p.L109L	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	682					activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
OR1L3	26735	broad.mit.edu	37	9	125437936	125437936	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125437936T>C	uc011lzb.1	+	1	528	c.528T>C	c.(526-528)CAT>CAC	p.H176H		NM_001005234	NP_001005234	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L,	176	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
PDCL	5082	broad.mit.edu	37	9	125582383	125582383	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125582383C>T	uc004bmz.1	-	4	983	c.887G>A	c.(886-888)AGC>AAC	p.S296N	uc004bmy.2_5'Flank|PDCL_uc004bna.2_3'UTR	NM_005388	NP_005379	Q13371	PHLP_HUMAN	phosducin-like	296					signal transduction|visual perception						0																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125760928	125760928	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125760928G>T	uc011lzh.1	+	10	1391	c.1257G>T	c.(1255-1257)CAG>CAT	p.Q419H	RABGAP1_uc004bnl.3_RNA	NM_012197	NP_036329	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	419					cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130294048	130294048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130294048C>T	uc004brh.2	-	2	267	c.65G>A	c.(64-66)GGG>GAG	p.G22E	FAM129B_uc004bri.2_Missense_Mutation_p.G9E|FAM129B_uc004brj.3_Missense_Mutation_p.G22E	NM_022833	NP_073744	Q96TA1	NIBL1_HUMAN	hypothetical protein LOC64855 isoform 1	22							protein binding				0																		---	---	---	---
ABL1	25	broad.mit.edu	37	9	133730285	133730285	+	Silent	SNP	G	A	A	rs141072111		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133730285G>A	uc004bzw.2	+	3	354	c.351G>A	c.(349-351)ACG>ACA	p.T117T	ABL1_uc004bzv.2_Silent_p.T136T	NM_005157	NP_005148	P00519	ABL1_HUMAN	c-abl oncogene 1, receptor tyrosine kinase	117	SH3.				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								---	---	---	---
DDX31	64794	broad.mit.edu	37	9	135537951	135537951	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135537951G>A	uc004cbq.1	-	2	674	c.522C>T	c.(520-522)AAC>AAT	p.N174N	DDX31_uc010mzu.1_Silent_p.N174N|DDX31_uc004cbr.1_Silent_p.N174N|DDX31_uc004cbs.1_Silent_p.N174N	NM_022779	NP_073616	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	174						nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)														---	---	---	---
REXO4	57109	broad.mit.edu	37	9	136279942	136279942	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136279942C>T	uc004cdm.2	-	2	615	c.415G>A	c.(415-417)GAC>AAC	p.D139N	ADAMTS13_uc004cdp.3_Intron|REXO4_uc011mde.1_Missense_Mutation_p.D2N|REXO4_uc011mdf.1_Missense_Mutation_p.D2N|REXO4_uc004cdn.2_Intron|REXO4_uc004cdo.2_Nonsense_Mutation_p.W79*	NM_020385	NP_065118	Q9GZR2	REXO4_HUMAN	XPMC2 prevents mitotic catastrophe 2 homolog	139						nucleolus	exonuclease activity|nucleic acid binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136310835	136310835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136310835G>A	uc004cdv.3	+	21	3070	c.2626G>A	c.(2626-2628)GCA>ACA	p.A876T	ADAMTS13_uc004cdp.3_Missense_Mutation_p.A103T|ADAMTS13_uc004cdt.1_Missense_Mutation_p.A876T|ADAMTS13_uc004cdu.1_Missense_Mutation_p.A845T|ADAMTS13_uc004cdw.3_Missense_Mutation_p.A876T|ADAMTS13_uc004cdx.3_Missense_Mutation_p.A845T|ADAMTS13_uc004cdy.1_RNA|ADAMTS13_uc004cdz.3_Missense_Mutation_p.A546T|ADAMTS13_uc004cds.1_Missense_Mutation_p.A401T|ADAMTS13_uc004cdr.1_RNA	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	876					cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
TMEM8C	389827	broad.mit.edu	37	9	136384042	136384042	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136384042T>C	uc011mdk.1	-	3	353	c.353A>G	c.(352-354)TAC>TGC	p.Y118C		NM_001080483	NP_001073952	A6NI61	TMM8C_HUMAN	transmembrane protein 8C	118	Helical; (Potential).					integral to membrane					0																		---	---	---	---
SARDH	1757	broad.mit.edu	37	9	136584048	136584048	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136584048C>A	uc004cep.3	-						SARDH_uc004ceo.2_Intron|SARDH_uc011mdn.1_Intron|SARDH_uc011mdo.1_Intron	NM_001134707	NP_001128179			sarcosine dehydrogenase precursor						glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)														---	---	---	---
AGPAT2	10555	broad.mit.edu	37	9	139571494	139571494	+	Silent	SNP	G	A	A	rs149658120		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139571494G>A	uc004cii.1	-	3	513	c.411C>T	c.(409-411)GGC>GGT	p.G137G	AGPAT2_uc004cij.1_Silent_p.G137G	NM_006412	NP_006403	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	137	Helical; (Potential).				phosphatidic acid biosynthetic process|positive regulation of cytokine production|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)														---	---	---	---
AGPAT2	10555	broad.mit.edu	37	9	139571597	139571597	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139571597C>T	uc004cii.1	-						AGPAT2_uc004cij.1_Intron	NM_006412	NP_006403			1-acylglycerol-3-phosphate O-acyltransferase 2						phosphatidic acid biosynthetic process|positive regulation of cytokine production|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)														---	---	---	---
LCN8	138307	broad.mit.edu	37	9	139651632	139651632	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139651632C>T	uc004cjb.1	-						LCN8_uc004cja.2_5'Flank|LCN8_uc004cjc.1_Intron	NM_178469	NP_848564			lipocalin 8						transport	extracellular region	binding			pancreas(1)	1	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139904360	139904360	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139904360C>T	uc011mem.1	-						ABCA2_uc011mel.1_Intron|ABCA2_uc004ckl.1_Intron|ABCA2_uc004ckm.1_Intron	NM_001606	NP_001597			ATP-binding cassette, sub-family A, member 2						cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
TMEM203	94107	broad.mit.edu	37	9	140099729	140099729	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140099729C>A	uc004clv.2	-	1	362	c.138G>T	c.(136-138)TGG>TGT	p.W46C	NDOR1_uc004clx.2_5'Flank|NDOR1_uc004clw.2_5'Flank|NDOR1_uc011mes.1_5'Flank|NDOR1_uc004cly.2_5'Flank	NM_053045	NP_444273	Q969S6	TM203_HUMAN	transmembrane protein 203	46						integral to membrane					0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)														---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140852062	140852062	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140852062C>T	uc004cog.2	+	10	1401	c.1256C>T	c.(1255-1257)GCG>GTG	p.A419V	CACNA1B_uc011mfd.1_5'UTR	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	419	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3180476	3180476	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3180476C>A	uc010qah.1	-	23	2709	c.2677G>T	c.(2677-2679)GAG>TAG	p.E893*	PITRM1_uc001igr.1_3'UTR|PITRM1_uc001igs.1_Nonsense_Mutation_p.E96*|PITRM1_uc001igt.1_Nonsense_Mutation_p.E991*|PITRM1_uc009xhv.1_Nonsense_Mutation_p.E557*|PITRM1_uc001igu.1_Nonsense_Mutation_p.E917*|PITRM1_uc010qai.1_Nonsense_Mutation_p.E962*			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;	893					proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
NET1	10276	broad.mit.edu	37	10	5498109	5498109	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5498109C>T	uc001iia.2	+	11	1395	c.1257C>T	c.(1255-1257)AAC>AAT	p.N419N	NET1_uc010qar.1_Silent_p.N238N|NET1_uc001iib.2_Silent_p.N365N|NET1_uc010qas.1_Silent_p.N238N	NM_001047160	NP_001040625	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming gene 1 isoform	419	PH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8006409	8006409	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8006409T>C	uc010qbd.1	+	3	936	c.936T>C	c.(934-936)CCT>CCC	p.P312P		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	312					maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15290697	15290697	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15290697G>A	uc001iob.2	-	5	702	c.695C>T	c.(694-696)ACG>ATG	p.T232M		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	232	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16932369	16932369	+	Splice_Site	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16932369C>T	uc001ioo.2	-	55	8807	c.8755_splice	c.e55+1	p.R2919_splice	CUBN_uc009xjq.1_Splice_Site|CUBN_uc009xjr.1_Splice_Site_p.R275_splice	NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
STAM	8027	broad.mit.edu	37	10	17747022	17747022	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17747022A>G	uc001ipj.1	+	11	1270	c.1054A>G	c.(1054-1056)AGA>GGA	p.R352G	STAM_uc009xjw.1_Intron	NM_003473	NP_003464	Q92783	STAM1_HUMAN	signal transducing adaptor molecule 1	352					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30336525	30336525	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30336525G>A	uc001iux.2	-	1	276	c.217C>T	c.(217-219)CGC>TGC	p.R73C	KIAA1462_uc001iuy.2_Missense_Mutation_p.R73C|KIAA1462_uc001iuz.2_5'UTR|KIAA1462_uc009xle.1_Missense_Mutation_p.R73C	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	73										ovary(4)	4																		---	---	---	---
MAP3K8	1326	broad.mit.edu	37	10	30748255	30748255	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30748255A>G	uc001ivi.1	+	8	1794	c.1098A>G	c.(1096-1098)GAA>GAG	p.E366E	MAP3K8_uc009xlf.1_Silent_p.E366E|MAP3K8_uc001ivj.1_Silent_p.E366E	NM_005204	NP_005195	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase	366	Protein kinase.				cell cycle|T cell costimulation	cytosol	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			breast(3)|central_nervous_system(1)	4		Prostate(175;0.151)																---	---	---	---
ARHGAP12	94134	broad.mit.edu	37	10	32097965	32097965	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32097965A>G	uc001ivz.1	-	18	2490	c.2220T>C	c.(2218-2220)CCT>CCC	p.P740P	ARHGAP12_uc001ivy.1_Silent_p.P686P|ARHGAP12_uc009xls.2_Silent_p.P691P|ARHGAP12_uc001iwb.1_Silent_p.P733P|ARHGAP12_uc001iwc.1_Silent_p.P708P|ARHGAP12_uc009xlq.1_Silent_p.P661P|ARHGAP12_uc001ivw.1_5'Flank|ARHGAP12_uc001ivx.1_Silent_p.P39P	NM_018287	NP_060757	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	740	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34558704	34558704	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34558704A>G	uc010qej.1	-	22	3309	c.3309T>C	c.(3307-3309)TCT>TCC	p.S1103S	PARD3_uc010qek.1_Silent_p.S1100S|PARD3_uc010qel.1_Silent_p.S1066S|PARD3_uc010qem.1_Silent_p.S1087S|PARD3_uc010qen.1_Silent_p.S1057S|PARD3_uc010qeo.1_Silent_p.S1020S|PARD3_uc010qep.1_Silent_p.S1013S|PARD3_uc010qeq.1_Silent_p.S991S	NM_019619	NP_062565	Q8TEW0	PARD3_HUMAN	partitioning-defective protein 3 homolog	1103					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
RASGEF1A	221002	broad.mit.edu	37	10	43696165	43696165	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43696165C>T	uc001jap.1	-	5	712	c.631G>A	c.(631-633)GTG>ATG	p.V211M	RASGEF1A_uc001jao.1_Missense_Mutation_p.V219M	NM_145313	NP_660356	Q8N9B8	RGF1A_HUMAN	RasGEF domain family, member 1A	211					cell migration|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
RASSF4	83937	broad.mit.edu	37	10	45488730	45488730	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45488730C>T	uc001jbo.2	+	11	1053	c.919C>T	c.(919-921)CGT>TGT	p.R307C	RASSF4_uc001jbp.2_Missense_Mutation_p.R338C|RASSF4_uc009xmn.2_Missense_Mutation_p.R237C|RASSF4_uc001jbq.2_Missense_Mutation_p.R204C|RASSF4_uc001jbt.2_Missense_Mutation_p.R264C	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	307	SARAH.				cell cycle|signal transduction		protein binding			large_intestine(1)	1																		---	---	---	---
FAM21C	253725	broad.mit.edu	37	10	46248126	46248126	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46248126A>G	uc001jcu.2	+	12	1193	c.1094A>G	c.(1093-1095)AAG>AGG	p.K365R	FAM21C_uc001jcs.1_Missense_Mutation_p.K310R|FAM21C_uc001jct.2_Missense_Mutation_p.K365R|FAM21C_uc010qfi.1_Missense_Mutation_p.K341R|FAM21C_uc010qfj.1_5'Flank	NM_015262	NP_056077	A8K5W5	A8K5W5_HUMAN	hypothetical protein LOC253725	365										ovary(1)	1																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61868760	61868760	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61868760G>A	uc001jky.2	-	27	3193	c.3001C>T	c.(3001-3003)CGT>TGT	p.R1001C	ANK3_uc001jkw.2_Missense_Mutation_p.R135C|ANK3_uc009xpa.2_Missense_Mutation_p.R135C|ANK3_uc001jkx.2_Missense_Mutation_p.R179C|ANK3_uc010qih.1_Missense_Mutation_p.R1002C|ANK3_uc001jkz.3_Missense_Mutation_p.R995C|ANK3_uc001jla.1_Missense_Mutation_p.R67C|ANK3_uc001jlb.1_Missense_Mutation_p.R519C	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1001	ZU5.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70450958	70450958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70450958C>T	uc001jok.3	+	12	6303	c.5798C>T	c.(5797-5799)CCG>CTG	p.P1933L		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	1933					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73544820	73544820	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73544820C>T	uc001jrx.3	+	41	6052	c.5675C>T	c.(5674-5676)GCG>GTG	p.A1892V		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1892	Cadherin 18.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
DNAJB12	54788	broad.mit.edu	37	10	74114622	74114622	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74114622T>C	uc010qjv.1	-	1	286	c.136A>G	c.(136-138)ATC>GTC	p.I46V	DNAJB12_uc001jsz.2_Missense_Mutation_p.I46V|DNAJB12_uc001jta.2_Missense_Mutation_p.I46V	NM_017626	NP_060096	Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	12					protein folding	endoplasmic reticulum|integral to membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
ECD	11319	broad.mit.edu	37	10	74894376	74894376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74894376C>T	uc001jtn.2	-	14	2143	c.1900G>A	c.(1900-1902)GAT>AAT	p.D634N	ECD_uc009xqx.2_Missense_Mutation_p.D667N|ECD_uc009xqy.2_Missense_Mutation_p.D591N|ECD_uc001jto.2_Missense_Mutation_p.D333N	NM_007265	NP_009196	O95905	SGT1_HUMAN	suppressor of S. cerevisiae gcr2 isoform 1	634					regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)																	---	---	---	---
SEC24C	9632	broad.mit.edu	37	10	75523277	75523277	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75523277C>A	uc001juw.2	+	8	1196	c.1017C>A	c.(1015-1017)AAC>AAA	p.N339K	SEC24C_uc010qkn.1_Intron|SEC24C_uc009xrj.1_Missense_Mutation_p.N197K|SEC24C_uc001jux.2_Missense_Mutation_p.N339K|SEC24C_uc010qko.1_Missense_Mutation_p.N220K|SEC24C_uc010qkp.1_Intron|SEC24C_uc010qkq.1_Intron	NM_004922	NP_004913	P53992	SC24C_HUMAN	SEC24-related protein C	339					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|zinc ion binding			skin(2)|central_nervous_system(1)	3	Prostate(51;0.0112)																	---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78799284	78799284	+	Splice_Site	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78799284A>G	uc001jxn.2	-	15	2036	c.1859_splice	c.e15+1	p.E620_splice	KCNMA1_uc001jxj.2_Splice_Site_p.E620_splice|KCNMA1_uc001jxk.1_Splice_Site_p.E235_splice|KCNMA1_uc009xrt.1_Splice_Site_p.E440_splice|KCNMA1_uc001jxl.1_Splice_Site_p.E274_splice|KCNMA1_uc001jxo.2_Splice_Site_p.E620_splice|KCNMA1_uc001jxm.2_Splice_Site_p.E620_splice|KCNMA1_uc001jxq.2_Splice_Site_p.E620_splice	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78844406	78844406	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78844406C>T	uc001jxn.2	-	12	1689	c.1512G>A	c.(1510-1512)TCG>TCA	p.S504S	KCNMA1_uc001jxj.2_Silent_p.S504S|KCNMA1_uc001jxk.1_Silent_p.S119S|KCNMA1_uc009xrt.1_Silent_p.S324S|KCNMA1_uc001jxl.1_Silent_p.S158S|KCNMA1_uc001jxo.2_Silent_p.S504S|KCNMA1_uc001jxm.2_Silent_p.S504S|KCNMA1_uc001jxq.2_Silent_p.S504S	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	504	RCK N-terminal.|Cytoplasmic (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81053157	81053157	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81053157A>C	uc001kaf.2	+	12	1549	c.977A>C	c.(976-978)TAT>TCT	p.Y326S	ZMIZ1_uc001kag.2_Missense_Mutation_p.Y202S|ZMIZ1_uc001kah.1_Missense_Mutation_p.Y208S	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	326					transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87615782	87615782	+	Intron	SNP	G	A	A	rs111458036		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87615782G>A	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94392365	94392365	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94392365T>C	uc001kic.2	+	13	1925	c.1617T>C	c.(1615-1617)AAT>AAC	p.N539N	KIF11_uc010qnq.1_Intron	NM_004523	NP_004514	P52732	KIF11_HUMAN	kinesin family member 11	539					blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94733809	94733809	+	Splice_Site	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94733809G>T	uc001kig.2	+	18	1840	c.1774_splice	c.e18-1	p.D592_splice	EXOC6_uc010qnr.1_Splice_Site_p.D608_splice|EXOC6_uc001kie.2_Splice_Site_p.D587_splice|EXOC6_uc009xub.2_Splice_Site_p.D591_splice|EXOC6_uc009xuc.2_Splice_Site_p.D489_splice|EXOC6_uc001kih.2_Splice_Site|EXOC6_uc001kii.2_Splice_Site_p.D166_splice	NM_019053	NP_061926			SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95079681	95079681	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95079681A>G	uc001kin.2	-	49	5669	c.5546T>C	c.(5545-5547)GTT>GCT	p.V1849A	MYOF_uc001kio.2_Missense_Mutation_p.V1836A|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1849	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
OPALIN	93377	broad.mit.edu	37	10	98105764	98105764	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98105764A>G	uc001kmj.2	-	6	799	c.360T>C	c.(358-360)CGT>CGC	p.R120R	OPALIN_uc010qor.1_Silent_p.R110R|OPALIN_uc001kmi.2_Silent_p.R110R|OPALIN_uc001kmk.2_Silent_p.R97R|OPALIN_uc010qos.1_RNA	NM_033207	NP_149984	Q96PE5	OPALI_HUMAN	transmembrane protein 10 isoform a	120						Golgi apparatus|integral to membrane|plasma membrane					0																		---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	99019153	99019153	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99019153A>G	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
HPS1	3257	broad.mit.edu	37	10	100182223	100182223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100182223C>T	uc010qpf.1	-	17	1892	c.1646G>A	c.(1645-1647)CGC>CAC	p.R549H	HPS1_uc001kpi.1_Missense_Mutation_p.R550H|HPS1_uc001kpj.1_Missense_Mutation_p.R457H|HPS1_uc001kpk.1_Missense_Mutation_p.R374H	NM_000195	NP_000186	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1 protein isoform a	549					lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity			skin(1)	1		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)										Hermansky-Pudlak_syndrome				---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101553677	101553677	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101553677G>A	uc001kqf.2	+	5	636	c.497G>A	c.(496-498)TGC>TAC	p.C166Y		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	166	Helical; Name=5; (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
FAM178A	55719	broad.mit.edu	37	10	102710474	102710474	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102710474A>C	uc001krt.3	+	17	3836	c.3294A>C	c.(3292-3294)GAA>GAC	p.E1098D	FAM178A_uc001krs.2_Missense_Mutation_p.E1098D	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1	1098											0																		---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103292822	103292822	+	Silent	SNP	G	T	T	rs61751508		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103292822G>T	uc001kta.2	+	9	1205	c.1092G>T	c.(1090-1092)ACG>ACT	p.T364T	BTRC_uc001ktb.2_Silent_p.T328T|BTRC_uc001ktc.2_Silent_p.T338T	NM_033637	NP_378663	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing protein	364	WD 2.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)														---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103295163	103295163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103295163G>A	uc001kta.2	+	11	1513	c.1400G>A	c.(1399-1401)CGA>CAA	p.R467Q	BTRC_uc001ktb.2_Missense_Mutation_p.R431Q|BTRC_uc001ktc.2_Missense_Mutation_p.R441Q	NM_033637	NP_378663	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing protein	467	WD 5.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)														---	---	---	---
PSD	5662	broad.mit.edu	37	10	104173805	104173805	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104173805G>A	uc001kvg.1	-	5	1801	c.1274C>T	c.(1273-1275)TCG>TTG	p.S425L	PSD_uc001kvh.1_Missense_Mutation_p.S46L|PSD_uc009xxd.1_Missense_Mutation_p.S425L	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	425					regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)														---	---	---	---
CUEDC2	79004	broad.mit.edu	37	10	104183797	104183797	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104183797C>A	uc001kvn.2	-	6	701	c.550G>T	c.(550-552)GAG>TAG	p.E184*	CUEDC2_uc001kvm.2_5'Flank	NM_024040	NP_076945	Q9H467	CUED2_HUMAN	CUE domain containing 2	184	CUE.					cytoplasm|nucleus	protein binding				0		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105793033	105793033	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105793033G>A	uc001kxr.2	-	53	4426	c.4257C>T	c.(4255-4257)TAC>TAT	p.Y1419Y	COL17A1_uc001kxq.2_5'Flank	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	1419	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105798255	105798255	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105798255G>A	uc001kxr.2	-	45	3148	c.2979C>T	c.(2977-2979)GGC>GGT	p.G993G		NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	993	Extracellular (Potential).|Triple-helical region.				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112343281	112343281	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112343281A>G	uc001kze.2	+	11	1070	c.944A>G	c.(943-945)GAA>GGA	p.E315G		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	315	Potential.				cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
EMX2	2018	broad.mit.edu	37	10	119305240	119305240	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119305240G>A	uc001ldh.3	+	2	1327	c.504G>A	c.(502-504)AGG>AGA	p.R168R	EMX2OS_uc001ldg.2_5'Flank|EMX2_uc001ldi.3_Intron	NM_004098	NP_004089	Q04743	EMX2_HUMAN	empty spiracles homeobox 2 isoform 1	168	Homeobox.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)														---	---	---	---
TIAL1	7073	broad.mit.edu	37	10	121339499	121339499	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121339499A>G	uc001lei.1	-	6	959	c.395T>C	c.(394-396)ATG>ACG	p.M132T	TIAL1_uc001leh.1_Missense_Mutation_p.M110T|TIAL1_uc001lej.1_Missense_Mutation_p.M149T|TIAL1_uc001lek.1_Missense_Mutation_p.M9T|TIAL1_uc009xzi.1_Missense_Mutation_p.M1T|TIAL1_uc010qtb.1_Missense_Mutation_p.M9T	NM_003252	NP_003243	Q01085	TIAR_HUMAN	TIA-1 related protein isoform 1	132	RRM 2.				apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)														---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123892188	123892188	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123892188G>A	uc001lfv.2	+	6	5998	c.5638G>A	c.(5638-5640)GCT>ACT	p.A1880T	TACC2_uc001lfw.2_Missense_Mutation_p.A71T|TACC2_uc009xzx.2_Missense_Mutation_p.A1880T|TACC2_uc010qtv.1_Missense_Mutation_p.A1929T|TACC2_uc001lfx.2_5'UTR|TACC2_uc001lfy.2_5'UTR	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1880						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124391375	124391375	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124391375C>T	uc001lgk.1	+	47	6070	c.5964C>T	c.(5962-5964)AAC>AAT	p.N1988N	DMBT1_uc001lgl.1_Silent_p.N1978N|DMBT1_uc001lgm.1_Silent_p.N1360N|DMBT1_uc009xzz.1_Silent_p.N1988N|DMBT1_uc010qtx.1_Silent_p.N708N|DMBT1_uc009yab.1_Silent_p.N691N|DMBT1_uc009yac.1_Silent_p.N282N	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1988					epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
FAM24A	118670	broad.mit.edu	37	10	124671216	124671216	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124671216C>T	uc001lgv.2	+	2	187	c.66C>T	c.(64-66)GCC>GCT	p.A22A		NM_001029888	NP_001025059	A6NFZ4	FA24A_HUMAN	family with sequence similarity 24, member A	22						extracellular region				ovary(2)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.124)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
BUB3	9184	broad.mit.edu	37	10	124917344	124917344	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124917344T>C	uc001lhe.2	+	4	607	c.365T>C	c.(364-366)CTG>CCG	p.L122P	BUB3_uc009yah.2_Missense_Mutation_p.L74P|BUB3_uc001lhf.3_Missense_Mutation_p.L122P|BUB3_uc001lhd.2_Missense_Mutation_p.L122P|BUB3_uc010qud.1_Missense_Mutation_p.L42P	NM_004725	NP_004716	O43684	BUB3_HUMAN	budding uninhibited by benzimidazoles 3 isoform	122	WD 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)																---	---	---	---
C10orf137	26098	broad.mit.edu	37	10	127412448	127412448	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127412448A>G	uc001liq.1	+	4	746	c.453A>G	c.(451-453)GGA>GGG	p.G151G	C10orf137_uc001lin.2_Silent_p.G151G|C10orf137_uc001lio.1_Silent_p.G151G|C10orf137_uc001lip.1_5'UTR	NM_015608	NP_056423	Q3B7T1	EDRF1_HUMAN	erythroid differentiation-related factor 1	151					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	binding			ovary(5)|large_intestine(3)|lung(2)	10		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128795065	128795065	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128795065C>A	uc001ljt.2	+	7	591	c.527C>A	c.(526-528)CCA>CAA	p.P176Q	DOCK1_uc010qun.1_Missense_Mutation_p.P176Q	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	176					apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
C10orf93	255352	broad.mit.edu	37	10	134751045	134751045	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134751045C>T	uc001llt.1	-						C10orf93_uc001llu.2_Missense_Mutation_p.R224H	NM_173572	NP_775843			hypothetical protein LOC255352								binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)														---	---	---	---
GPR123	84435	broad.mit.edu	37	10	134942224	134942224	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134942224C>A	uc001llx.3	+	7	1328	c.892C>A	c.(892-894)CTG>ATG	p.L298M	GPR123_uc001llw.2_Missense_Mutation_p.L1017M	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	298	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)														---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135195102	135195102	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135195102G>A	uc001lmv.2	+	3	887	c.807G>A	c.(805-807)TCG>TCA	p.S269S	PAOX_uc001lmw.2_RNA|PAOX_uc001lmx.2_Silent_p.S269S|PAOX_uc001lmy.2_Silent_p.S269S|PAOX_uc001lmz.2_RNA|PAOX_uc001lna.2_RNA|PAOX_uc001lnb.2_RNA|PAOX_uc001lnc.2_RNA	NM_152911	NP_690875	Q6QHF9	PAOX_HUMAN	polyamine oxidase isoform 1	407					polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)														---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135195153	135195153	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135195153C>A	uc001lmv.2	+	3	938	c.858C>A	c.(856-858)ACC>ACA	p.T286T	PAOX_uc001lmw.2_RNA|PAOX_uc001lmx.2_Silent_p.T286T|PAOX_uc001lmy.2_Silent_p.T286T|PAOX_uc001lmz.2_RNA|PAOX_uc001lna.2_RNA|PAOX_uc001lnb.2_RNA|PAOX_uc001lnc.2_RNA	NM_152911	NP_690875	Q6QHF9	PAOX_HUMAN	polyamine oxidase isoform 1	424					polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)														---	---	---	---
RIC8A	60626	broad.mit.edu	37	11	211202	211202	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:211202C>T	uc001log.2	+	5	1147	c.822C>T	c.(820-822)CAC>CAT	p.H274H	RIC8A_uc001lof.2_Silent_p.H274H|RIC8A_uc001loh.2_Silent_p.H267H	NM_021932	NP_068751	Q9NPQ8	RIC8A_HUMAN	resistance to inhibitors of cholinesterase 8	274						cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity				0		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1250474	1250474	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1250474C>T	uc009ycr.1	+	25	3145	c.3019C>T	c.(3019-3021)CGC>TGC	p.R1007C	MUC5B_uc009yct.1_Missense_Mutation_p.R351C|MUC5B_uc001ltb.2_Missense_Mutation_p.R351C|MUC5B_uc001lta.2_Missense_Mutation_p.R19C	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	351	TIL 1.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
TRPM5	29850	broad.mit.edu	37	11	2427880	2427880	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2427880G>T	uc001lwm.3	-						TRPM5_uc010qxl.1_Intron|TRPM5_uc009ydn.2_Intron	NM_014555	NP_055370			transient receptor potential cation channel,							integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)														---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3721906	3721906	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3721906C>T	uc001lyh.2	-	24	3967	c.3676G>A	c.(3676-3678)GTT>ATT	p.V1226I	NUP98_uc001lyi.2_Missense_Mutation_p.V1226I|NUP98_uc001lyg.2_Missense_Mutation_p.V191I	NM_016320	NP_057404	P52948	NUP98_HUMAN	nucleoporin 98kD isoform 1	1243					carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
OR52J3	119679	broad.mit.edu	37	11	5068158	5068158	+	Missense_Mutation	SNP	G	A	A	rs143834741		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5068158G>A	uc010qyv.1	+	1	403	c.403G>A	c.(403-405)GCA>ACA	p.A135T		NM_001001916	NP_001001916	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|lung(1)|skin(1)	3		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51B2	79345	broad.mit.edu	37	11	5344589	5344589	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5344589T>C	uc001mao.1	-	1	994	c.939A>G	c.(937-939)TAA>TAG	p.*313*	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_033180	NP_149420	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B,	313					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5730360	5730360	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5730360C>T	uc001mbr.2	+	8	1256	c.979C>T	c.(979-981)CGC>TGC	p.R327C	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|TRIM22_uc009yes.2_Missense_Mutation_p.R323C|TRIM22_uc010qzm.1_Missense_Mutation_p.R155C|TRIM22_uc009yeu.2_Missense_Mutation_p.R138C|OR56B1_uc001mbs.1_Intron|OR56B1_uc009yev.1_Intron	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	327	B30.2/SPRY.				immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)														---	---	---	---
OR52E6	390078	broad.mit.edu	37	11	5862840	5862840	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5862840A>G	uc010qzq.1	-	1	288	c.288T>C	c.(286-288)TTT>TTC	p.F96F	TRIM5_uc001mbq.1_Intron	NM_001005167	NP_001005167	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR56A4	120793	broad.mit.edu	37	11	6023400	6023400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6023400C>T	uc010qzv.1	-	1	979	c.979G>A	c.(979-981)GTC>ATC	p.V327I		NM_001005179	NP_001005179	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A,	275	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
CYB5R2	51700	broad.mit.edu	37	11	7694000	7694000	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7694000C>T	uc001mfm.2	-	2	295	c.57G>A	c.(55-57)CCG>CCA	p.P19P	CYB5R2_uc001mfn.2_RNA|CYB5R2_uc009yfk.2_Silent_p.P19P|CYB5R2_uc009yfl.1_Silent_p.P19P	NM_016229	NP_057313	Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase b5R.2	19	FAD-binding FR-type.				sterol biosynthetic process	membrane|soluble fraction	cytochrome-b5 reductase activity				0				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
BTBD10	84280	broad.mit.edu	37	11	13435077	13435077	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13435077T>C	uc001mkz.2	-	6	1065	c.808A>G	c.(808-810)AGT>GGT	p.S270G	BTBD10_uc010rcl.1_Missense_Mutation_p.S278G|BTBD10_uc001mla.2_Missense_Mutation_p.S254G|BTBD10_uc009ygn.2_RNA|BTBD10_uc010rcm.1_Missense_Mutation_p.S222G|BTBD10_uc010rcn.1_Missense_Mutation_p.S239G|BTBD10_uc009ygo.2_Missense_Mutation_p.S222G	NM_032320	NP_115696	Q9BSF8	BTBDA_HUMAN	K+ channel tetramerization protein	270						nucleus					0				Epithelial(150;0.0214)														---	---	---	---
FAR1	84188	broad.mit.edu	37	11	13729476	13729476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13729476C>T	uc001mld.2	+	4	550	c.395C>T	c.(394-396)ACG>ATG	p.T132M	FAR1_uc009ygp.2_Missense_Mutation_p.T132M	NM_032228	NP_115604	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	132					ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	18028253	18028253	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18028253C>T	uc001mnm.2	-	3	317	c.237G>A	c.(235-237)GGG>GGA	p.G79G	SERGEF_uc009yhd.2_RNA|SERGEF_uc001mnn.2_Silent_p.G79G|SERGEF_uc010rcz.1_5'UTR|SERGEF_uc001mno.1_5'UTR	NM_012139	NP_036271	Q9UGK8	SRGEF_HUMAN	deafness locus associated putative guanine	79	RCC1 2.				negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19970272	19970272	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19970272C>T	uc010rdm.1	+	11	2721	c.2360C>T	c.(2359-2361)ACG>ATG	p.T787M	NAV2_uc001mpp.2_Missense_Mutation_p.T700M|NAV2_uc001mpr.3_Missense_Mutation_p.T764M	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	787						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
DBX1	120237	broad.mit.edu	37	11	20181498	20181498	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20181498G>A	uc001mpw.1	-							NM_001029865	NP_001025036			developing brain homeobox 1						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
HTATIP2	10553	broad.mit.edu	37	11	20385903	20385903	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20385903G>A	uc009yia.1	+	2	186	c.120G>A	c.(118-120)GAG>GAA	p.E40E	HTATIP2_uc009yib.1_Silent_p.E40E|HTATIP2_uc001mpx.2_Silent_p.E74E|HTATIP2_uc001mpz.2_Silent_p.E40E|HTATIP2_uc001mpy.3_Silent_p.E40E	NM_006410	NP_006401	Q9BUP3	HTAI2_HUMAN	HIV-1 Tat interactive protein 2, 30kDa isoform	40	NADP.				angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0																		---	---	---	---
SLC6A5	9152	broad.mit.edu	37	11	20625844	20625844	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20625844G>T	uc001mqd.2	+	3	826	c.553G>T	c.(553-555)GGG>TGG	p.G185W	SLC6A5_uc009yic.2_Intron	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	185	Cytoplasmic (Potential).				synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)													---	---	---	---
FBXO3	26273	broad.mit.edu	37	11	33772171	33772171	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33772171C>T	uc001muz.2	-	8	874	c.846G>A	c.(844-846)GGG>GGA	p.G282G	FBXO3_uc010rej.1_5'UTR|FBXO3_uc001muy.2_Silent_p.G169G|FBXO3_uc009ykb.2_RNA|FBXO3_uc001mva.1_Silent_p.G282G|FBXO3_uc001mvb.1_Silent_p.G277G|FBXO3_uc010rek.1_RNA	NM_012175	NP_036307	Q9UK99	FBX3_HUMAN	F-box only protein 3 isoform 1	282	ApaG.				proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)														---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36595732	36595732	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36595732G>A	uc001mwu.3	+	2	1002	c.878G>A	c.(877-879)TGC>TAC	p.C293Y	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	293	RING-type.	Zinc 2 (By similarity).			histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
API5	8539	broad.mit.edu	37	11	43356827	43356827	+	Splice_Site	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43356827G>T	uc010rfh.1	+	12	1452	c.1279_splice	c.e12-1	p.D427_splice	API5_uc010rfg.1_Splice_Site_p.D416_splice|API5_uc001mxf.2_Splice_Site_p.D427_splice|API5_uc010rfi.1_Splice_Site_p.D373_splice|API5_uc001mxg.2_Splice_Site_p.D301_splice	NM_001142930	NP_001136402			apoptosis inhibitor 5 isoform a						anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
ALKBH3	221120	broad.mit.edu	37	11	43911304	43911304	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43911304T>C	uc001mxs.2	+	6	739	c.296T>C	c.(295-297)GTG>GCG	p.V99A	ALKBH3_uc009ykp.2_RNA|ALKBH3_uc001mxt.2_RNA|ALKBH3_uc009ykq.2_5'UTR	NM_139178	NP_631917	Q96Q83	ALKB3_HUMAN	AlkB homolog 3	99					DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation	mitochondrion|nucleoplasm	damaged DNA binding|DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0					Vitamin C(DB00126)								Direct_reversal_of_damage					---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44289061	44289061	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44289061C>T	uc001myb.2	-	3	993	c.889G>A	c.(889-891)GCT>ACT	p.A297T		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	297					hair follicle development						0																		---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44297062	44297062	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44297062C>T	uc001myb.2	-	2	717	c.613G>A	c.(613-615)GCC>ACC	p.A205T		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	205					hair follicle development						0																		---	---	---	---
ZNF408	79797	broad.mit.edu	37	11	46727164	46727164	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46727164C>A	uc001nde.1	+	5	2144	c.1914C>A	c.(1912-1914)CCC>CCA	p.P638P	ZNF408_uc010rgw.1_Silent_p.P630P	NM_024741	NP_079017	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	638					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding				0																		---	---	---	---
F2	2147	broad.mit.edu	37	11	46744948	46744948	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46744948C>A	uc001ndf.3	+	6	482	c.439C>A	c.(439-441)CAT>AAT	p.H147N	F2_uc001ndg.3_RNA	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein	147	Kringle 1.				activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
ACP2	53	broad.mit.edu	37	11	47264672	47264672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47264672C>T	uc001nei.2	-	9	976	c.859G>A	c.(859-861)GAC>AAC	p.D287N	ACP2_uc010rhe.1_Missense_Mutation_p.D259N|ACP2_uc009ylj.2_Missense_Mutation_p.D215N|ACP2_uc010rhf.1_Missense_Mutation_p.D255N|ACP2_uc010rhg.1_Missense_Mutation_p.D224N|ACP2_uc010rhh.1_Missense_Mutation_p.D100N|ACP2_uc010rhi.1_Missense_Mutation_p.D100N|ACP2_uc009ylk.2_Missense_Mutation_p.D254N	NM_001610	NP_001601	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal isoform 1	287	Lumenal (Potential).	Proton donor (By similarity).				integral to membrane|lysosomal lumen|lysosomal membrane	acid phosphatase activity			ovary(1)	1																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47307054	47307054	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47307054G>A	uc001ner.1	+	14	2655	c.2464G>A	c.(2464-2466)GCA>ACA	p.A822T	MADD_uc001neq.2_Missense_Mutation_p.A822T|MADD_uc001nev.1_Missense_Mutation_p.A779T|MADD_uc001nes.1_Missense_Mutation_p.A779T|MADD_uc001net.1_Missense_Mutation_p.A822T|MADD_uc009yln.1_Missense_Mutation_p.A779T|MADD_uc001neu.1_Missense_Mutation_p.A779T|MADD_uc001nex.2_Missense_Mutation_p.A822T|MADD_uc001nez.2_Missense_Mutation_p.A779T|MADD_uc001new.2_Missense_Mutation_p.A822T	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	822					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
KBTBD4	55709	broad.mit.edu	37	11	47599015	47599015	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47599015A>G	uc001nfx.2	-	2	708	c.537T>C	c.(535-537)AAT>AAC	p.N179N	NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Silent_p.N204N|KBTBD4_uc001nfz.2_Silent_p.N195N|KBTBD4_uc001nfy.2_Silent_p.N179N|NDUFS3_uc010rhn.1_5'Flank|NDUFS3_uc001nga.2_5'Flank	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	179	BACK.									ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NUP160	23279	broad.mit.edu	37	11	47859139	47859139	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47859139A>G	uc001ngm.2	-	5	870	c.785T>C	c.(784-786)GTA>GCA	p.V262A	NUP160_uc009ylw.2_RNA	NM_015231	NP_056046	Q12769	NU160_HUMAN	nucleoporin 160kDa	262					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48161113	48161113	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48161113C>A	uc001ngp.3	+	11	2583	c.2228C>A	c.(2227-2229)CCT>CAT	p.P743H	PTPRJ_uc010rhr.1_Missense_Mutation_p.P188H	NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	743	Extracellular (Potential).|Fibronectin type-III 8.				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
OR4S1	256148	broad.mit.edu	37	11	48327840	48327840	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48327840G>A	uc010rhu.1	+	1	66	c.66G>A	c.(64-66)CAG>CAA	p.Q22Q		NM_001004725	NP_001004725	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR4C46	119749	broad.mit.edu	37	11	51515845	51515845	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51515845T>C	uc010ric.1	+	1	564	c.564T>C	c.(562-564)ACT>ACC	p.T188T		NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C,	188	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035854	55035854	+	Intron	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035854T>A	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035855	55035855	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035855A>G	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
SPRYD5	84767	broad.mit.edu	37	11	55659079	55659079	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55659079A>G	uc010rip.1	+	7	1422	c.1330A>G	c.(1330-1332)AGG>GGG	p.R444G	SPRYD5_uc010riq.1_Missense_Mutation_p.R301G	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	444	B30.2/SPRY.					intracellular	zinc ion binding				0		all_epithelial(135;0.226)																---	---	---	---
OR8K5	219453	broad.mit.edu	37	11	55927697	55927697	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55927697C>T	uc010rja.1	-	1	97	c.97G>A	c.(97-99)GTC>ATC	p.V33I		NM_001004058	NP_001004058	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)																---	---	---	---
OR5T2	219464	broad.mit.edu	37	11	56000210	56000210	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56000210C>A	uc010rjc.1	-	1	452	c.452G>T	c.(451-453)TGC>TTC	p.C151F		NM_001004746	NP_001004746	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T,	151	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)																	---	---	---	---
P2RX3	5024	broad.mit.edu	37	11	57117371	57117371	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57117371C>T	uc001nju.2	+	7	780	c.704C>T	c.(703-705)ACG>ATG	p.T235M		NM_002559	NP_002550	P56373	P2RX3_HUMAN	purinergic receptor P2X3	235	Extracellular (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0																OREG0020966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PRG3	10394	broad.mit.edu	37	11	57146997	57146997	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57146997C>T	uc001njv.1	-	3	455	c.345G>A	c.(343-345)GTG>GTA	p.V115V		NM_006093	NP_006084	Q9Y2Y8	PRG3_HUMAN	proteoglycan 3 precursor	115	C-type lectin.				basophil activation|histamine biosynthetic process|immune response|leukotriene biosynthetic process|negative regulation of translation|neutrophil activation|positive regulation of interleukin-8 biosynthetic process|superoxide anion generation		sugar binding				0																		---	---	---	---
TIMM10	26519	broad.mit.edu	37	11	57296267	57296267	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57296267C>A	uc001nkm.1	-	3	343	c.196G>T	c.(196-198)GGC>TGC	p.G66C		NM_012456	NP_036588	P62072	TIM10_HUMAN	translocase of inner mitochondrial membrane 10	66					protein import into mitochondrial inner membrane|sensory perception of sound|transmembrane transport	mitochondrial inner membrane presequence translocase complex|mitochondrial intermembrane space protein transporter complex	zinc ion binding				0																		---	---	---	---
MPEG1	219972	broad.mit.edu	37	11	58979300	58979300	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58979300A>G	uc001nnu.3	-	1	1195	c.1039T>C	c.(1039-1041)TAC>CAC	p.Y347H		NM_001039396	NP_001034485	Q2M385	MPEG1_HUMAN	macrophage expressed gene 1 precursor	347	Extracellular (Potential).					integral to membrane				ovary(1)|skin(1)	2		all_epithelial(135;0.125)																---	---	---	---
MS4A13	503497	broad.mit.edu	37	11	60296882	60296882	+	Silent	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60296882T>G	uc001nps.2	+	6	674	c.351T>G	c.(349-351)GGT>GGG	p.G117G	MS4A13_uc009ync.2_Silent_p.G77G|MS4A13_uc009ynd.2_Silent_p.G58G	NM_001012417	NP_001012417	Q5J8X5	M4A13_HUMAN	membrane-spanning 4-domains, subfamily A, member	117	Helical; (Potential).					integral to membrane					0																		---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63656411	63656411	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63656411T>C	uc001nxw.2	+						MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron|MARK2_uc009yox.2_Silent_p.G5G|MARK2_uc001nxz.3_5'UTR	NM_001039469	NP_001034558			MAP/microtubule affinity-regulating kinase 2						cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
SLC22A11	55867	broad.mit.edu	37	11	64323478	64323478	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64323478T>C	uc001oai.2	+	1	381	c.7T>C	c.(7-9)TTC>CTC	p.F3L	SLC22A11_uc001oah.1_Missense_Mutation_p.F3L|SLC22A11_uc001oaj.2_Missense_Mutation_p.F3L|SLC22A11_uc009ypq.2_Missense_Mutation_p.F3L	NM_018484	NP_060954	Q9NSA0	S22AB_HUMAN	solute carrier family 22 member 11	3	Cytoplasmic (Potential).				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)											OREG0004031	type=REGULATORY REGION|Gene=SLC22A11|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
SCYL1	57410	broad.mit.edu	37	11	65298235	65298235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65298235G>A	uc001oea.1	+	7	1062	c.985G>A	c.(985-987)GTT>ATT	p.V329I	SCYL1_uc009yqk.2_Missense_Mutation_p.V329I|SCYL1_uc001oeb.1_Missense_Mutation_p.V329I|SCYL1_uc001oec.1_Missense_Mutation_p.V329I|SCYL1_uc001oed.1_Missense_Mutation_p.V186I|SCYL1_uc001oee.1_5'UTR	NM_020680	NP_065731	Q96KG9	NTKL_HUMAN	SCY1-like 1 isoform A	329					regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			skin(1)	1																		---	---	---	---
SNX32	254122	broad.mit.edu	37	11	65618601	65618601	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65618601C>T	uc001ofr.2	+	7	806	c.679C>T	c.(679-681)CGG>TGG	p.R227W		NM_152760	NP_689973	Q86XE0	SNX32_HUMAN	sorting nexin 6B	227					cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)														---	---	---	---
CPT1A	1374	broad.mit.edu	37	11	68542897	68542897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68542897C>T	uc001oog.3	-	13	1632	c.1462G>A	c.(1462-1464)GTC>ATC	p.V488I	CPT1A_uc001oof.3_Missense_Mutation_p.V488I|CPT1A_uc009ysj.2_Intron	NM_001876	NP_001867	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A liver isoform	488	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			skin(2)	2	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		L-Carnitine(DB00583)|Perhexiline(DB01074)													---	---	---	---
ANO1	55107	broad.mit.edu	37	11	69995855	69995855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69995855G>A	uc001opj.2	+	12	1603	c.1298G>A	c.(1297-1299)CGA>CAA	p.R433Q	ANO1_uc001opk.1_Missense_Mutation_p.R405Q|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.R168Q	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	433	Cytoplasmic (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity	p.R433*(1)		ovary(1)|pancreas(1)	2																		---	---	---	---
ANO1	55107	broad.mit.edu	37	11	70017068	70017068	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70017068T>G	uc001opj.2	+	22	2578	c.2273T>G	c.(2272-2274)ATC>AGC	p.I758S	ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.I467S|ANO1_uc010rql.1_5'UTR	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	758	Cytoplasmic (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71734199	71734199	+	Intron	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71734199A>T	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc009ysx.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc009ysy.1_Intron|NUMA1_uc001orp.2_Intron|NUMA1_uc001orq.2_Intron	NM_006185	NP_006176			nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
SERPINH1	871	broad.mit.edu	37	11	75277741	75277741	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75277741G>A	uc001owr.2	+	2	576	c.347G>A	c.(346-348)CGC>CAC	p.R116H	SERPINH1_uc009yuf.2_Missense_Mutation_p.R116H|SERPINH1_uc009yug.2_Missense_Mutation_p.R116H|SERPINH1_uc001ows.2_Missense_Mutation_p.R116H|SERPINH1_uc001owt.2_5'Flank	NM_001235	NP_001226	P50454	SERPH_HUMAN	serine (or cysteine) proteinase inhibitor, clade	116					regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)																	---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75776823	75776823	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75776823T>G	uc001oxc.2	+	13	1537	c.1296T>G	c.(1294-1296)AAT>AAG	p.N432K	UVRAG_uc010rrw.1_Missense_Mutation_p.N331K|UVRAG_uc001oxd.2_Missense_Mutation_p.N60K|UVRAG_uc010rrx.1_Missense_Mutation_p.N60K	NM_003369	NP_003360	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	432					DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92088561	92088561	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92088561G>A	uc001pdj.3	+	1	3300	c.3283G>A	c.(3283-3285)GAC>AAC	p.D1095N		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1095	Cadherin 10.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92533874	92533874	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92533874A>G	uc001pdj.3	+	9	7712	c.7695A>G	c.(7693-7695)GAA>GAG	p.E2565E		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2565	Cadherin 23.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
PIWIL4	143689	broad.mit.edu	37	11	94340675	94340675	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94340675G>A	uc001pfa.2	+	14	1920	c.1709G>A	c.(1708-1710)TGC>TAC	p.C570Y	PIWIL4_uc010rue.1_RNA|PIWIL4_uc009ywk.1_RNA	NM_152431	NP_689644	Q7Z3Z4	PIWL4_HUMAN	piwi-like 4	570	Piwi.				cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding			skin(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
CWC15	51503	broad.mit.edu	37	11	94696586	94696586	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94696586T>A	uc001pfd.3	-	8	777	c.654A>T	c.(652-654)GAA>GAT	p.E218D		NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	218					nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
BIRC2	329	broad.mit.edu	37	11	102220626	102220626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102220626C>T	uc001pgy.2	+	2	1440	c.41C>T	c.(40-42)TCG>TTG	p.S14L	BIRC2_uc010ruq.1_Intron|BIRC2_uc010rur.1_Missense_Mutation_p.S14L	NM_001166	NP_001157	Q13490	BIRC2_HUMAN	baculoviral IAP repeat-containing protein 2	14					cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102742328	102742328	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102742328T>C	uc001phk.2	-	4	666	c.621A>G	c.(619-621)TCA>TCG	p.S207S		NM_002426	NP_002417	P39900	MMP12_HUMAN	matrix metalloproteinase 12 preproprotein	207					positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
DDI1	414301	broad.mit.edu	37	11	103907911	103907911	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103907911G>A	uc001phr.2	+	1	604	c.361G>A	c.(361-363)GCT>ACT	p.A121T	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	121					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)														---	---	---	---
KBTBD3	143879	broad.mit.edu	37	11	105924490	105924490	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105924490T>C	uc001pja.2	-	4	1566	c.926A>G	c.(925-927)CAA>CGA	p.Q309R	KBTBD3_uc001pjb.2_Missense_Mutation_p.Q309R|KBTBD3_uc009yxm.2_Missense_Mutation_p.Q230R	NM_198439	NP_940841	Q8NAB2	KBTB3_HUMAN	BTB and kelch domain containing 3	305	Kelch 1.									ovary(1)|central_nervous_system(1)	2		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.43e-05)|Epithelial(105;0.00418)|all cancers(92;0.0299)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107925673	107925673	+	Silent	SNP	C	T	T	rs147410964	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107925673C>T	uc001pjv.2	+	7	1438	c.771C>T	c.(769-771)TCC>TCT	p.S257S	CUL5_uc001pju.2_RNA	NM_003478	NP_003469	Q93034	CUL5_HUMAN	Vasopressin-activated calcium-mobilizing	257					cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108117798	108117798	+	Missense_Mutation	SNP	C	T	T	rs138398778		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108117798C>T	uc001pkb.1	+	8	1394	c.1009C>T	c.(1009-1011)CGT>TGT	p.R337C	ATM_uc009yxr.1_Missense_Mutation_p.R337C	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	337			R -> C (in a colorectal adenocarcinoma sample; somatic mutation).|R -> H (in a colorectal adenocarcinoma sample; somatic mutation).		cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	p.R337C(2)|p.R337S(2)|p.R337H(1)		haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
LAYN	143903	broad.mit.edu	37	11	111414815	111414815	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111414815T>C	uc001plr.1	+	3	613	c.277T>C	c.(277-279)TTC>CTC	p.F93L	LAYN_uc001plp.1_Missense_Mutation_p.F85L|LAYN_uc001plq.1_Missense_Mutation_p.F93L|LAYN_uc001pls.1_Missense_Mutation_p.F85L|LAYN_uc010rwg.1_5'UTR|LAYN_uc010rwh.1_5'UTR	NM_178834	NP_849156	Q6UX15	LAYN_HUMAN	layilin	93	C-type lectin.|Extracellular (Potential).					cell surface|integral to membrane|ruffle	hyaluronic acid binding|sugar binding				0		all_cancers(61;9.06e-10)|all_epithelial(67;1.34e-05)|Melanoma(852;1.74e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Breast(348;0.086)		Epithelial(105;1.5e-06)|BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|all cancers(92;2.45e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0476)														---	---	---	---
C11orf1	64776	broad.mit.edu	37	11	111753154	111753154	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111753154C>T	uc001pmd.2	+	2	445	c.108C>T	c.(106-108)GGC>GGT	p.G36G	C11orf1_uc001pme.2_Silent_p.G76G	NM_022761	NP_073598	Q9H5F2	CK001_HUMAN	hypothetical protein LOC64776	36						nucleus					0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)														---	---	---	---
HTR3B	9177	broad.mit.edu	37	11	113802574	113802574	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113802574T>C	uc001pok.2	+	4	420	c.353T>C	c.(352-354)ATC>ACC	p.I118T	HTR3B_uc001pol.2_Missense_Mutation_p.I107T	NM_006028	NP_006019	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B	118	Extracellular (Potential).				synaptic transmission	integral to plasma membrane|postsynaptic membrane	serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)														---	---	---	---
FAM55D	54827	broad.mit.edu	37	11	114453246	114453246	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114453246G>A	uc001ppc.2	-	3	775	c.594C>T	c.(592-594)GGC>GGT	p.G198G	FAM55D_uc001ppd.2_Intron	NM_001077639	NP_001071107	Q6UWF7	FA55D_HUMAN	hypothetical protein LOC54827 isoform 1	198						extracellular region				ovary(2)|skin(2)	4		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.82e-06)|Epithelial(105;0.000129)|all cancers(92;0.000938)														---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116744643	116744643	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116744643T>C	uc001ppy.2	-	12	1419	c.1383A>G	c.(1381-1383)CAA>CAG	p.Q461Q	SIK3_uc001ppz.2_Silent_p.Q360Q|SIK3_uc001pqa.2_Silent_p.Q413Q	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK	461						cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
TAGLN	6876	broad.mit.edu	37	11	117073731	117073731	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117073731T>C	uc001pqm.2	+	2	123	c.2T>C	c.(1-3)ATG>ACG	p.M1T	uc001pqk.1_5'Flank|TAGLN_uc001pql.1_RNA|TAGLN_uc001pqn.2_Missense_Mutation_p.M1T|TAGLN_uc001pqo.2_Missense_Mutation_p.M1T|TAGLN_uc001pqp.2_Missense_Mutation_p.M1T|uc001pqq.1_5'Flank	NM_003186	NP_003177	Q01995	TAGL_HUMAN	transgelin	1					muscle organ development	cytoplasm	actin binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)														---	---	---	---
AMICA1	120425	broad.mit.edu	37	11	118071335	118071335	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118071335A>G	uc001psk.2	-						AMICA1_uc001psg.2_Intron|AMICA1_uc001psh.2_Intron|AMICA1_uc009yzw.1_Intron|AMICA1_uc001psi.2_Intron|AMICA1_uc001psj.2_Intron|AMICA1_uc010rxw.1_Intron|AMICA1_uc010rxx.1_Intron|AMICA1_uc001psl.1_Intron	NM_001098526	NP_001091996			adhesion molecule, interacts with CXADR antigen						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
TTC36	143941	broad.mit.edu	37	11	118399499	118399499	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118399499C>T	uc001ptg.1	+	2	300	c.300C>T	c.(298-300)GAC>GAT	p.D100D	TTC36_uc010ryb.1_RNA|TTC36_uc010ryc.1_Silent_p.D41D|TMEM25_uc010ryd.1_5'Flank|TMEM25_uc001ptk.3_5'Flank|TMEM25_uc010rye.1_5'Flank|TMEM25_uc001pth.2_5'Flank|TMEM25_uc009zad.2_5'Flank|TMEM25_uc001pti.2_5'Flank|TMEM25_uc010ryf.1_5'Flank|TMEM25_uc001ptl.2_5'Flank|TMEM25_uc001ptm.2_5'Flank|TMEM25_uc001ptn.2_5'Flank	NM_001080441	NP_001073910	A6NLP5	TTC36_HUMAN	tetratricopeptide repeat domain 36	100	TPR 2.						binding				0																		---	---	---	---
TREH	11181	broad.mit.edu	37	11	118533631	118533631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118533631C>T	uc001pty.1	-	4	427	c.382G>A	c.(382-384)GCA>ACA	p.A128T	TREH_uc009zaj.1_Missense_Mutation_p.A128T|TREH_uc001ptz.1_Silent_p.G7G|TREH_uc009zak.2_Missense_Mutation_p.A128T	NM_007180	NP_009111	O43280	TREA_HUMAN	trehalase precursor	128					polysaccharide digestion|trehalose catabolic process	anchored to plasma membrane	alpha,alpha-trehalase activity			pancreas(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)														---	---	---	---
C2CD2L	9854	broad.mit.edu	37	11	118982005	118982005	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118982005G>T	uc001pvo.2	+	6	1190	c.831G>T	c.(829-831)CAG>CAT	p.Q277H	DPAGT1_uc010ryz.1_5'Flank|C2CD2L_uc001pvn.2_Missense_Mutation_p.Q277H	NM_014807	NP_055622	O14523	C2C2L_HUMAN	transmembrane protein 24	277						integral to membrane					0																		---	---	---	---
OAF	220323	broad.mit.edu	37	11	120096472	120096472	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120096472A>G	uc001pxb.2	+	2	575	c.334A>G	c.(334-336)ATC>GTC	p.I112V		NM_178507	NP_848602	Q86UD1	OAF_HUMAN	OAF homolog precursor	112											0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)														---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120690602	120690602	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120690602G>A	uc001pxn.2	+	6	771	c.484G>A	c.(484-486)GCC>ACC	p.A162T	GRIK4_uc009zav.1_Missense_Mutation_p.A162T|GRIK4_uc009zaw.1_Missense_Mutation_p.A162T|GRIK4_uc009zax.1_Missense_Mutation_p.A162T	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	162	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121038788	121038788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121038788A>G	uc010rzo.1	+	18	5612	c.5612A>G	c.(5611-5613)AAA>AGA	p.K1871R		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1871	ZP.				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)														---	---	---	---
BLID	414899	broad.mit.edu	37	11	121986495	121986495	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121986495G>A	uc001pyf.2	-	1	429	c.136C>T	c.(136-138)CCA>TCA	p.P46S	LOC399959_uc009zba.2_Intron	NM_001001786	NP_001001786	Q8IZY5	BLID_HUMAN	BRCC2 protein	46					apoptosis	mitochondrion					0		Breast(109;0.0164)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;2.08e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.101)												OREG0021435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UBASH3B	84959	broad.mit.edu	37	11	122659945	122659945	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122659945C>T	uc001pyi.3	+	6	1269	c.909C>T	c.(907-909)ACC>ACT	p.T303T		NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,	303	SH3.					cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)														---	---	---	---
HSPA8	3312	broad.mit.edu	37	11	122928610	122928610	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122928610T>C	uc001pyo.2	-	9	1851	c.1773A>G	c.(1771-1773)GAA>GAG	p.E591E	HSPA8_uc009zbc.2_Silent_p.E355E|HSPA8_uc001pyp.2_Intron|HSPA8_uc010rzu.1_Silent_p.E514E	NM_006597	NP_006588	P11142	HSP7C_HUMAN	heat shock 70kDa protein 8 isoform 1	591					cellular membrane organization|interspecies interaction between organisms|mRNA metabolic process|negative regulation of transcription, DNA-dependent|neurotransmitter secretion|post-Golgi vesicle-mediated transport|protein folding|response to unfolded protein|transcription, DNA-dependent	cell surface|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|melanosome|plasma membrane|ribonucleoprotein complex	ATP binding|ATPase activity, coupled|protein binding			central_nervous_system(7)|lung(1)	8		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)														---	---	---	---
OR10G8	219869	broad.mit.edu	37	11	123900482	123900482	+	Silent	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123900482T>A	uc001pzp.1	+	1	153	c.153T>A	c.(151-153)TCT>TCA	p.S51S		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	51	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)														---	---	---	---
OR8B12	219858	broad.mit.edu	37	11	124413190	124413190	+	Missense_Mutation	SNP	G	A	A	rs148702196		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124413190G>A	uc010sam.1	-	1	361	c.361C>T	c.(361-363)CGC>TGC	p.R121C		NM_001005195	NP_001005195	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)|skin(1)	3		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0213)														---	---	---	---
NFRKB	4798	broad.mit.edu	37	11	129754692	129754692	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129754692C>T	uc001qfi.2	-	7	891	c.690G>A	c.(688-690)GCG>GCA	p.A230A	NFRKB_uc001qfg.2_Silent_p.A255A|NFRKB_uc001qfh.2_Silent_p.A253A|NFRKB_uc010sbw.1_Silent_p.A242A	NM_001143835	NP_001137307	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	230					DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)														---	---	---	---
SNX19	399979	broad.mit.edu	37	11	130785348	130785348	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130785348C>A	uc001qgk.3	-	1	1035	c.487G>T	c.(487-489)GGT>TGT	p.G163C	SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Missense_Mutation_p.G163C|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	163	PXA.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)														---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6687040	6687040	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6687040A>G	uc001qpo.2	-	37	5436	c.5272T>C	c.(5272-5274)TAT>CAT	p.Y1758H	CHD4_uc001qpn.2_Missense_Mutation_p.Y1751H|CHD4_uc001qpp.2_Missense_Mutation_p.Y1783H|uc001qpq.1_5'Flank	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1758	Required for interaction with PCNT.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6701231	6701231	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6701231G>T	uc001qpo.2	-						CHD4_uc001qpn.2_Intron|CHD4_uc001qpp.2_Intron	NM_001273	NP_001264			chromodomain helicase DNA binding protein 4						chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
ACRBP	84519	broad.mit.edu	37	12	6749557	6749557	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6749557G>T	uc001qpu.1	-	7	1257	c.1209C>A	c.(1207-1209)CCC>CCA	p.P403P	LPAR5_uc010sff.1_5'Flank|ACRBP_uc001qpt.1_5'Flank|ACRBP_uc010sfg.1_Silent_p.P370P	NM_032489	NP_115878	Q8NEB7	ACRBP_HUMAN	proacrosin binding protein sp32 precursor	403						acrosomal vesicle|extracellular region				central_nervous_system(1)	1																		---	---	---	---
USP5	8078	broad.mit.edu	37	12	6964649	6964649	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6964649G>A	uc001qri.3	+	2	255	c.196G>A	c.(196-198)GGC>AGC	p.G66S	USP5_uc001qrh.3_Missense_Mutation_p.G66S	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	66					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4																		---	---	---	---
PHB2	11331	broad.mit.edu	37	12	7077645	7077645	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7077645T>C	uc001qsd.2	-	4	616	c.406A>G	c.(406-408)ATT>GTT	p.I136V	PHB2_uc010sft.1_Missense_Mutation_p.I136V|PHB2_uc010sfu.1_Missense_Mutation_p.I136V|PHB2_uc001qse.1_5'Flank|PHB2_uc001qsf.1_5'Flank|PHB2_uc009zfn.1_5'Flank|SCARNA12_uc001qsg.2_5'Flank	NM_001144831	NP_001138303	Q99623	PHB2_HUMAN	prohibitin 2 isoform 1	136					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial inner membrane|nucleus	estrogen receptor binding|receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
CLEC4A	50856	broad.mit.edu	37	12	8281918	8281918	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8281918T>C	uc001qtz.1	+	3	505	c.258T>C	c.(256-258)CAT>CAC	p.H86H	CLEC4A_uc009zga.1_Silent_p.H47H|CLEC4A_uc001qub.1_Intron|CLEC4A_uc001quc.1_Intron|CLEC4A_uc009zgb.1_Intron	NM_016184	NP_057268	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A isoform	86	Extracellular (Potential).				cell adhesion|cell surface receptor linked signaling pathway|innate immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity				0				Kidney(36;0.0915)														---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14664529	14664529	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14664529G>A	uc001rcc.1	-	7	1122	c.961C>T	c.(961-963)CTG>TTG	p.L321L		NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	321					lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
ART4	420	broad.mit.edu	37	12	14993873	14993873	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14993873G>T	uc001rcl.1	-	2	725	c.359C>A	c.(358-360)GCT>GAT	p.A120D	ART4_uc009zid.1_Intron|ART4_uc009zie.1_Intron|ART4_uc001rcm.1_Missense_Mutation_p.A120D	NM_021071	NP_066549	Q93070	NAR4_HUMAN	ADP-ribosyltransferase 4 precursor	120					arginine metabolic process|protein ADP-ribosylation	anchored to membrane|plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity				0																		---	---	---	---
CMAS	55907	broad.mit.edu	37	12	22208418	22208418	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22208418A>G	uc001rfm.2	+	3	512	c.433A>G	c.(433-435)ACT>GCT	p.T145A	CMAS_uc001rfn.2_RNA	NM_018686	NP_061156	Q8NFW8	NEUA_HUMAN	cytidine monophospho-N-acetylneuraminic acid	145					lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25398281	25398281	+	Missense_Mutation	SNP	C	T	T	rs112445441		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25398281C>T	uc001rgp.1	-	2	219	c.38G>A	c.(37-39)GGC>GAC	p.G13D	KRAS_uc001rgq.1_Missense_Mutation_p.G13D|KRAS_uc001rgr.2_RNA	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	13	GTP.		G -> R (in pylocytic astrocytoma; somatic mutation; increase activation of the Ras pathway).|G -> D (in a breast carcinoma cell line and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G13D(2647)|p.G13C(182)|p.G13S(58)|p.G13R(41)|p.G13V(27)|p.G13A(24)|p.G13G(11)|p.G13E(4)|p.G12_G13insG(4)|p.G13N(3)|p.G13I(1)|p.G13_V14>DI(1)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			G13D(NCIH647_LUNG)|G13D(MDAMB231_BREAST)|G13D(NCIH747_LARGE_INTESTINE)|G13D(T84_LARGE_INTESTINE)|G13D(LOVO_LARGE_INTESTINE)|G13D(DLD1_LARGE_INTESTINE)|G13D(DV90_LUNG)|G13D(HCT15_LARGE_INTESTINE)|G13D(HCT116_LARGE_INTESTINE)|G13D(TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NOMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
TWF1	5756	broad.mit.edu	37	12	44191543	44191543	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44191543A>T	uc001rob.2	-	7	728	c.700T>A	c.(700-702)TTG>ATG	p.L234M	TWF1_uc001rnz.2_Missense_Mutation_p.L95M|TWF1_uc001roa.2_Missense_Mutation_p.L227M|TWF1_uc001roc.2_Missense_Mutation_p.L95M	NM_002822	NP_002813	Q12792	TWF1_HUMAN	twinfilin 1	193	ADF-H 2.					actin cytoskeleton|cytoplasm	actin binding|protein tyrosine kinase activity			stomach(1)	1	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)														---	---	---	---
NELL2	4753	broad.mit.edu	37	12	44915909	44915909	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44915909T>C	uc001rog.2	-	18	2644	c.2049A>G	c.(2047-2049)ACA>ACG	p.T683T	NELL2_uc001rof.3_Silent_p.T682T|NELL2_uc001roh.2_Silent_p.T683T|NELL2_uc009zkd.2_Silent_p.T635T|NELL2_uc010skz.1_Silent_p.T733T|NELL2_uc010sla.1_Silent_p.T706T	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	683	VWFC 3.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)														---	---	---	---
DDN	23109	broad.mit.edu	37	12	49391517	49391517	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49391517C>A	uc001rsv.1	-	2	1160	c.1142G>T	c.(1141-1143)TGG>TTG	p.W381L	uc001rsw.2_5'Flank	NM_015086	NP_055901	O94850	DEND_HUMAN	dendrin	381	Interaction with ACTN1.					dendritic spine membrane|endoplasmic reticulum membrane|nucleus|perikaryon				large_intestine(1)	1																		---	---	---	---
GPD1	2819	broad.mit.edu	37	12	50498517	50498517	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50498517A>G	uc001rvz.2	+	2	235	c.202A>G	c.(202-204)AAG>GAG	p.K68E	GPD1_uc010smp.1_Missense_Mutation_p.K68E|GPD1_uc001rwa.2_Missense_Mutation_p.K68E	NM_005276	NP_005267	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	68					glycerol-3-phosphate catabolic process|triglyceride biosynthetic process	cytosol|glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|protein homodimerization activity				0					NADH(DB00157)													---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52094954	52094954	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52094954C>T	uc001ryw.2	+	8	1133	c.955C>T	c.(955-957)CTG>TTG	p.L319L	SCN8A_uc010snl.1_Silent_p.L184L|SCN8A_uc001ryx.1_Silent_p.L184L|SCN8A_uc001ryz.1_Silent_p.L184L|SCN8A_uc001ryy.2_Silent_p.L184L	NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	319	I.				axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
GDF11	10220	broad.mit.edu	37	12	56143376	56143376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56143376C>T	uc001shq.2	+	3	971	c.934C>T	c.(934-936)CGC>TGC	p.R312C	GDF11_uc010spv.1_Missense_Mutation_p.R312C	NM_005811	NP_005802	O95390	GDF11_HUMAN	growth differentiation factor 11 precursor	312					growth|mesoderm development|skeletal system development	extracellular space	cytokine activity|growth factor activity	p.R312H(1)		kidney(1)	1																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56481660	56481660	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56481660C>T	uc001sjh.2	+	6	888	c.695C>T	c.(694-696)GCC>GTC	p.A232V	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.A173V|ERBB3_uc001sji.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	232	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56563427	56563427	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56563427C>A	uc001skb.2	-	24	2614	c.2508G>T	c.(2506-2508)AAG>AAT	p.K836N	SMARCC2_uc001skd.2_Missense_Mutation_p.K867N|SMARCC2_uc001ska.2_Missense_Mutation_p.K867N|SMARCC2_uc001skc.2_Missense_Mutation_p.K866N|SMARCC2_uc010sqf.1_Missense_Mutation_p.K756N	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	836	Glu-rich.				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
SLC39A5	283375	broad.mit.edu	37	12	56629344	56629344	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56629344G>A	uc010sqj.1	+	8	1062	c.805G>A	c.(805-807)GCA>ACA	p.A269T	SLC39A5_uc010sqi.1_Missense_Mutation_p.A160T|SLC39A5_uc010sqk.1_Missense_Mutation_p.A269T	NM_173596	NP_775867	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (metal ion	269	Extracellular (Potential).				zinc ion transport	basolateral plasma membrane|integral to membrane	metal ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
STAT2	6773	broad.mit.edu	37	12	56749230	56749230	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56749230C>T	uc001slc.2	-	5	546	c.468G>A	c.(466-468)ATG>ATA	p.M156I	STAT2_uc001sld.2_Missense_Mutation_p.M152I|STAT2_uc010sqn.1_Missense_Mutation_p.M152I	NM_005419	NP_005410	P52630	STAT2_HUMAN	signal transducer and activator of transcription	156					interspecies interaction between organisms|JAK-STAT cascade|regulation of transcription from RNA polymerase II promoter|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	cytosol|nucleoplasm|plasma membrane	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|lung(1)|kidney(1)	3																		---	---	---	---
INHBE	83729	broad.mit.edu	37	12	57849901	57849901	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57849901T>C	uc001snw.2	+	2	547	c.323T>C	c.(322-324)CTG>CCG	p.L108P		NM_031479	NP_113667	P58166	INHBE_HUMAN	activin beta E precursor	108					growth	extracellular region	growth factor activity|hormone activity			breast(2)|central_nervous_system(1)	3																OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57864396	57864396	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57864396G>A	uc001snx.2	+	12	1951	c.1873G>A	c.(1873-1875)GAG>AAG	p.E625K	GLI1_uc009zpq.2_Missense_Mutation_p.E497K	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	625					epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)															---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57920381	57920381	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57920381C>A	uc001soj.1	+	7	1677	c.1453C>A	c.(1453-1455)CCA>ACA	p.P485T	MBD6_uc001sok.1_Missense_Mutation_p.P352T|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	485	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
FAM119B	25895	broad.mit.edu	37	12	58166907	58166907	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58166907G>A	uc001sqg.2	+	2	410	c.285G>A	c.(283-285)CTG>CTA	p.L95L	METTL1_uc010ssd.1_5'Flank|METTL1_uc009zqc.2_5'Flank|FAM119B_uc001sqf.2_Silent_p.L95L|FAM119B_uc009zqd.2_Intron	NM_015433	NP_056248	Q96AZ1	MT21B_HUMAN	hypothetical protein LOC25895 isoform a	95	Helical; (Potential).					integral to membrane|intracellular	methyltransferase activity				0	all_cancers(7;9.07e-82)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)																	---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64491077	64491077	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64491077G>A	uc010ssp.1	+	15	1791	c.1735G>A	c.(1735-1737)GTT>ATT	p.V579I	SRGAP1_uc001srv.2_Missense_Mutation_p.V516I	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	579	Rho-GAP.				axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812728	64812728	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812728A>G	uc001ssb.2	+	6	769	c.343A>G	c.(343-345)ACA>GCA	p.T115A	XPOT_uc009zqm.1_Missense_Mutation_p.T25A	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	115	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812733	64812733	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812733G>A	uc001ssb.2	+	6	774	c.348G>A	c.(346-348)GAG>GAA	p.E116E	XPOT_uc009zqm.1_Silent_p.E26E	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	116	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812808	64812808	+	Silent	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812808C>G	uc001ssb.2	+	6	849	c.423C>G	c.(421-423)CTC>CTG	p.L141L	XPOT_uc009zqm.1_Silent_p.L51L	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	141	Necessary for interaction with Ran, nuclear localization and nuclear import.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66547166	66547166	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66547166T>C	uc001stc.2	-	2	236	c.160A>G	c.(160-162)ACA>GCA	p.T54A	LLPH_uc010ssx.1_RNA|TMBIM4_uc001std.2_Missense_Mutation_p.T23A|TMBIM4_uc009zqr.2_Missense_Mutation_p.T101A|TMBIM4_uc001ste.2_RNA|TMBIM4_uc001stf.2_Missense_Mutation_p.T54A|TMBIM4_uc009zqs.2_Missense_Mutation_p.T54A	NM_016056	NP_057140	Q9HC24	TMBI4_HUMAN	transmembrane BAX inhibitor motif containing 4	54	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71139707	71139707	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71139707T>C	uc001swi.1	-	6	1314	c.898A>G	c.(898-900)AAT>GAT	p.N300D	PTPRR_uc001swh.1_Missense_Mutation_p.N55D|PTPRR_uc009zrs.2_Missense_Mutation_p.N149D|PTPRR_uc010stq.1_Missense_Mutation_p.N188D|PTPRR_uc010str.1_Missense_Mutation_p.N149D	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	300	Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)														---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71977612	71977612	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71977612G>A	uc001swl.2	+	18	1870	c.1822G>A	c.(1822-1824)GTC>ATC	p.V608I	LGR5_uc001swm.2_Missense_Mutation_p.V584I|LGR5_uc001swn.1_RNA	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	608	Helical; Name=2; (Potential).					integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	72667257	72667257	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72667257G>A	uc001sxa.2	+	1	729	c.699G>A	c.(697-699)CTG>CTA	p.L233L	LOC283392_uc010stv.1_5'UTR	NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	233	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
NAP1L1	4673	broad.mit.edu	37	12	76449858	76449858	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76449858C>T	uc001sxw.2	-	7	925	c.513G>A	c.(511-513)TGG>TGA	p.W171*	NAP1L1_uc001sxv.2_Nonsense_Mutation_p.W129*|NAP1L1_uc001sxz.2_Nonsense_Mutation_p.W102*|NAP1L1_uc001sxx.2_Nonsense_Mutation_p.W171*|NAP1L1_uc001sxy.2_Nonsense_Mutation_p.W108*|NAP1L1_uc010sty.1_Nonsense_Mutation_p.W128*|NAP1L1_uc010stz.1_5'UTR|NAP1L1_uc010sua.1_Nonsense_Mutation_p.W171*|NAP1L1_uc001syb.2_Nonsense_Mutation_p.W171*|NAP1L1_uc001sya.2_Nonsense_Mutation_p.W129*|NAP1L1_uc001syc.2_Nonsense_Mutation_p.W182*	NM_139207	NP_631946	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	171					DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)																---	---	---	---
MYF5	4617	broad.mit.edu	37	12	81110900	81110900	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81110900T>A	uc001szg.2	+	1	193	c.58T>A	c.(58-60)TGC>AGC	p.C20S		NM_005593	NP_005584	P13349	MYF5_HUMAN	myogenic factor 5	20					muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88472895	88472895	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88472895C>T	uc001tar.2	-	39	5682	c.5338G>A	c.(5338-5340)GTT>ATT	p.V1780I	CEP290_uc001taq.2_Missense_Mutation_p.V840I	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1780	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																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95442864	95442864	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95442864C>T	uc001tdm.3	-	9	1367	c.1111G>A	c.(1111-1113)GAT>AAT	p.D371N	NR2C1_uc010suu.1_Missense_Mutation_p.D371N|NR2C1_uc001tdo.3_Missense_Mutation_p.D371N|NR2C1_uc001tdn.3_Missense_Mutation_p.D371N	NM_003297	NP_003288	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	371					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96292234	96292234	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96292234C>A	uc001tek.1	-	7	777	c.543G>T	c.(541-543)CAG>CAT	p.Q181H		NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	181	Potential.									skin(1)	1																		---	---	---	---
APAF1	317	broad.mit.edu	37	12	99076985	99076985	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99076985G>A	uc001tfz.2	+	15	2688	c.2111G>A	c.(2110-2112)TGC>TAC	p.C704Y	APAF1_uc001tfy.2_Missense_Mutation_p.C693Y|APAF1_uc001tga.2_Missense_Mutation_p.C693Y|APAF1_uc001tgb.2_Missense_Mutation_p.C704Y|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Missense_Mutation_p.C113Y	NM_181861	NP_863651	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1 isoform	704	WD 3.				activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
NR1H4	9971	broad.mit.edu	37	12	100957089	100957089	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100957089T>C	uc001tht.1	+	9	1311	c.1283T>C	c.(1282-1284)GTG>GCG	p.V428A	NR1H4_uc001thp.1_Missense_Mutation_p.V414A|NR1H4_uc001thq.1_Missense_Mutation_p.V418A|NR1H4_uc010svj.1_RNA|NR1H4_uc001thr.1_Missense_Mutation_p.V418A|NR1H4_uc010svk.1_Missense_Mutation_p.V367A|NR1H4_uc001ths.1_Missense_Mutation_p.V424A	NM_005123	NP_005114	Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	428	Ligand-binding.				bile acid metabolic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
GAS2L3	283431	broad.mit.edu	37	12	101005888	101005888	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101005888T>C	uc001thu.2	+	6	640	c.414T>C	c.(412-414)GAT>GAC	p.D138D	GAS2L3_uc009zty.2_Silent_p.D138D|GAS2L3_uc001thv.2_Silent_p.D34D	NM_174942	NP_777602	Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	138	CH.				cell cycle arrest					skin(1)	1																		---	---	---	---
IGF1	3479	broad.mit.edu	37	12	102811694	102811694	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102811694C>A	uc001tjp.3	-	4	709	c.490G>T	c.(490-492)GGG>TGG	p.G164W	IGF1_uc001tjn.2_Intron|IGF1_uc001tjm.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111285	NP_001104755	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 3	164					anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104042605	104042605	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104042605C>T	uc001tjw.2	+							NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105538653	105538653	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105538653A>G	uc001tld.2	+						KIAA1033_uc010swr.1_Intron|KIAA1033_uc010sws.1_Intron	NM_015275	NP_056090			hypothetical protein LOC23325						endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
RIC8B	55188	broad.mit.edu	37	12	107254141	107254141	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107254141T>G	uc001tlx.2	+	8	1527	c.1402T>G	c.(1402-1404)TCA>GCA	p.S468A	RIC8B_uc001tlw.2_Missense_Mutation_p.S468A|RIC8B_uc001tly.2_Missense_Mutation_p.S428A|RIC8B_uc001tlz.2_RNA|RIC8B_uc009zur.2_RNA	NM_018157	NP_060627	Q9NVN3	RIC8B_HUMAN	resistance to inhibitors of cholinesterase 8	468					regulation of G-protein coupled receptor protein signaling pathway	cell cortex|cytosol|plasma membrane	G-protein alpha-subunit binding|guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
ISCU	23479	broad.mit.edu	37	12	108958107	108958107	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108958107C>T	uc010sxc.1	+	2	272	c.167C>T	c.(166-168)TCT>TTT	p.S56F	SART3_uc001tmz.1_5'Flank|SART3_uc009zux.1_5'Flank|SART3_uc010swx.1_5'Flank|SART3_uc010swz.1_5'Flank|SART3_uc001tna.1_5'Flank|SART3_uc001tnb.2_5'Flank|ISCU_uc010sxa.1_Missense_Mutation_p.S56F|ISCU_uc010sxb.1_Missense_Mutation_p.S56F|ISCU_uc001tnc.3_Missense_Mutation_p.S31F|ISCU_uc009zuy.2_Missense_Mutation_p.S31F|ISCU_uc010sxd.1_Missense_Mutation_p.S56F	NM_213595	NP_998760	Q9H1K1	ISCU_HUMAN	iron-sulfur cluster assembly enzyme isoform	56					iron-sulfur cluster assembly|nitrogen fixation	cytosol|mitochondrion|nucleus	iron ion binding|iron-sulfur cluster binding|protein complex scaffold				0																		---	---	---	---
TRPV4	59341	broad.mit.edu	37	12	110226433	110226433	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110226433G>A	uc001tpj.1	-	12	2075	c.1980C>T	c.(1978-1980)TGC>TGT	p.C660C	TRPV4_uc001tpg.1_Silent_p.C626C|TRPV4_uc001tph.1_Silent_p.C613C|TRPV4_uc001tpi.1_Silent_p.C553C|TRPV4_uc001tpk.1_Silent_p.C660C|TRPV4_uc001tpl.1_Silent_p.C600C	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	660					actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
VPS29	51699	broad.mit.edu	37	12	110933822	110933822	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110933822C>T	uc001tqy.2	-	2	250	c.190G>A	c.(190-192)GAT>AAT	p.D64N	VPS29_uc001tqw.2_RNA|VPS29_uc001tqx.2_Missense_Mutation_p.D68N|VPS29_uc001tqz.2_RNA	NM_016226	NP_057310	Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 isoform 1	64					protein transport	endosome membrane	metal ion binding|phosphoserine phosphatase activity				0																		---	---	---	---
PLBD2	196463	broad.mit.edu	37	12	113825620	113825620	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113825620C>A	uc001tve.2	+	11	1546	c.1511C>A	c.(1510-1512)GCT>GAT	p.A504D	PLBD2_uc001tvf.2_Missense_Mutation_p.A472D	NM_173542	NP_775813	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2 isoform 1	504					lipid catabolic process	lysosomal lumen	hydrolase activity				0																		---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116428813	116428813	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116428813T>C	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119773072	119773072	+	Splice_Site	SNP	G	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119773072G>C	uc001txe.2	+	1	555	c.90_splice	c.e1+1	p.Q30_splice		NM_178499	NP_848594			coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)														---	---	---	---
UNC119B	84747	broad.mit.edu	37	12	121154782	121154782	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121154782A>G	uc001tyz.2	+	4	1027	c.580A>G	c.(580-582)ATC>GTC	p.I194V		NM_001080533	NP_001074002	A6NIH7	U119B_HUMAN	unc-119 homolog B	194										haematopoietic_and_lymphoid_tissue(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
B3GNT4	79369	broad.mit.edu	37	12	122691078	122691078	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122691078C>T	uc001ubx.2	+	3	498	c.280C>T	c.(280-282)CGT>TGT	p.R94C	B3GNT4_uc001uby.2_Missense_Mutation_p.R69C	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	94	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)														---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122966486	122966486	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122966486T>C	uc001ucn.2	-						ZCCHC8_uc001ucm.2_Intron|ZCCHC8_uc009zxp.2_Intron|ZCCHC8_uc009zxq.2_Intron	NM_017612	NP_060082			zinc finger, CCHC domain containing 8							catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)														---	---	---	---
GPR109A	338442	broad.mit.edu	37	12	123187233	123187233	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123187233G>A	uc001ucx.1	-	1	672	c.598C>T	c.(598-600)CCC>TCC	p.P200S	GPR81_uc001ucw.1_Intron	NM_177551	NP_808219	Q8TDS4	HCAR2_HUMAN	G protein-coupled receptor 109A	200	Helical; Name=5; (Potential).				negative regulation of lipid catabolic process|neutrophil apoptosis|positive regulation of adiponectin secretion|positive regulation of neutrophil apoptosis	integral to membrane|plasma membrane	nicotinic acid receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)													---	---	---	---
SBNO1	55206	broad.mit.edu	37	12	123810084	123810084	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123810084G>A	uc010tap.1	-	14	1938	c.1938C>T	c.(1936-1938)GGC>GGT	p.G646G	SBNO1_uc010tao.1_Silent_p.G645G|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Silent_p.G646G|SBNO1_uc001ueu.2_Silent_p.G645G|SBNO1_uc001uev.2_Silent_p.G644G|SBNO1_uc009zxy.1_Silent_p.G611G	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	646							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124092063	124092063	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124092063G>A	uc001ufi.2	+	4	355	c.331G>A	c.(331-333)GAG>AAG	p.E111K	DDX55_uc001ufh.2_5'UTR|DDX55_uc001ufj.1_Intron|DDX55_uc001ufk.2_5'UTR	NM_020936	NP_065987	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	111	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132446241	132446241	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132446241G>A	uc001ujn.2	+	1	1112	c.1077G>A	c.(1075-1077)CCG>CCA	p.P359P	EP400_uc001ujl.2_Silent_p.P359P|EP400_uc001ujm.2_Silent_p.P359P|EP400_uc001ujj.1_Silent_p.P359P|EP400_uc001ujk.2_Silent_p.P359P	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	359					histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
P2RX2	22953	broad.mit.edu	37	12	133197638	133197638	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133197638G>A	uc001ukj.1	+	8	826	c.826G>A	c.(826-828)GCA>ACA	p.A276T	P2RX2_uc001uki.1_Missense_Mutation_p.A276T|P2RX2_uc001ukk.1_Missense_Mutation_p.A276T|P2RX2_uc001ukl.1_Missense_Mutation_p.A252T|P2RX2_uc001ukm.1_Missense_Mutation_p.A204T|P2RX2_uc001ukn.1_Missense_Mutation_p.A184T|P2RX2_uc009zyt.1_Missense_Mutation_p.A276T|P2RX2_uc001uko.1_Missense_Mutation_p.A242T	NM_170682	NP_733782	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X2 isoform A	276	Extracellular (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|protein homooligomerization	integral to membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20242596	20242596	+	Missense_Mutation	SNP	G	A	A	rs145688067		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20242596G>A	uc001umh.2	+	11	2263	c.2254G>A	c.(2254-2256)GCA>ACA	p.A752T	MPHOSPH8_uc001umg.2_Missense_Mutation_p.A752T	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	752					cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)														---	---	---	---
GJB6	10804	broad.mit.edu	37	13	20797345	20797345	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20797345G>A	uc001umz.3	-	3	828	c.275C>T	c.(274-276)GCC>GTC	p.A92V	GJB6_uc001unc.3_Missense_Mutation_p.A92V|GJB6_uc001una.3_Missense_Mutation_p.A92V|GJB6_uc001und.3_Missense_Mutation_p.A92V|GJB6_uc001unb.3_Missense_Mutation_p.A92V	NM_006783	NP_006774	O95452	CXB6_HUMAN	gap junction protein, beta 6	92	Helical; (Potential).				cell communication|sensory perception of sound	connexon complex|integral to membrane|intracellular membrane-bounded organelle				ovary(1)	1		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)														---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22070218	22070218	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22070218T>C	uc001uof.2	-	10	1037	c.1015A>G	c.(1015-1017)AGT>GGT	p.S339G	EFHA1_uc010tct.1_Missense_Mutation_p.S129G	NM_152726	NP_689939	Q8IYU8	EFHA1_HUMAN	EF-hand domain family, member A1	339							calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)														---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23824814	23824814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23824814G>A	uc001uom.2	+	4	498	c.343G>A	c.(343-345)GCG>ACG	p.A115T	SGCG_uc009zzv.2_Missense_Mutation_p.A115T|SGCG_uc009zzw.2_Missense_Mutation_p.A115T	NM_000231	NP_000222	Q13326	SGCG_HUMAN	gamma sarcoglycan	115	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)														---	---	---	---
C1QTNF9	338872	broad.mit.edu	37	13	24890284	24890284	+	Missense_Mutation	SNP	C	T	T	rs143537751		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24890284C>T	uc001upj.2	+	2	204	c.143C>T	c.(142-144)GCG>GTG	p.A48V	C1QTNF9_uc001upe.2_RNA	NM_178540	NP_848635	P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	48	Collagen-like 1.					collagen	hormone activity				0		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)														---	---	---	---
ATP12A	479	broad.mit.edu	37	13	25262595	25262595	+	Missense_Mutation	SNP	G	A	A	rs149324896		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25262595G>A	uc001upp.2	+	4	554	c.367G>A	c.(367-369)GCC>ACC	p.A123T	ATP12A_uc010aaa.2_Missense_Mutation_p.A123T	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A	123	Helical; (Potential).				ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)													---	---	---	---
ATP12A	479	broad.mit.edu	37	13	25264616	25264616	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25264616C>T	uc001upp.2	+						ATP12A_uc010aaa.2_Intron	NM_001676	NP_001667			hydrogen/potassium-exchanging ATPase 12A						ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)													---	---	---	---
GSX1	219409	broad.mit.edu	37	13	28367816	28367816	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28367816C>T	uc001urr.1	+	2	574	c.526C>T	c.(526-528)CGT>TGT	p.R176C		NM_145657	NP_663632	Q9H4S2	GSX1_HUMAN	GS homeobox 1	176	Homeobox.				positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28834653	28834653	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28834653G>A	uc001urz.2	+	7	888	c.880G>A	c.(880-882)GCA>ACA	p.A294T	PAN3_uc010tdo.1_Missense_Mutation_p.A440T|PAN3_uc001ury.2_Missense_Mutation_p.A128T|PAN3_uc001urx.2_Missense_Mutation_p.A240T	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	440	Interaction with polyadenylate-binding protein.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32366011	32366011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32366011G>A	uc001utt.2	+	15	1285	c.1214G>A	c.(1213-1215)GGC>GAC	p.G405D	RXFP2_uc010aba.2_Missense_Mutation_p.G364D	NM_130806	NP_570718	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	405	Extracellular (Potential).					integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)														---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33012780	33012780	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33012780C>T	uc010abe.1	-						N4BP2L2_uc001uug.2_Intron|N4BP2L2_uc010abd.1_Intron|N4BP2L2_uc001uuh.2_Intron|N4BP2L2_uc001uuj.2_Intron|N4BP2L2_uc010tdz.1_Intron	NM_033111	NP_149102			phosphonoformate immuno-associated protein 5												0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)														---	---	---	---
SPG20	23111	broad.mit.edu	37	13	36909438	36909438	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36909438T>C	uc001uvn.2	-	3	800	c.530A>G	c.(529-531)CAA>CGA	p.Q177R	SPG20_uc010ten.1_Missense_Mutation_p.Q177R|SPG20_uc001uvm.2_Missense_Mutation_p.Q177R|SPG20_uc001uvo.2_Missense_Mutation_p.Q177R|SPG20_uc001uvq.2_Missense_Mutation_p.Q177R|SPG20_uc001uvp.2_Missense_Mutation_p.Q177R	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	177					cell death	cytoplasm	ubiquitin protein ligase binding				0		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39587850	39587850	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39587850T>C	uc001uwy.2	-	11	2412	c.1539A>G	c.(1537-1539)TCA>TCG	p.S513S	C13orf23_uc001uwz.2_Silent_p.S491S	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	513	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
NAA16	79612	broad.mit.edu	37	13	41943312	41943312	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41943312C>T	uc001uyf.2	+	15	2164	c.1840C>T	c.(1840-1842)CAT>TAT	p.H614Y	NAA16_uc010tfg.1_RNA	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform	614					N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1																		---	---	---	---
TPT1	7178	broad.mit.edu	37	13	45911676	45911676	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45911676T>C	uc001uzy.1	-						TPT1_uc001uzz.1_Intron|SNORA31_uc001vaa.1_RNA	NM_003295	NP_003286			tumor protein, translationally-controlled 1						anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)														---	---	---	---
TPT1	7178	broad.mit.edu	37	13	45914128	45914128	+	Splice_Site	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45914128C>A	uc001uzy.1	-	3	386	c.293_splice	c.e3+1	p.S98_splice	TPT1_uc001uzz.1_Splice_Site_p.S64_splice|SNORA31_uc001vaa.1_5'Flank|LOC100190939_uc010tfr.1_5'Flank|LOC100190939_uc001vac.2_5'Flank	NM_003295	NP_003286			tumor protein, translationally-controlled 1						anti-apoptosis|response to virus	extracellular space|multivesicular body	calcium ion binding|protein binding				0		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000232)														---	---	---	---
NEK5	341676	broad.mit.edu	37	13	52639595	52639595	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52639595C>T	uc001vge.2	-	22	2215	c.2075G>A	c.(2074-2076)CGT>CAT	p.R692H		NM_199289	NP_954983	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	692							ATP binding|metal ion binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)	1		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)														---	---	---	---
SUGT1	10910	broad.mit.edu	37	13	53239778	53239778	+	Silent	SNP	C	T	T	rs148803576		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53239778C>T	uc001vhc.2	+	10	750	c.525C>T	c.(523-525)GAC>GAT	p.D175D	SUGT1_uc001vha.2_RNA|SUGT1_uc001vhb.2_Silent_p.D143D|SUGT1_uc010thb.1_Silent_p.D87D|SUGT1_uc001vhd.2_Silent_p.D32D	NM_001130912	NP_001124384	Q9Y2Z0	SUGT1_HUMAN	suppressor of G2 allele of SKP1 isoform a	175	CS.				mitosis	kinetochore|ubiquitin ligase complex	binding				0		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.25e-08)														---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58208795	58208795	+	Silent	SNP	G	A	A	rs79688799	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58208795G>A	uc001vhq.1	+	1	3007	c.2115G>A	c.(2113-2115)TCG>TCA	p.S705S	PCDH17_uc010aec.1_Silent_p.S705S	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	705	Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60413550	60413550	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60413550G>A	uc001vht.2	-	23	2989	c.2770C>T	c.(2770-2772)CAG>TAG	p.Q924*	DIAPH3_uc001vhu.2_Nonsense_Mutation_p.Q661*	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	924	FH2.				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)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60566595	60566595	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60566595C>T	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.2_5'Flank|DIAPH3_uc001vhw.1_Intron|DIAPH3_uc010aed.1_Intron|DIAPH3_uc010aee.1_Intron	NM_001042517	NP_001035982			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)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60737769	60737769	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60737769A>G	uc001vht.2	-	1	351	c.132T>C	c.(130-132)CCT>CCC	p.P44P	DIAPH3_uc001vhw.1_Silent_p.P44P|DIAPH3_uc010aed.1_Silent_p.P44P|DIAPH3_uc010aee.1_Silent_p.P44P	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	44					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)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67802393	67802393	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67802393G>A	uc001vik.2	-	2	872	c.180C>T	c.(178-180)GCC>GCT	p.A60A	PCDH9_uc001vil.2_Silent_p.A60A|PCDH9_uc010thl.1_Silent_p.A60A|PCDH9_uc001vin.3_Silent_p.A60A	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	60	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
C13orf34	79866	broad.mit.edu	37	13	73327858	73327858	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73327858G>T	uc001viv.1	+	11	1632	c.1513G>T	c.(1513-1515)GGA>TGA	p.G505*	C13orf34_uc010aen.1_Nonsense_Mutation_p.G580*|C13orf34_uc010thr.1_Nonsense_Mutation_p.G435*|C13orf34_uc001viw.1_Nonsense_Mutation_p.G454*	NM_024808	NP_079084	Q6PGQ7	BORA_HUMAN	aurora borealis	505					cell division|mitosis|regulation of mitosis|regulation of mitotic spindle organization|regulation of protein localization		protein kinase binding				0		Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.000227)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76210812	76210812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76210812G>A	uc001vjt.1	+	1	354	c.19G>A	c.(19-21)GCA>ACA	p.A7T	LMO7_uc010thv.1_Intron	NM_005358	NP_005349	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 1	Error:Variant_position_missing_in_Q8WWI1_after_alignment						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77657276	77657276	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77657276C>T	uc001vkf.2	-	64	10904	c.10813G>A	c.(10813-10815)GGG>AGG	p.G3605R	MYCBP2_uc010aev.2_Missense_Mutation_p.G3009R|MYCBP2_uc001vke.2_Missense_Mutation_p.G225R	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3605					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
SLITRK6	84189	broad.mit.edu	37	13	86370288	86370288	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86370288A>T	uc001vll.1	-	2	815	c.356T>A	c.(355-357)ATC>AAC	p.I119N	SLITRK6_uc010afe.1_5'Flank	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	119	Extracellular (Potential).|LRR 2.					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)														---	---	---	---
GPC5	2262	broad.mit.edu	37	13	93518632	93518632	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93518632G>A	uc010tif.1	+	8	2025	c.1659G>A	c.(1657-1659)GCG>GCA	p.A553A		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	553						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103257246	103257246	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103257246T>G	uc001vpi.3	+	2	372	c.269T>G	c.(268-270)GTT>GGT	p.V90G		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	90					proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110835372	110835372	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110835372C>T	uc001vqw.3	-	28	2185	c.2063G>A	c.(2062-2064)GGC>GAC	p.G688D	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	688	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111117854	111117854	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111117854G>A	uc001vqx.2	+	25	2168	c.1879G>A	c.(1879-1881)GGC>AGC	p.G627S		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	627	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111926266	111926266	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111926266T>C	uc001vrs.2	+	11	1492	c.1242T>C	c.(1240-1242)CCT>CCC	p.P414P	ARHGEF7_uc001vrr.2_Silent_p.P393P|ARHGEF7_uc001vrt.2_Silent_p.P364P|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Silent_p.P236P|ARHGEF7_uc001vrv.3_Silent_p.P236P|ARHGEF7_uc001vrw.3_Silent_p.P236P|ARHGEF7_uc001vrx.3_Silent_p.P236P|ARHGEF7_uc010tjo.1_Silent_p.P311P|ARHGEF7_uc010tjp.1_Silent_p.P158P|ARHGEF7_uc010agn.1_Silent_p.P158P	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	414	DH.				apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113477733	113477733	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113477733T>C	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc001vsm.1_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
GAS6	2621	broad.mit.edu	37	13	114526521	114526521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114526521G>A	uc001vud.2	-	13	1633	c.1480C>T	c.(1480-1482)CGG>TGG	p.R494W	GAS6_uc001vug.2_Missense_Mutation_p.R195W|GAS6_uc001vuf.2_Missense_Mutation_p.R221W	NM_000820	NP_000811	Q14393	GAS6_HUMAN	growth arrest-specific 6 isoform 1 precursor	537	Laminin G-like 2.				cell proliferation|leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|post-translational protein modification|proteolysis|regulation of growth	endoplasmic reticulum lumen|extracellular space|Golgi lumen|platelet alpha granule lumen	calcium ion binding|receptor agonist activity			central_nervous_system(4)	4	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)																---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20853225	20853225	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20853225A>G	uc001vxe.2	-	21	3066	c.3026T>C	c.(3025-3027)GTG>GCG	p.V1009A	TEP1_uc010ahk.2_Missense_Mutation_p.V359A|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Missense_Mutation_p.V901A|TEP1_uc010tlh.1_5'Flank	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1009					telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20871992	20871992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20871992G>A	uc001vxe.2	-	6	1124	c.1084C>T	c.(1084-1086)CGT>TGT	p.R362C	TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	362	TROVE.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
SALL2	6297	broad.mit.edu	37	14	21993076	21993076	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21993076A>G	uc001wbe.2	-	2	1068	c.786T>C	c.(784-786)TCT>TCC	p.S262S	SALL2_uc010tly.1_Silent_p.S260S|SALL2_uc010tlz.1_Intron|SALL2_uc001wbf.3_Intron|SALL2_uc010tma.1_Intron|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	262	Poly-Ser.						DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)														---	---	---	---
RBM23	55147	broad.mit.edu	37	14	23374162	23374162	+	Silent	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23374162T>A	uc001whg.2	-	9	985	c.786A>T	c.(784-786)CCA>CCT	p.P262P	RBM23_uc001whh.2_Silent_p.P246P|RBM23_uc001whi.2_Silent_p.P228P|RBM23_uc010tne.1_Silent_p.P92P|RBM23_uc001whj.2_Silent_p.P12P|RBM23_uc001whk.1_Silent_p.P262P	NM_001077351	NP_001070819	Q86U06	RBM23_HUMAN	RNA binding motif protein 23 isoform 1	262					mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)														---	---	---	---
MYH7	4625	broad.mit.edu	37	14	23902741	23902741	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23902741C>A	uc001wjx.2	-	3	307	c.201G>T	c.(199-201)AAG>AAT	p.K67N		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	67	Myosin head-like.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)														---	---	---	---
PCK2	5106	broad.mit.edu	37	14	24572963	24572963	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24572963A>G	uc001wlt.2	+	10	1845	c.1713A>G	c.(1711-1713)ACA>ACG	p.T571T	NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_Intron|PCK2_uc010tnw.1_Silent_p.T437T|PCK2_uc010tnx.1_Silent_p.T437T|PCK2_uc001wlu.3_Silent_p.T405T	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase	571					gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
FOXG1	2290	broad.mit.edu	37	14	29237047	29237047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29237047G>A	uc001wqe.2	+	1	761	c.562G>A	c.(562-564)GCG>ACG	p.A188T		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	188	Fork-head.				axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)														---	---	---	---
PPP2R3C	55012	broad.mit.edu	37	14	35564337	35564337	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35564337G>A	uc001wss.2	-	10	1246	c.892C>T	c.(892-894)CTC>TTC	p.L298F	PPP2R3C_uc001wst.2_Missense_Mutation_p.L182F|PPP2R3C_uc010tpr.1_Missense_Mutation_p.L182F|PPP2R3C_uc001wsu.2_Intron	NM_017917	NP_060387	Q969Q6	P2R3C_HUMAN	serine/threonine-protein phosphatase 2A	298	EF-hand 1.					centrosome|nucleus	calcium ion binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)														---	---	---	---
SSTR1	6751	broad.mit.edu	37	14	38678777	38678777	+	Silent	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38678777C>A	uc001wul.1	+	3	800	c.183C>A	c.(181-183)ATC>ATA	p.I61I	SSTR1_uc010amu.1_Intron	NM_001049	NP_001040	P30872	SSR1_HUMAN	somatostatin receptor 1	61	Helical; Name=1; (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity			central_nervous_system(3)|ovary(1)|lung(1)	5	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)													---	---	---	---
CDKL1	8814	broad.mit.edu	37	14	50846843	50846843	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50846843C>A	uc010anu.1	-	8	1078	c.1078G>T	c.(1078-1080)GGT>TGT	p.G360C	CDKL1_uc001wxz.2_Intron	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	Error:Variant_position_missing_in_Q00532_after_alignment						cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)																	---	---	---	---
NIN	51199	broad.mit.edu	37	14	51192775	51192775	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51192775C>T	uc001wym.2	-	30	6279	c.6088G>A	c.(6088-6090)GAA>AAA	p.E2030K	NIN_uc001wyi.2_Missense_Mutation_p.E2030K|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Missense_Mutation_p.E1317K|NIN_uc010tqp.1_Missense_Mutation_p.E2036K	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	2030	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
NIN	51199	broad.mit.edu	37	14	51219236	51219236	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51219236C>T	uc001wym.2	-	21	5141	c.4950G>A	c.(4948-4950)CAG>CAA	p.Q1650Q	NIN_uc001wyi.2_Silent_p.Q1650Q|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Silent_p.Q937Q|NIN_uc010tqp.1_Silent_p.Q1656Q|NIN_uc001wyo.2_Silent_p.Q1650Q	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	1650	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51561483	51561483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51561483C>T	uc001wyx.3	-	1	940	c.175G>A	c.(175-177)GAC>AAC	p.D59N	TRIM9_uc001wyy.2_Missense_Mutation_p.D59N|TRIM9_uc001wyz.3_Missense_Mutation_p.D59N	NM_015163	NP_055978	Q9C026	TRIM9_HUMAN	tripartite motif protein 9 isoform 1	59					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)																	---	---	---	---
C14orf166	51637	broad.mit.edu	37	14	52466489	52466489	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52466489A>G	uc010aod.2	+	5	567	c.437A>G	c.(436-438)CAT>CGT	p.H146R	C14orf166_uc001wzm.3_Missense_Mutation_p.H12R|C14orf166_uc001wzn.3_Missense_Mutation_p.H12R	NM_016039	NP_057123	Q9Y224	CN166_HUMAN	homeobox prox 1	146						microtubule organizing center|nucleus|perinuclear region of cytoplasm|tRNA-splicing ligase complex	identical protein binding				0	Breast(41;0.0639)|all_epithelial(31;0.101)																	---	---	---	---
BMP4	652	broad.mit.edu	37	14	54417278	54417278	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54417278C>T	uc001xal.3	-	3	886	c.699G>A	c.(697-699)GGG>GGA	p.G233G	BMP4_uc010aoh.2_Silent_p.G233G|BMP4_uc001xao.3_Silent_p.G233G|BMP4_uc001xan.3_Silent_p.G233G	NM_130851	NP_570912	P12644	BMP4_HUMAN	bone morphogenetic protein 4 preproprotein	233					activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway	extracellular space|proteinaceous extracellular matrix	BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity				0																		---	---	---	---
BMP4	652	broad.mit.edu	37	14	54418933	54418933	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54418933G>T	uc001xal.3	-	2	195	c.8C>A	c.(7-9)CCT>CAT	p.P3H	BMP4_uc010aoh.2_Missense_Mutation_p.P3H|BMP4_uc001xao.3_Missense_Mutation_p.P3H|BMP4_uc001xan.3_Missense_Mutation_p.P3H	NM_130851	NP_570912	P12644	BMP4_HUMAN	bone morphogenetic protein 4 preproprotein	3					activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway	extracellular space|proteinaceous extracellular matrix	BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity				0																		---	---	---	---
C14orf105	55195	broad.mit.edu	37	14	57960431	57960431	+	Missense_Mutation	SNP	C	A	A	rs117025852	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57960431C>A	uc001xcy.2	-	1	146	c.3G>T	c.(1-3)ATG>ATT	p.M1I	C14orf105_uc010trl.1_Missense_Mutation_p.M1I|C14orf105_uc010trm.1_5'UTR|C14orf105_uc010trn.1_5'UTR|C14orf105_uc001xcz.2_Missense_Mutation_p.M1I|C14orf105_uc010aox.1_RNA|C14orf105_uc010aoy.1_5'UTR	NM_018168	NP_060638	Q9NVL8	CN105_HUMAN	hypothetical protein LOC55195	1											0																		---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60591468	60591468	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60591468A>G	uc001xer.3	+	8	2399	c.1877A>G	c.(1876-1878)CAG>CGG	p.Q626R	C14orf135_uc001xeq.2_Missense_Mutation_p.Q626R|C14orf135_uc010apm.2_RNA	NM_022495	NP_071940	Q63HM2	CN135_HUMAN	hepatitis C virus F protein-binding protein 2	860						integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	62016477	62016477	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62016477G>T	uc001xfn.2	+	14	2285	c.1980G>T	c.(1978-1980)GAG>GAT	p.E660D	PRKCH_uc010tsa.1_Missense_Mutation_p.E499D|PRKCH_uc010tsb.1_Missense_Mutation_p.E228D|PRKCH_uc001xfo.2_RNA	NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta	660	AGC-kinase C-terminal.				intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63863413	63863413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63863413C>T	uc001xgd.1	-	6	1161	c.571G>A	c.(571-573)GAA>AAA	p.E191K	PPP2R5E_uc010tsf.1_Missense_Mutation_p.E115K|PPP2R5E_uc010tsg.1_Missense_Mutation_p.E115K|PPP2R5E_uc001xge.2_Missense_Mutation_p.E191K|PPP2R5E_uc010tsh.1_Missense_Mutation_p.E191K|PPP2R5E_uc001xgf.1_RNA	NM_006246	NP_006237	Q16537	2A5E_HUMAN	epsilon isoform of regulatory subunit B56,	191					signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
SGPP1	81537	broad.mit.edu	37	14	64165381	64165381	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64165381A>G	uc001xgj.2	-							NM_030791	NP_110418			sphingosine-1-phosphate phosphatase 1							endoplasmic reticulum membrane|integral to membrane	dihydrosphingosine-1-phosphate phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)														---	---	---	---
TMEM229B	161145	broad.mit.edu	37	14	67940214	67940214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67940214G>A	uc001xjk.2	-	3	837	c.427C>T	c.(427-429)CGC>TGC	p.R143C	TMEM229B_uc001xjj.1_RNA	NM_182526	NP_872332	Q8NBD8	T229B_HUMAN	transmembrane protein 229B	143	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(1)	1																		---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71455319	71455319	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71455319C>T	uc001xmo.2	+	7	2793	c.2347C>T	c.(2347-2349)CGT>TGT	p.R783C	PCNX_uc001xmn.3_Missense_Mutation_p.R783C|PCNX_uc010are.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	783						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72055785	72055785	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72055785G>A	uc001xms.2	+	2	1544	c.1196G>A	c.(1195-1197)AGC>AAC	p.S399N	SIPA1L1_uc001xmt.2_Missense_Mutation_p.S399N|SIPA1L1_uc001xmu.2_Missense_Mutation_p.S399N|SIPA1L1_uc001xmv.2_Missense_Mutation_p.S399N	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	399					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73566386	73566386	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73566386T>A	uc001xno.2	+	9	1003	c.795T>A	c.(793-795)AAT>AAA	p.N265K	RBM25_uc001xnn.3_Missense_Mutation_p.N265K|RBM25_uc010ttu.1_Missense_Mutation_p.N265K|RBM25_uc001xnp.2_Missense_Mutation_p.N60K	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	265					apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
C14orf43	91748	broad.mit.edu	37	14	74203800	74203800	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74203800G>A	uc001xot.2	-	3	2433	c.1650C>T	c.(1648-1650)GAC>GAT	p.D550D	C14orf43_uc001xou.2_Silent_p.D550D|C14orf43_uc010tud.1_Silent_p.D550D|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	550					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75139565	75139565	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75139565A>G	uc001xqb.2	-	11	1896	c.1391T>C	c.(1390-1392)CTG>CCG	p.L464P	KIAA0317_uc010tut.1_Missense_Mutation_p.L303P|KIAA0317_uc001xqc.2_Missense_Mutation_p.L464P	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	464					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86087980	86087980	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86087980G>A	uc001xvr.2	+	2	889	c.122G>A	c.(121-123)CGC>CAC	p.R41H	FLRT2_uc010atd.2_Missense_Mutation_p.R41H	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	41	Extracellular (Potential).|LRRNT.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91780228	91780228	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91780228G>A	uc010aty.2	-	15	2031	c.1932C>T	c.(1930-1932)AAC>AAT	p.N644N		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	644	Potential.				microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92406952	92406952	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92406952G>A	uc001xzx.3	-	3	554	c.81C>T	c.(79-81)TGC>TGT	p.C27C	FBLN5_uc010aud.2_Silent_p.C32C|FBLN5_uc010aue.2_Silent_p.C27C	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor	27					cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)																---	---	---	---
LGMN	5641	broad.mit.edu	37	14	93176196	93176196	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93176196T>G	uc001yav.2	-	12	1167	c.841A>C	c.(841-843)ATG>CTG	p.M281L	LGMN_uc001yat.2_Missense_Mutation_p.M281L|LGMN_uc001yau.2_Missense_Mutation_p.M281L|LGMN_uc001yaw.2_Missense_Mutation_p.M281L|LGMN_uc010aul.2_Missense_Mutation_p.M162L|LGMN_uc001yax.2_Missense_Mutation_p.M281L|LGMN_uc001yay.2_Missense_Mutation_p.M281L	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein	281					hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)														---	---	---	---
SERPINA6	866	broad.mit.edu	37	14	94780499	94780499	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94780499A>G	uc001ycv.2	-	2	591	c.487T>C	c.(487-489)TGG>CGG	p.W163R	SERPINA6_uc010auv.2_RNA	NM_001756	NP_001747	P08185	CBG_HUMAN	corticosteroid binding globulin precursor	163					regulation of proteolysis|transport	extracellular space	serine-type endopeptidase inhibitor activity|steroid binding			skin(3)|ovary(1)|central_nervous_system(1)	5		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)													---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99871571	99871571	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99871571G>T	uc001ygc.2	-	10	1232	c.1062C>A	c.(1060-1062)GCC>GCA	p.A354A		NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	354					peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)																---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102695911	102695911	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102695911C>T	uc001ylm.2	-	11	1291	c.1065G>A	c.(1063-1065)TCG>TCA	p.S355S	RAGE_uc010txv.1_Silent_p.S325S|RAGE_uc001yln.2_Silent_p.S173S|RAGE_uc001ylh.2_Intron|RAGE_uc001yli.2_RNA|RAGE_uc001yll.2_RNA|RAGE_uc001ylj.2_RNA|RAGE_uc001ylk.2_RNA	NM_014226	NP_055041	Q9UQ07	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase	355					signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
TNFAIP2	7127	broad.mit.edu	37	14	103601572	103601572	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103601572G>A	uc001ymm.1	+	11	1971	c.1840G>A	c.(1840-1842)GCT>ACT	p.A614T	TNFAIP2_uc010awo.1_Missense_Mutation_p.A274T|TNFAIP2_uc010txz.1_Missense_Mutation_p.A283T|TNFAIP2_uc010tya.1_Missense_Mutation_p.A97T	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	614					angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)															---	---	---	---
TDRD9	122402	broad.mit.edu	37	14	104482383	104482383	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104482383G>A	uc001yom.3	+	22	2319	c.2289G>A	c.(2287-2289)GCG>GCA	p.A763A	TDRD9_uc001yon.3_Silent_p.A501A	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	763					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding	p.A478A(1)		ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)																---	---	---	---
PACS2	23241	broad.mit.edu	37	14	105833659	105833659	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105833659C>A	uc001yqt.2	+	5	708	c.533C>A	c.(532-534)CCC>CAC	p.P178H	PACS2_uc001yqs.2_Missense_Mutation_p.P111H|PACS2_uc001yqv.2_Missense_Mutation_p.P178H|PACS2_uc001yqu.2_Missense_Mutation_p.P178H	NM_015197	NP_056012	Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	178					apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)														---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25953366	25953366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25953366C>T	uc010ayu.2	-	11	2532	c.2426G>A	c.(2425-2427)CGC>CAC	p.R809H		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	809	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28277199	28277199	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28277199A>G	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266			oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										Oculocutaneous_Albinism				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28421604	28421604	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28421604G>A	uc001zbj.2	-	63	9762	c.9656C>T	c.(9655-9657)GCG>GTG	p.A3219V		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3219	RCC1 10.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31819407	31819407	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31819407G>A	uc001zfq.2	-	5	850	c.757C>T	c.(757-759)CAG>TAG	p.Q253*	OTUD7A_uc001zfr.2_Nonsense_Mutation_p.Q253*	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	253	OTU.|Catalytic (By similarity).|TRAF-binding (By similarity).					cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
AVEN	57099	broad.mit.edu	37	15	34159951	34159951	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34159951G>C	uc001zhj.2	-	5	774	c.718C>G	c.(718-720)CCC>GCC	p.P240A		NM_020371	NP_065104	Q9NQS1	AVEN_HUMAN	cell death regulator aven	240					anti-apoptosis|apoptosis	endomembrane system|intracellular|membrane|membrane fraction	protein binding			kidney(1)	1		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)														---	---	---	---
C15orf55	256646	broad.mit.edu	37	15	34648763	34648763	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34648763C>T	uc001zif.2	+	7	2625	c.2470C>T	c.(2470-2472)CAG>TAG	p.Q824*	C15orf55_uc010ucc.1_Nonsense_Mutation_p.Q852*|C15orf55_uc010ucd.1_Nonsense_Mutation_p.Q842*	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	824						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)				T	BRD3|BRD4	lethal midline carcinoma								---	---	---	---
RTF1	23168	broad.mit.edu	37	15	41772868	41772868	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41772868C>T	uc001zny.2	+	18	2128	c.2116C>T	c.(2116-2118)CGA>TGA	p.R706*		NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component	706					histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	41988756	41988756	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41988756T>C	uc001zog.1	+	3	1639	c.1548T>C	c.(1546-1548)AAT>AAC	p.N516N	MGA_uc010ucy.1_Silent_p.N516N|MGA_uc010ucz.1_Silent_p.N516N	NM_001080541	NP_001074010	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 2	516						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
ZSCAN29	146050	broad.mit.edu	37	15	43661966	43661966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43661966G>A	uc001zrk.1	-	1	293	c.146C>T	c.(145-147)CCG>CTG	p.P49L	ZSCAN29_uc001zrj.1_5'Flank|ZSCAN29_uc010bdf.1_Missense_Mutation_p.P48L|ZSCAN29_uc001zrl.1_RNA|ZSCAN29_uc010bdg.1_Missense_Mutation_p.P48L|ZSCAN29_uc001zrm.2_Missense_Mutation_p.P48L|TUBGCP4_uc001zrn.2_5'Flank|TUBGCP4_uc001zro.2_5'Flank	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	49	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)														---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45402837	45402837	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45402837C>T	uc010bea.2	-						DUOX2_uc001zun.2_Intron	NM_014080	NP_054799			dual oxidase 2 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)														---	---	---	---
FBN1	2200	broad.mit.edu	37	15	48741074	48741074	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48741074T>G	uc001zwx.1	-	46	5890	c.5562A>C	c.(5560-5562)CAA>CAC	p.Q1854H	FBN1_uc010beo.1_RNA	NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1854	EGF-like 31; calcium-binding.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)														---	---	---	---
ONECUT1	3175	broad.mit.edu	37	15	53081051	53081051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53081051C>T	uc002aci.1	-	1	1159	c.1031G>A	c.(1030-1032)CGG>CAG	p.R344Q		NM_004498	NP_004489	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	344	CUT.				endocrine pancreas development	nucleus	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding				0				all cancers(107;0.0708)														---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57545469	57545469	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57545469A>G	uc002aec.2	+	15	1482	c.1198A>G	c.(1198-1200)ATG>GTG	p.M400V	TCF12_uc010ugm.1_Missense_Mutation_p.M452V|TCF12_uc010ugn.1_Missense_Mutation_p.M420V|TCF12_uc002aea.2_Missense_Mutation_p.M424V|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Missense_Mutation_p.M424V|TCF12_uc002aed.2_Missense_Mutation_p.M400V|TCF12_uc002aee.2_Missense_Mutation_p.M230V|TCF12_uc010bft.2_Missense_Mutation_p.M254V|TCF12_uc010ugo.1_Missense_Mutation_p.M164V|TCF12_uc010ugp.1_Missense_Mutation_p.M58V|TCF12_uc010ugq.1_Missense_Mutation_p.M34V|TCF12_uc010ugr.1_Missense_Mutation_p.M13V	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	400					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58285256	58285256	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58285256G>A	uc002aex.2	-	6	629	c.571C>T	c.(571-573)CTG>TTG	p.L191L	ALDH1A2_uc002aey.2_Silent_p.L191L|ALDH1A2_uc010ugv.1_Silent_p.L170L|ALDH1A2_uc010ugw.1_Silent_p.L162L|ALDH1A2_uc002aew.2_Silent_p.L95L	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	191					negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
GCNT3	9245	broad.mit.edu	37	15	59911456	59911456	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59911456G>A	uc002age.2	+	3	1468	c.1019G>A	c.(1018-1020)CGG>CAG	p.R340Q	GCNT3_uc002agd.2_Missense_Mutation_p.R340Q	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	340	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|membrane fraction	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62994288	62994288	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62994288C>T	uc002alb.3	+	15	1794	c.1794C>T	c.(1792-1794)GCC>GCT	p.A598A		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	598					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
IGDCC4	57722	broad.mit.edu	37	15	65677433	65677433	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65677433G>T	uc002aou.1	-	19	3411	c.3201C>A	c.(3199-3201)AGC>AGA	p.S1067R	IGDCC4_uc002aot.1_Missense_Mutation_p.S655R	NM_020962	NP_066013	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member	1067	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3																OREG0023195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC24A1	9187	broad.mit.edu	37	15	65946296	65946296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65946296C>T	uc010ujf.1	+	10	3466	c.3179C>T	c.(3178-3180)GCG>GTG	p.A1060V	SLC24A1_uc010uje.1_Intron|SLC24A1_uc010ujg.1_Missense_Mutation_p.A1030V|SLC24A1_uc010ujh.1_Missense_Mutation_p.A1042V|SLC24A1_uc010uji.1_Missense_Mutation_p.A387V	NM_004727	NP_004718	O60721	NCKX1_HUMAN	solute carrier family 24	1060	Helical; (Potential).				response to light intensity|visual perception	integral to plasma membrane|membrane fraction|outer membrane	calcium, potassium:sodium antiporter activity|protein binding|symporter activity				0																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68617468	68617468	+	Splice_Site	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68617468C>T	uc002ari.2	-	18	2409	c.2322_splice	c.e18+1	p.S774_splice	ITGA11_uc010bib.2_Splice_Site_p.S774_splice	NM_001004439	NP_001004439			integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)													---	---	---	---
NOX5	79400	broad.mit.edu	37	15	69329504	69329504	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69329504G>A	uc002ars.1	+	8	1345	c.1325G>A	c.(1324-1326)CGC>CAC	p.R442H	NOX5_uc002arp.1_Missense_Mutation_p.R424H|NOX5_uc002arq.1_Missense_Mutation_p.R396H|NOX5_uc010bid.1_Missense_Mutation_p.R407H|NOX5_uc002arr.1_Missense_Mutation_p.R414H|NOX5_uc010bie.1_Missense_Mutation_p.R242H|NOX5_uc010bif.1_RNA	NM_024505	NP_078781	Q96PH1	NOX5_HUMAN	NADPH oxidase, EF-hand calcium binding domain 5	442	FAD-binding FR-type.|Helical; (Potential).				angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2																		---	---	---	---
GLCE	26035	broad.mit.edu	37	15	69548140	69548140	+	5'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69548140C>T	uc002ary.1	+	3						NM_015554	NP_056369			D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2																		---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71193355	71193355	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71193355C>T	uc002asw.2	+	4	535	c.288C>T	c.(286-288)AGC>AGT	p.S96S	LRRC49_uc002asu.2_Silent_p.S86S|LRRC49_uc002asx.2_Silent_p.S52S|LRRC49_uc010ukf.1_Silent_p.S101S|LRRC49_uc002asy.2_5'UTR|LRRC49_uc002asz.2_Silent_p.S68S	NM_017691	NP_060161	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	96						cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73470705	73470705	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73470705T>C	uc002avm.3	+	7	1370	c.1228T>C	c.(1228-1230)TGC>CGC	p.C410R	NEO1_uc010ukx.1_Missense_Mutation_p.C410R|NEO1_uc010uky.1_Missense_Mutation_p.C410R|NEO1_uc010ukz.1_5'UTR|NEO1_uc002avn.3_Missense_Mutation_p.C55R	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	410	Extracellular (Potential).|Ig-like C2-type 4.				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73594972	73594972	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73594972C>T	uc002avm.3	+	29	4463	c.4321C>T	c.(4321-4323)CTG>TTG	p.L1441L	NEO1_uc010ukx.1_Silent_p.L1430L|NEO1_uc010uky.1_Silent_p.L1388L|NEO1_uc010ukz.1_Silent_p.L854L|NEO1_uc002avn.3_Silent_p.L1079L	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	1441	Cytoplasmic (Potential).				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75968797	75968797	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75968797A>G	uc002baw.2	-	10	6156	c.6063T>C	c.(6061-6063)CAT>CAC	p.H2021H		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	2021	Extracellular (Potential).|CSPG 14.|Cysteine-containing.|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3																		---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78921917	78921917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78921917C>T	uc002bed.1	-	5	842	c.730G>A	c.(730-732)GTG>ATG	p.V244M	CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Missense_Mutation_p.V62M	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4	244	Helical; (Potential).				regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83332377	83332377	+	Intron	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83332377A>C	uc010uoh.1	-						AP3B2_uc010uoi.1_Intron|AP3B2_uc010uoj.1_Intron|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Intron|AP3B2_uc002biy.1_5'Flank	NM_004644	NP_004635			adaptor-related protein complex 3, beta 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84237297	84237297	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84237297A>G	uc002bjw.2	+	4	399	c.204A>G	c.(202-204)CTA>CTG	p.L68L	SH3GL3_uc010uot.1_Silent_p.L68L|SH3GL3_uc002bjx.2_5'UTR|SH3GL3_uc002bju.2_Silent_p.L76L|SH3GL3_uc002bjv.2_RNA	NM_003027	NP_003018	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	68	Required for dimerization upon membrane association (By similarity).|BAR.				central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ZSCAN2	54993	broad.mit.edu	37	15	85164068	85164068	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85164068C>T	uc002bkr.2	+	3	868	c.642C>T	c.(640-642)GGC>GGT	p.G214G	ZSCAN2_uc010bmz.1_Silent_p.G212G|ZSCAN2_uc010bna.2_Silent_p.G64G|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1	214					cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)														---	---	---	---
SEMA4B	10509	broad.mit.edu	37	15	90766851	90766851	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90766851C>T	uc002boy.2	+	9	1205	c.922C>T	c.(922-924)CTG>TTG	p.L308L	SEMA4B_uc002boz.2_Silent_p.L308L|SEMA4B_uc010uqd.1_Silent_p.L146L|SEMA4B_uc002bpa.2_Silent_p.L146L|SEMA4B_uc010bnv.1_5'UTR	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)															---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92647631	92647631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92647631C>T	uc002bqx.2	+	4	1069	c.868C>T	c.(868-870)CCC>TCC	p.P290S	SLCO3A1_uc002bqy.2_Missense_Mutation_p.P290S|SLCO3A1_uc010boc.1_RNA|SLCO3A1_uc002bqz.1_Missense_Mutation_p.P232S	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,	290	Cytoplasmic (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94901781	94901781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94901781G>A	uc002btj.2	+	9	1306	c.1241G>A	c.(1240-1242)GGC>GAC	p.G414D	MCTP2_uc010urg.1_Silent_p.G392G|MCTP2_uc002bti.2_Missense_Mutation_p.G414D|MCTP2_uc010boj.2_Missense_Mutation_p.G143D|MCTP2_uc010bok.2_Missense_Mutation_p.G414D|MCTP2_uc002btk.3_Missense_Mutation_p.G2D|MCTP2_uc002btl.2_Missense_Mutation_p.G2D	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1	414	C2 2.				calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)															---	---	---	---
SYNM	23336	broad.mit.edu	37	15	99671044	99671044	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99671044G>A	uc002bup.2	+	6	2599	c.2479G>A	c.(2479-2481)GAG>AAG	p.E827K	SYNM_uc002buo.2_Missense_Mutation_p.E827K|SYNM_uc002buq.2_Intron	NM_145728	NP_663780	O15061	SYNEM_HUMAN	desmuslin isoform A	827	Tail.				intermediate filament cytoskeleton organization	adherens junction|costamere|intermediate filament|neurofilament cytoskeleton	intermediate filament binding|structural constituent of cytoskeleton|structural constituent of muscle|vinculin binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CHSY1	22856	broad.mit.edu	37	15	101775430	101775430	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101775430C>T	uc002bwt.1	-	3	1156	c.673G>A	c.(673-675)GTG>ATG	p.V225M		NM_014918	NP_055733	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	225	Lumenal (Potential).				chondroitin sulfate biosynthetic process	Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity				0	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
TM2D3	80213	broad.mit.edu	37	15	102182749	102182749	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102182749G>A	uc002bxi.2	-	6	707	c.677C>T	c.(676-678)ACG>ATG	p.T226M	TM2D3_uc010usg.1_Intron|TM2D3_uc002bxh.2_Missense_Mutation_p.T161M|TM2D3_uc002bxj.2_Missense_Mutation_p.T200M|TM2D3_uc002bxk.2_Missense_Mutation_p.T161M	NM_078474	NP_510883	Q9BRN9	TM2D3_HUMAN	TM2 domain containing 3 isoform a	226	Helical; (Potential).					integral to membrane				ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
TARSL2	123283	broad.mit.edu	37	15	102224299	102224299	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102224299G>A	uc002bxm.2	-	12	1684	c.1629C>T	c.(1627-1629)CAC>CAT	p.H543H	TARSL2_uc002bxl.2_Silent_p.H88H|TARSL2_uc010usi.1_RNA	NM_152334	NP_689547	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	543					threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	339512	339512	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:339512C>T	uc002cgp.1	-	10	2567	c.2390G>A	c.(2389-2391)CGC>CAC	p.R797H	AXIN1_uc002cgq.1_Missense_Mutation_p.R761H	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	797	DIX.				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)																---	---	---	---
SOLH	6650	broad.mit.edu	37	16	597827	597827	+	Missense_Mutation	SNP	G	A	A	rs145625644		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:597827G>A	uc002chi.2	+	4	1352	c.989G>A	c.(988-990)CGT>CAT	p.R330H	SOLH_uc002chh.1_Missense_Mutation_p.R330H	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes	330					proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)																---	---	---	---
JMJD8	339123	broad.mit.edu	37	16	733072	733072	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:733072G>A	uc002ciw.1	-	8	715	c.658C>T	c.(658-660)CCA>TCA	p.P220S	JMJD8_uc002cix.1_Missense_Mutation_p.P220S|JMJD8_uc002ciy.1_Missense_Mutation_p.P190S	NM_001005920	NP_001005920	Q96S16	JMJD8_HUMAN	jumonji domain containing 8	269	JmjC.									breast(1)	1																		---	---	---	---
BAIAP3	8938	broad.mit.edu	37	16	1394670	1394670	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1394670C>A	uc002clk.1	+	19	1833	c.1833C>A	c.(1831-1833)TGC>TGA	p.C611*	BAIAP3_uc002clj.2_Nonsense_Mutation_p.C593*|BAIAP3_uc010uuz.1_Nonsense_Mutation_p.C576*|BAIAP3_uc010uva.1_Nonsense_Mutation_p.C548*|BAIAP3_uc010uvc.1_Nonsense_Mutation_p.C540*	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	611					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
RPS2	6187	broad.mit.edu	37	16	2012162	2012162	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2012162G>A	uc002cnn.2	-	6	1007	c.819C>T	c.(817-819)CTC>CTT	p.L273L	RPS2_uc010bsa.1_RNA|RPS2_uc002cnl.2_Silent_p.L215L|RPS2_uc002cnm.2_RNA|RPS2_uc002cno.2_Silent_p.L273L|SNHG9_uc002cnr.2_5'Flank	NM_002952	NP_002943	P15880	RS2_HUMAN	ribosomal protein S2	273					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleoplasm	fibroblast growth factor 1 binding|fibroblast growth factor 3 binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
CASKIN1	57524	broad.mit.edu	37	16	2240127	2240127	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2240127A>G	uc010bsg.1	-	3	223	c.191T>C	c.(190-192)TTG>TCG	p.L64S		NM_020764	NP_065815	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	64	ANK 1.				signal transduction	cytoplasm				skin(2)	2																		---	---	---	---
MLST8	64223	broad.mit.edu	37	16	2258499	2258499	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2258499G>A	uc002coz.2	+	8	866	c.747G>A	c.(745-747)ACG>ACA	p.T249T	MLST8_uc002coy.2_Silent_p.T249T|MLST8_uc002cpa.2_Silent_p.T65T|MLST8_uc002cpb.2_Silent_p.T248T|MLST8_uc010uvx.1_Silent_p.T183T|MLST8_uc002cpc.2_Silent_p.T249T|MLST8_uc002cpd.2_Silent_p.T183T|MLST8_uc002cpe.2_Silent_p.T249T|MLST8_uc002cpg.2_Silent_p.T268T|MLST8_uc002cph.2_RNA|MLST8_uc002cpf.2_Silent_p.T249T	NM_022372	NP_071767	Q9BVC4	LST8_HUMAN	G protein beta subunit-like	249	WD 6.				insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|T cell costimulation	cytosol	protein binding				0																		---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3843382	3843382	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3843382C>T	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4164627	4164627	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4164627C>T	uc002cvx.2	-	2	1356	c.817G>A	c.(817-819)GGA>AGA	p.G273R		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	273	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4164980	4164980	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4164980A>G	uc002cvx.2	-	2	1003	c.464T>C	c.(463-465)GTG>GCG	p.V155A		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	155	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
TFAP4	7023	broad.mit.edu	37	16	4312636	4312636	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4312636G>A	uc010uxg.1	-	2	410	c.156C>T	c.(154-156)ATC>ATT	p.I52I		NM_003223	NP_003214	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer	52	Basic motif.				DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
MGRN1	23295	broad.mit.edu	37	16	4701990	4701990	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4701990C>T	uc002cwz.2	+	3	370	c.234C>T	c.(232-234)CAC>CAT	p.H78H	MGRN1_uc002cxa.2_Silent_p.H78H|MGRN1_uc010btx.2_Silent_p.H78H|MGRN1_uc010btw.2_Silent_p.H78H|MGRN1_uc002cxb.2_Silent_p.H78H|MGRN1_uc010uxo.1_Silent_p.H78H|MGRN1_uc010uxp.1_Silent_p.H78H|MGRN1_uc010uxq.1_RNA	NM_001142290	NP_001135762	O60291	MGRN1_HUMAN	mahogunin, ring finger 1 isoform 3	78					endosome to lysosome transport|negative regulation of cAMP-mediated signaling|negative regulation of G-protein coupled receptor protein signaling pathway|protein monoubiquitination	cytosol|early endosome|nucleus|plasma membrane|plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
C16orf89	146556	broad.mit.edu	37	16	5110282	5110282	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5110282C>T	uc010bud.2	-						ALG1_uc002cyj.2_Intron|C16orf89_uc002cyk.3_Intron	NM_152459	NP_689672			hypothetical protein LOC146556 isoform 1							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7102105	7102105	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7102105T>C	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			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)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7645632	7645632	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7645632C>T	uc002cys.2	+	8	1538	c.550C>T	c.(550-552)CGT>TGT	p.R184C	A2BP1_uc010buf.1_Missense_Mutation_p.R184C|A2BP1_uc002cyr.1_Missense_Mutation_p.R183C|A2BP1_uc002cyt.2_Missense_Mutation_p.R184C|A2BP1_uc010uxz.1_Missense_Mutation_p.R227C|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Missense_Mutation_p.R184C|A2BP1_uc010uyb.1_Missense_Mutation_p.R184C|A2BP1_uc002cyw.2_Missense_Mutation_p.R204C|A2BP1_uc002cyy.2_Missense_Mutation_p.R204C|A2BP1_uc002cyx.2_Missense_Mutation_p.R204C|A2BP1_uc010uyc.1_Missense_Mutation_p.R204C	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	184	RRM.	Interaction with RNA.			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)														---	---	---	---
NUBP1	4682	broad.mit.edu	37	16	10850626	10850626	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10850626C>T	uc002daa.1	+	6	463	c.440C>T	c.(439-441)CCC>CTC	p.P147L	NUBP1_uc010bum.1_Intron|NUBP1_uc002dab.1_Missense_Mutation_p.P136L	NM_002484	NP_002475	P53384	NUBP1_HUMAN	nucleotide binding protein 1	147					cell growth|cellular iron ion homeostasis|iron-sulfur cluster assembly	cytosol	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding|nucleoside-triphosphatase activity|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
BFAR	51283	broad.mit.edu	37	16	14758878	14758878	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14758878A>G	uc002dco.2	+	7	1391	c.1110A>G	c.(1108-1110)TCA>TCG	p.S370S	BFAR_uc002dcp.2_Silent_p.S245S|BFAR_uc010uzh.1_Silent_p.S242S	NM_016561	NP_057645	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	370	Helical; (Potential).				anti-apoptosis|apoptosis	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	structural molecule activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15110081	15110081	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15110081G>A	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16248763	16248763	+	Silent	SNP	G	A	A	rs146265944		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16248763G>A	uc002den.3	-	28	4045	c.4008C>T	c.(4006-4008)CAC>CAT	p.H1336H	ABCC6_uc010bvo.2_RNA|ABCC6_uc002dem.2_Silent_p.H88H	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1336	Cytoplasmic (By similarity).|ABC transporter 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16302688	16302688	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16302688G>A	uc002den.3	-	7	728	c.691C>T	c.(691-693)CTG>TTG	p.L231L	ABCC6_uc010bvo.2_RNA|ABCC6_uc010uzz.1_Silent_p.L243L	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	231	Cytoplasmic (By similarity).				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
GPRC5B	51704	broad.mit.edu	37	16	19883873	19883873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19883873A>G	uc002dgt.2	-	2	403	c.295T>C	c.(295-297)TTC>CTC	p.F99L	GPRC5B_uc010vav.1_Missense_Mutation_p.F125L	NM_016235	NP_057319	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, family C, group 5,	99	Helical; Name=2; (Potential).									lung(1)|breast(1)|skin(1)	3																		---	---	---	---
ACSM1	116285	broad.mit.edu	37	16	20702489	20702489	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20702489G>A	uc002dhm.1	-	1	90	c.22C>T	c.(22-24)CGG>TGG	p.R8W	ACSM1_uc002dhn.1_RNA|ACSM1_uc010bwg.1_Missense_Mutation_p.R8W	NM_052956	NP_443188	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member	8					benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21042447	21042447	+	Missense_Mutation	SNP	G	A	A	rs146173789		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21042447G>A	uc010vbe.1	-	37	5359	c.5359C>T	c.(5359-5361)CGC>TGC	p.R1787C		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1787	AAA 2 (By similarity).				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)														---	---	---	---
IL4R	3566	broad.mit.edu	37	16	27353456	27353456	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27353456T>C	uc002don.2	+	4	327	c.85T>C	c.(85-87)TTG>CTG	p.L29L	IL4R_uc002dom.2_Silent_p.L29L|IL4R_uc002dop.3_Silent_p.L14L|IL4R_uc010bxy.2_Silent_p.L29L|IL4R_uc002doo.2_5'UTR	NM_000418	NP_000409	P24394	IL4RA_HUMAN	interleukin 4 receptor alpha chain isoform a	29	Extracellular (Potential).				immune response|production of molecular mediator involved in inflammatory response	integral to plasma membrane	identical protein binding|interleukin-4 receptor activity|receptor signaling protein activity			ovary(1)|skin(1)	2																		---	---	---	---
IL27	246778	broad.mit.edu	37	16	28513323	28513323	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28513323C>T	uc002dqc.2	-	4	459	c.436G>A	c.(436-438)GAT>AAT	p.D146N	uc010vct.1_Intron	NM_145659	NP_663634	Q8NEV9	IL27A_HUMAN	interleukin 27 precursor	146					inflammatory response|innate immune response|positive regulation of interferon-gamma biosynthetic process|regulation of defense response to virus|regulation of T cell proliferation|regulation of T-helper 1 cell differentiation	extracellular space	cytokine activity|interleukin-27 receptor binding				0																		---	---	---	---
KCTD13	253980	broad.mit.edu	37	16	29922371	29922371	+	Silent	SNP	G	A	A	rs143894366		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29922371G>A	uc002duv.2	-	5	872	c.681C>T	c.(679-681)TAC>TAT	p.Y227Y	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|ASPHD1_uc002duu.3_Intron|ASPHD1_uc010bzi.2_Intron|KCTD13_uc010vee.1_RNA	NM_178863	NP_849194	Q8WZ19	BACD1_HUMAN	potassium channel tetramerisation domain	227					cell migration|DNA replication|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0																		---	---	---	---
HIRIP3	8479	broad.mit.edu	37	16	30005496	30005496	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30005496T>C	uc002dve.2	-	4	1431	c.970A>G	c.(970-972)AAG>GAG	p.K324E	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvg.1_5'Flank|INO80E_uc002dvh.1_5'Flank|INO80E_uc002dvi.1_5'Flank|INO80E_uc002dvj.1_5'Flank|INO80E_uc002dvk.1_5'Flank|HIRIP3_uc002dvf.2_Intron	NM_003609	NP_003600	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	324					chromatin assembly or disassembly	nucleus	protein binding			central_nervous_system(1)	1																		---	---	---	---
TBX6	6911	broad.mit.edu	37	16	30100291	30100291	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30100291G>T	uc010veh.1	-	4	654	c.594C>A	c.(592-594)ACC>ACA	p.T198T	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TBX6_uc002dwk.1_Silent_p.T198T	NM_004608	NP_004599	O95947	TBX6_HUMAN	T-box 6	198	T-box.				anatomical structure morphogenesis|mesoderm development|multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ZNF668	79759	broad.mit.edu	37	16	31072722	31072722	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31072722A>G	uc010caf.2	-	3	1884	c.1527T>C	c.(1525-1527)GCT>GCC	p.A509A	ZNF668_uc002eao.2_Silent_p.A509A	NM_024706	NP_078982	Q96K58	ZN668_HUMAN	zinc finger protein 668	509					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(4)	4																		---	---	---	---
MYST1	84148	broad.mit.edu	37	16	31131803	31131803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31131803C>T	uc002eay.2	+	3	448	c.430C>T	c.(430-432)CGC>TGC	p.R144C	MYST1_uc002eax.2_Missense_Mutation_p.R144C	NM_032188	NP_115564	Q9H7Z6	MYST1_HUMAN	MYST histone acetyltransferase 1 isoform 1	144					histone H4-K16 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex|MSL complex	histone acetyltransferase activity|metal ion binding|methylated histone residue binding|transcription factor binding			ovary(1)	1																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31383801	31383801	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31383801G>A	uc002ebu.1	+	18	2330	c.2263G>A	c.(2263-2265)GCC>ACC	p.A755T	ITGAX_uc002ebt.2_Missense_Mutation_p.A755T	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	755	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49671711	49671711	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49671711G>T	uc002efs.2	-	5	1650	c.1352C>A	c.(1351-1353)CCC>CAC	p.P451H	ZNF423_uc010vgn.1_Missense_Mutation_p.P334H	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	451	C2H2-type 10.				cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ADCY7	113	broad.mit.edu	37	16	50332842	50332842	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50332842C>A	uc002egd.1	+	7	1244	c.976C>A	c.(976-978)CTC>ATC	p.L326I	ADCY7_uc002egb.1_Missense_Mutation_p.L326I|ADCY7_uc002egc.1_Missense_Mutation_p.L326I	NM_001114	NP_001105	P51828	ADCY7_HUMAN	adenylate cyclase 7	326	Cytoplasmic (Potential).|Guanylate cyclase 1.				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)													---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50744697	50744697	+	Missense_Mutation	SNP	C	T	T	rs149338478	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50744697C>T	uc002egm.1	+	4	980	c.875C>T	c.(874-876)GCG>GTG	p.A292V	NOD2_uc010cbk.1_Missense_Mutation_p.A265V|NOD2_uc002egl.1_Missense_Mutation_p.A70V|NOD2_uc010cbl.1_Missense_Mutation_p.A70V|NOD2_uc010cbm.1_Missense_Mutation_p.A70V|NOD2_uc010cbn.1_RNA|NOD2_uc010cbo.1_RNA|NOD2_uc010cbp.1_5'Flank|NOD2_uc010cbq.1_5'Flank|NOD2_uc010cbr.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	292					activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
SALL1	6299	broad.mit.edu	37	16	51174686	51174686	+	Missense_Mutation	SNP	C	T	T	rs148915594		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51174686C>T	uc010vgs.1	-	2	1478	c.1447G>A	c.(1447-1449)GGG>AGG	p.G483R	SALL1_uc010vgr.1_Missense_Mutation_p.G386R|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	483	C2H2-type 2.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)															---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55519218	55519218	+	Silent	SNP	C	T	T	rs151071926		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55519218C>T	uc002ehz.3	+	4	848	c.537C>T	c.(535-537)GGC>GGT	p.G179G	MMP2_uc010vhd.1_Silent_p.G103G|MMP2_uc010ccc.2_Silent_p.G129G	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	179	Collagenase-like 1.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)													---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55525756	55525756	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55525756C>T	uc002ehz.3	+	8	1535	c.1224C>T	c.(1222-1224)GCC>GCT	p.A408A	MMP2_uc010vhd.1_Silent_p.A332A|MMP2_uc010ccc.2_Silent_p.A358A|MMP2_uc002eia.3_5'Flank	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	408	Collagenase-like 2.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			large_intestine(3)|ovary(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	11		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)													---	---	---	---
CETP	1071	broad.mit.edu	37	16	57016121	57016121	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57016121C>T	uc002eki.2	+	14	1350	c.1293C>T	c.(1291-1293)ACC>ACT	p.T431T	CETP_uc002ekj.2_Silent_p.T371T	NM_000078	NP_000069	P11597	CETP_HUMAN	cholesteryl ester transfer protein, plasma	431					cholesterol homeostasis|cholesterol metabolic process|high-density lipoprotein particle remodeling|lipoprotein metabolic process|low-density lipoprotein particle remodeling|phosphatidylcholine metabolic process|phospholipid homeostasis|receptor-mediated endocytosis|regulation of cholesterol efflux|triglyceride homeostasis|triglyceride metabolic process|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle|vesicle	cholesterol binding|cholesterol transporter activity|phosphatidylcholine binding|phospholipid transporter activity|triglyceride binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57092035	57092035	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57092035C>T	uc002ekk.1	+	28	4030	c.3805C>T	c.(3805-3807)CAG>TAG	p.Q1269*	NLRC5_uc002ekn.2_Intron|NLRC5_uc002ekl.2_Nonsense_Mutation_p.Q1073*|NLRC5_uc002ekm.2_Nonsense_Mutation_p.Q1043*|NLRC5_uc010ccr.1_RNA|NLRC5_uc010ccs.1_RNA|NLRC5_uc002eko.1_RNA|NLRC5_uc002ekp.1_Nonsense_Mutation_p.Q184*|NLRC5_uc002ekq.1_5'UTR|NLRC5_uc002ekr.1_Nonsense_Mutation_p.Q156*	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	1269					defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
CCDC113	29070	broad.mit.edu	37	16	58288046	58288046	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58288046G>A	uc002ene.2	+	3	452	c.373G>A	c.(373-375)GAC>AAC	p.D125N	CCDC113_uc010vid.1_Intron	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1	125	Potential.					protein complex					0																		---	---	---	---
GOT2	2806	broad.mit.edu	37	16	58757658	58757658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58757658C>T	uc002eof.1	-	2	352	c.238G>A	c.(238-240)GTC>ATC	p.V80I	GOT2_uc010vim.1_Missense_Mutation_p.V80I	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	80					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PLEKHG4	25894	broad.mit.edu	37	16	67319435	67319435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67319435G>A	uc002eso.3	+	13	4973	c.2438G>A	c.(2437-2439)CGC>CAC	p.R813H	PLEKHG4_uc002esp.3_Missense_Mutation_p.R620H|PLEKHG4_uc002esq.3_Missense_Mutation_p.R813H|PLEKHG4_uc010cef.2_Missense_Mutation_p.R813H|PLEKHG4_uc002ess.3_Missense_Mutation_p.R813H|PLEKHG4_uc010ceg.2_Missense_Mutation_p.R732H	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	813	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)														---	---	---	---
LRRC36	55282	broad.mit.edu	37	16	67412553	67412553	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67412553T>A	uc002esv.2	+	12	1887	c.1868T>A	c.(1867-1869)ATT>AAT	p.I623N	LRRC36_uc002esw.2_RNA|LRRC36_uc002esx.2_Missense_Mutation_p.I502N|LRRC36_uc010vjk.1_Missense_Mutation_p.I398N|LRRC36_uc010vjl.1_Missense_Mutation_p.I95N|LRRC36_uc002esy.2_Missense_Mutation_p.I133N	NM_018296	NP_060766	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36 isoform 1	623	Potential.										0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)														---	---	---	---
EDC4	23644	broad.mit.edu	37	16	67909972	67909972	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67909972G>A	uc002eur.2	+	2	373	c.207G>A	c.(205-207)ATG>ATA	p.M69I	EDC4_uc010cer.2_5'UTR|EDC4_uc010vkg.1_Missense_Mutation_p.M1I|EDC4_uc010ces.1_5'Flank|EDC4_uc002eus.2_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	69					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)														---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70154529	70154529	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70154529T>A	uc002eyf.1	+	3	1091	c.134T>A	c.(133-135)GTG>GAG	p.V45E	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	45					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)														---	---	---	---
DDX19B	11269	broad.mit.edu	37	16	70363885	70363885	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70363885C>A	uc002eyo.2	+	9	1066	c.937C>A	c.(937-939)CTG>ATG	p.L313M	DDX19B_uc010vly.1_Missense_Mutation_p.L313M|DDX19A_uc002eys.2_Intron|DDX19B_uc010vlv.1_Missense_Mutation_p.L287M|DDX19B_uc010vlw.1_Missense_Mutation_p.L204M|DDX19B_uc002eyp.2_Missense_Mutation_p.L282M|DDX19B_uc002eyq.2_Missense_Mutation_p.L204M|DDX19B_uc002eyr.2_Missense_Mutation_p.L162M|DDX19B_uc010vlx.1_Missense_Mutation_p.L162M|uc002eyt.2_Intron	NM_007242	NP_009173	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform	313	Helicase C-terminal.				mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			kidney(1)	1		Ovarian(137;0.0694)																---	---	---	---
MARVELD3	91862	broad.mit.edu	37	16	71674764	71674764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71674764C>T	uc002fau.2	+	3	1130	c.1067C>T	c.(1066-1068)ACC>ATC	p.T356I	PHLPP2_uc002fav.2_RNA|MARVELD3_uc010cge.2_3'UTR	NM_001017967	NP_001017967	Q96A59	MALD3_HUMAN	MARVEL domain containing 3 isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane				skin(1)	1		Ovarian(137;0.125)																---	---	---	---
DHX38	9785	broad.mit.edu	37	16	72138432	72138432	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72138432G>A	uc002fcb.2	+	15	2413	c.2058G>A	c.(2056-2058)ACG>ACA	p.T686T	DHX38_uc010vmp.1_Intron	NM_014003	NP_054722	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	686	Helicase ATP-binding.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1		Ovarian(137;0.125)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72831435	72831435	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72831435C>T	uc002fck.2	-	9	5819	c.5146G>A	c.(5146-5148)GCA>ACA	p.A1716T	ZFHX3_uc002fcl.2_Missense_Mutation_p.A802T	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1716					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)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72993844	72993844	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72993844C>T	uc002fck.2	-	2	874	c.201G>A	c.(199-201)TCG>TCA	p.S67S	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	67					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)																---	---	---	---
TERF2IP	54386	broad.mit.edu	37	16	75690483	75690483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75690483C>T	uc002fet.1	+	3	1271	c.1174C>T	c.(1174-1176)CGG>TGG	p.R392W		NM_018975	NP_061848	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting	392	Nuclear localization signal (Potential).				negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1																		---	---	---	---
PKD1L2	114780	broad.mit.edu	37	16	81171067	81171067	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81171067C>T	uc002fgh.1	-	34	5694	c.5694G>A	c.(5692-5694)CCG>CCA	p.P1898P	PKD1L2_uc002fgf.1_5'Flank|PKD1L2_uc002fgg.1_RNA	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1898	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83159089	83159089	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83159089C>T	uc002fgx.2	+	4	586	c.466C>T	c.(466-468)CCA>TCA	p.P156S	CDH13_uc010chh.2_Missense_Mutation_p.P156S|CDH13_uc010vns.1_Missense_Mutation_p.P203S|CDH13_uc010vnt.1_5'UTR|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	156	Cadherin 1.				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)														---	---	---	---
COTL1	23406	broad.mit.edu	37	16	84623721	84623721	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84623721T>C	uc002fid.2	-	3	457	c.308A>G	c.(307-309)GAG>GGG	p.E103G	COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_RNA	NM_021149	NP_066972	Q14019	COTL1_HUMAN	coactosin-like 1	103	ADF-H.					cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1																		---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84906600	84906600	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84906600G>A	uc010voh.1	+	10	1211	c.984G>A	c.(982-984)TCG>TCA	p.S328S	CRISPLD2_uc010vog.1_Intron|CRISPLD2_uc002fio.2_Silent_p.S327S|CRISPLD2_uc002fim.2_Silent_p.S328S|CRISPLD2_uc002fin.3_Silent_p.S328S	NM_031476	NP_113664	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain	328	LCCL 1.					extracellular region|transport vesicle					0																		---	---	---	---
COX4I1	1327	broad.mit.edu	37	16	85834824	85834824	+	Silent	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85834824A>C	uc002fje.2	+	2	177	c.13A>C	c.(13-15)AGG>CGG	p.R5R	COX4NB_uc002fjd.2_5'Flank|COX4NB_uc010vol.1_5'Flank|COX4I1_uc002fjf.2_Silent_p.R5R|COX4I1_uc002fjg.1_Silent_p.R5R|COX4I1_uc010vom.1_5'UTR	NM_001861	NP_001852	P13073	COX41_HUMAN	cytochrome c oxidase subunit IV isoform 1	5					respiratory electron transport chain	mitochondrial inner membrane|nucleus	cytochrome-c oxidase activity|protein binding			lung(1)	1		Renal(780;0.228)																---	---	---	---
TRAPPC2L	51693	broad.mit.edu	37	16	88925094	88925094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88925094C>T	uc002fmc.2	+	2	154	c.101C>T	c.(100-102)ACA>ATA	p.T34I	GALNS_uc002fly.3_5'Flank|GALNS_uc010cid.2_5'Flank|GALNS_uc002flz.3_5'Flank|GALNS_uc002fma.2_5'Flank|TRAPPC2L_uc010cie.2_RNA|TRAPPC2L_uc002fmd.3_Missense_Mutation_p.T34I|TRAPPC2L_uc002fme.3_Missense_Mutation_p.T34I|TRAPPC2L_uc002fmf.2_5'Flank|uc002fmg.2_5'Flank	NM_016209	NP_057293	Q9UL33	TPC2L_HUMAN	trafficking protein particle complex 2-like	34					ER to Golgi vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm					0				BRCA - Breast invasive adenocarcinoma(80;0.0477)														---	---	---	---
FAM101B	359845	broad.mit.edu	37	17	293243	293243	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:293243G>A	uc002frj.2	-	2	421	c.147C>T	c.(145-147)ATC>ATT	p.I49I		NM_182705	NP_874364	Q8N5W9	F101B_HUMAN	hypothetical protein LOC359845	119											0		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.0216)														---	---	---	---
SGSM2	9905	broad.mit.edu	37	17	2279115	2279115	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2279115C>T	uc002fun.3	+	17	2470	c.2295C>T	c.(2293-2295)GCC>GCT	p.A765A	SGSM2_uc002fum.3_Silent_p.A810A|SGSM2_uc010vqw.1_Silent_p.A765A|SGSM2_uc002fup.1_5'UTR|SGSM2_uc002fuq.2_5'Flank	NM_001098509	NP_001091979	O43147	SGSM2_HUMAN	RUN and TBC1 domain containing 1 isoform 2	765	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)														---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2901577	2901577	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2901577G>A	uc010ckd.2	+	14	1197	c.1107G>A	c.(1105-1107)ACG>ACA	p.T369T	RAP1GAP2_uc010cke.2_Silent_p.T354T	NM_015085	NP_055900	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2 isoform 1	369	Rap-GAP.				regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
MYBBP1A	10514	broad.mit.edu	37	17	4442989	4442989	+	Silent	SNP	G	A	A	rs138002559	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4442989G>A	uc002fyb.3	-	26	3770	c.3708C>T	c.(3706-3708)GGC>GGT	p.G1236G	MYBBP1A_uc002fxz.3_Silent_p.G1236G|SPNS2_uc002fxx.2_3'UTR|SPNS2_uc002fxy.2_3'UTR|MYBBP1A_uc002fya.3_Silent_p.G181G|MYBBP1A_uc010vsa.1_Silent_p.G278G	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	1236	Required for nuclear and nucleolar localization (By similarity).				nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
EIF4A1	1973	broad.mit.edu	37	17	7480019	7480019	+	Intron	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7480019T>A	uc002gho.1	+						EIF4A1_uc002ghr.1_Intron|EIF4A1_uc002ghq.1_Intron|EIF4A1_uc002ghp.1_Intron|SNORD10_uc002ght.2_5'Flank|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407			eukaryotic translation initiation factor 4A						nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
AURKB	9212	broad.mit.edu	37	17	8108369	8108369	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8108369G>A	uc002gkm.2	-						AURKB_uc010cnu.2_Intron|AURKB_uc002gkn.2_Intron|AURKB_uc010vuu.1_Intron|AURKB_uc002gko.2_Intron	NM_004217	NP_004208			aurora kinase B						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|mitotic prometaphase|protein localization to kinetochore	chromosome passenger complex|condensed nuclear chromosome, centromeric region|cytosol|spindle	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
WDR16	146845	broad.mit.edu	37	17	9532147	9532147	+	Intron	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9532147A>G	uc002gly.2	+						WDR16_uc002glz.2_Intron|WDR16_uc010coc.2_Intron	NM_145054	NP_659491			WD40-repeat protein upregulated in HCC isoform							cytoplasm|intracellular membrane-bounded organelle	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10447054	10447054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10447054C>T	uc010coi.2	-	8	843	c.715G>A	c.(715-717)GTG>ATG	p.V239M	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.V239M|MYH2_uc010coj.2_Missense_Mutation_p.V239M	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	239	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11607512	11607512	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11607512T>C	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			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)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11837339	11837339	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11837339C>T	uc002gne.2	+	65	12508	c.12440C>T	c.(12439-12441)GCC>GTC	p.A4147V	DNAH9_uc010coo.2_Missense_Mutation_p.A3365V|DNAH9_uc002gnf.2_Missense_Mutation_p.A459V	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	4147					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)														---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18023246	18023246	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18023246G>A	uc010vxh.1	+	2	1470	c.1132G>A	c.(1132-1134)GTC>ATC	p.V378I		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	378	Myosin head-like.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)																	---	---	---	---
FLII	2314	broad.mit.edu	37	17	18151293	18151293	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18151293C>T	uc002gsr.1	-	19	2296	c.2245G>A	c.(2245-2247)GTG>ATG	p.V749M	FLII_uc002gsq.1_Missense_Mutation_p.V620M|FLII_uc010cpy.1_Missense_Mutation_p.V738M|FLII_uc010vxn.1_Missense_Mutation_p.V718M|FLII_uc010vxo.1_Missense_Mutation_p.V694M|FLII_uc002gss.1_Missense_Mutation_p.V748M	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	749	Interaction with ACTL6A.				multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)															OREG0024225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ALDH3A1	218	broad.mit.edu	37	17	19642929	19642929	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19642929G>T	uc010cqu.2	-	7	1338	c.1008C>A	c.(1006-1008)TTC>TTA	p.F336L	ALDH3A1_uc010vzd.1_Missense_Mutation_p.F336L|ALDH3A1_uc002gwj.2_Missense_Mutation_p.F336L|ALDH3A1_uc010cqv.2_Missense_Mutation_p.F335L|ALDH3A1_uc002gwk.2_Missense_Mutation_p.F453L|ALDH3A1_uc002gwl.1_Missense_Mutation_p.F263L	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	336					cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)													---	---	---	---
ALDH3A1	218	broad.mit.edu	37	17	19646727	19646727	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19646727A>G	uc010cqu.2	-	2	542	c.212T>C	c.(211-213)ATC>ACC	p.I71T	ALDH3A1_uc010vzd.1_Missense_Mutation_p.I71T|ALDH3A1_uc002gwj.2_Missense_Mutation_p.I71T|ALDH3A1_uc010cqv.2_Missense_Mutation_p.I71T|ALDH3A1_uc002gwk.2_5'UTR|ALDH3A1_uc002gwl.1_5'UTR	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	71					cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)													---	---	---	---
AKAP10	11216	broad.mit.edu	37	17	19823397	19823397	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19823397G>A	uc002gwo.2	-	12	1923	c.1786C>T	c.(1786-1788)CAA>TAA	p.Q596*	AKAP10_uc002gwp.1_Nonsense_Mutation_p.Q596*|AKAP10_uc010cqw.1_Nonsense_Mutation_p.Q538*	NM_007202	NP_009133	O43572	AKA10_HUMAN	A-kinase anchor protein 10 precursor	596					blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)																	---	---	---	---
GIT1	28964	broad.mit.edu	37	17	27901773	27901773	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27901773C>T	uc002hef.2	-	20	2447	c.2233G>A	c.(2233-2235)GCC>ACC	p.A745T	GIT1_uc002heg.2_Missense_Mutation_p.A754T|GIT1_uc010wbg.1_Missense_Mutation_p.A731T|GIT1_uc010csb.1_3'UTR	NM_014030	NP_054749	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interactor 1	745	Interaction with PXN and TGFB1I1 (By similarity).				regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|focal adhesion	ARF GTPase activator activity|protein binding|zinc ion binding				0				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)														---	---	---	---
NF1	4763	broad.mit.edu	37	17	29685651	29685651	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29685651G>A	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010cso.2_Intron|NF1_uc010wbt.1_Intron|NF1_uc010wbu.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
SLFN5	162394	broad.mit.edu	37	17	33591816	33591816	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33591816A>C	uc002hjf.3	+	4	1870	c.1753A>C	c.(1753-1755)ACT>CCT	p.T585P	SLFN5_uc010wcg.1_Intron	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	585	ATP (Potential).				cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)														---	---	---	---
GAS2L2	246176	broad.mit.edu	37	17	34072681	34072681	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34072681A>G	uc002hjv.1	-	6	1863	c.1835T>C	c.(1834-1836)ATG>ACG	p.M612T		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	612					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
MRM1	79922	broad.mit.edu	37	17	34964326	34964326	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34964326G>A	uc002hne.2	+						MRM1_uc002hnf.2_Intron	NM_024864	NP_079140			mitochondrial rRNA methyltransferase 1 homolog						RNA processing	mitochondrion	RNA binding|RNA methyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)														---	---	---	---
KRTAP1-5	83895	broad.mit.edu	37	17	39182975	39182975	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39182975G>T	uc002hvu.2	-	1	480	c.433C>A	c.(433-435)CAA>AAA	p.Q145K		NM_031957	NP_114163	Q9BYS1	KRA15_HUMAN	keratin associated protein 1.5	145	15 X 5 AA repeats of C-C-[QEPVRC]- [TPIVLE]-[SRHVP].					keratin filament					0		Breast(137;0.00043)	STAD - Stomach adenocarcinoma(17;0.000371)															---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40359649	40359649	+	Silent	SNP	G	A	A	rs147503881		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40359649G>A	uc002hzh.2	-	16	2173	c.2004C>T	c.(2002-2004)TAC>TAT	p.Y668Y		NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription	668	SH2.				2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)													---	---	---	---
ITGA2B	3674	broad.mit.edu	37	17	42457968	42457968	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42457968C>A	uc002igt.1	-	14	1471	c.1439G>T	c.(1438-1440)AGA>ATA	p.R480I	ITGA2B_uc002igu.1_5'UTR	NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein	480	Extracellular (Potential).|FG-GAP 7.				axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)													---	---	---	---
EFTUD2	9343	broad.mit.edu	37	17	42942391	42942391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42942391C>T	uc002ihn.2	-	14	1453	c.1192G>A	c.(1192-1194)GAG>AAG	p.E398K	EFTUD2_uc010wje.1_Missense_Mutation_p.E363K|EFTUD2_uc010wjf.1_Missense_Mutation_p.E388K	NM_004247	NP_004238	Q15029	U5S1_HUMAN	elongation factor Tu GTP binding domain	398						Cajal body|catalytic step 2 spliceosome|cytoplasm|nuclear speck	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(33;0.109)														OREG0024466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NMT1	4836	broad.mit.edu	37	17	43182260	43182260	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43182260A>G	uc002ihz.2	+	11	1384	c.1366A>G	c.(1366-1368)ATG>GTG	p.M456V	NMT1_uc002iia.2_RNA	NM_021079	NP_066565	P30419	NMT1_HUMAN	N-myristoyltransferase 1	456					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation	actin cytoskeleton|cell junction|cytosol	glycylpeptide N-tetradecanoyltransferase activity				0		Prostate(33;0.155)																---	---	---	---
LRRC37A2	474170	broad.mit.edu	37	17	44626102	44626102	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44626102C>T	uc002ikn.1	+	9	3600	c.3597C>T	c.(3595-3597)AAC>AAT	p.N1199N	ARL17A_uc002iko.3_Intron|LRRC37A2_uc002ikq.1_Silent_p.N160N|LRRC37A2_uc010dax.1_Silent_p.N129N	NM_001006607	NP_001006608	A6NM11	L37A2_HUMAN	c114 SLIT-like testicular protein precursor	1199	Extracellular (Potential).					integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)														---	---	---	---
GOSR2	9570	broad.mit.edu	37	17	45017916	45017916	+	3'UTR	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45017916C>A	uc002ila.2	+	6					GOSR2_uc010wkh.1_Intron|GOSR2_uc002ikz.2_Intron	NM_004287	NP_004278			golgi SNAP receptor complex member 2 isoform A						cellular membrane fusion|ER to Golgi vesicle-mediated transport|protein transport	Golgi membrane|integral to membrane	transporter activity			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(9;0.102)															---	---	---	---
HOXB8	3218	broad.mit.edu	37	17	46691803	46691803	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46691803G>A	uc002inw.2	-	1	499	c.264C>T	c.(262-264)TAC>TAT	p.Y88Y		NM_024016	NP_076921	P17481	HXB8_HUMAN	homeobox B8	88						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
HLF	3131	broad.mit.edu	37	17	53392780	53392780	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53392780G>A	uc002iug.1	+	3	1169	c.644G>A	c.(643-645)CGC>CAC	p.R215H	HLF_uc010dce.1_Missense_Mutation_p.R130H|HLF_uc002iuh.2_Missense_Mutation_p.R130H|HLF_uc010wni.1_Missense_Mutation_p.R162H	NM_002126	NP_002117	Q16534	HLF_HUMAN	hepatic leukemia factor	215					multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2								T	TCF3	ALL								---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54428336	54428336	+	Intron	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54428336A>C	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
TRIM25	7706	broad.mit.edu	37	17	54981777	54981777	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54981777C>A	uc002iut.2	-	3	826	c.766G>T	c.(766-768)GAG>TAG	p.E256*	TRIM25_uc010dcj.2_Nonsense_Mutation_p.E48*	NM_005082	NP_005073	Q14258	TRI25_HUMAN	tripartite motif-containing 25	256	Interaction with influenza A virus NS1.|Potential.				innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|response to virus	cell junction|cytosol|nucleus	sequence-specific DNA binding transcription factor activity|ubiquitin-protein ligase activity|zinc ion binding			lung(1)|breast(1)|skin(1)	3	Breast(9;6.15e-08)																	---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55752431	55752431	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55752431A>G	uc002iuz.1	+	12	1062	c.889A>G	c.(889-891)AAT>GAT	p.N297D	MSI2_uc010wnm.1_Missense_Mutation_p.N293D	NM_138962	NP_620412	Q96DH6	MSI2H_HUMAN	musashi 2 isoform a	297						cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
ACE	1636	broad.mit.edu	37	17	61574303	61574303	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61574303G>A	uc002jau.1	+	24	3670	c.3648G>A	c.(3646-3648)GGG>GGA	p.G1216G	ACE_uc002jav.1_Silent_p.G642G|ACE_uc010ddv.1_Silent_p.G443G|ACE_uc010wpj.1_Silent_p.G601G|ACE_uc002jaw.1_RNA|ACE_uc010wpk.1_Silent_p.G421G	NM_000789	NP_000780	P12821	ACE_HUMAN	angiotensin I converting enzyme 1 isoform 1	1216	Extracellular (Potential).|Peptidase M2 2.				arachidonic acid secretion|hormone catabolic process|kidney development|peptide catabolic process|regulation of smooth muscle cell migration	endosome|external side of plasma membrane|extracellular space|integral to membrane|membrane fraction|plasma membrane	actin binding|bradykinin receptor binding|carboxypeptidase activity|chloride ion binding|drug binding|metallopeptidase activity|peptidyl-dipeptidase activity|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4					Benazepril(DB00542)|Captopril(DB01197)|Deserpidine(DB01089)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)													---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61895288	61895288	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61895288G>A	uc002jbu.2	+	19	2604	c.2347G>A	c.(2347-2349)GGA>AGA	p.G783R	DDX42_uc002jbv.2_Missense_Mutation_p.G783R|DDX42_uc002jbx.2_Missense_Mutation_p.G519R|DDX42_uc002jby.2_Missense_Mutation_p.G329R|DDX42_uc010wps.1_Missense_Mutation_p.G151R	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	783	Gly-rich.|Necessary for interaction with TP53BP2.				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
SCN4A	6329	broad.mit.edu	37	17	62020337	62020337	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62020337C>T	uc002jds.1	-	23	4214	c.4137G>A	c.(4135-4137)CAG>CAA	p.Q1379Q		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	1379	IV.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)													---	---	---	---
ERN1	2081	broad.mit.edu	37	17	62141446	62141446	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62141446C>T	uc002jdz.2	-	10	1100	c.987G>A	c.(985-987)AAG>AAA	p.K329K		NM_001433	NP_001424	O75460	ERN1_HUMAN	endoplasmic reticulum to nucleus signalling 1	329	Lumenal (Potential).				activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9																OREG0024657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63526100	63526100	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63526100G>A	uc002jfi.2	-	11	2815	c.2526C>T	c.(2524-2526)ATC>ATT	p.I842I	AXIN2_uc002jfh.2_Silent_p.I777I	NM_004655	NP_004646	Q9Y2T1	AXIN2_HUMAN	axin 2	842	DIX.				cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67125775	67125775	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67125775G>A	uc002jhw.1	-	7	1084	c.909C>T	c.(907-909)CTC>CTT	p.L303L		NM_080284	NP_525023	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A, member 6	303	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67178424	67178424	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67178424C>A	uc010dfa.1	-	23	3518	c.2639G>T	c.(2638-2640)AGA>ATA	p.R880I	ABCA10_uc010wqt.1_RNA|ABCA10_uc010dfb.1_Missense_Mutation_p.R481I	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10	880					transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67221504	67221504	+	Translation_Start_Site	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67221504C>A	uc010dfa.1	-	4	875	c.-4G>T	c.(-6--2)AAGGA>AATGA		ABCA10_uc010wqt.1_RNA|ABCA10_uc010dfc.1_Translation_Start_Site	NM_080282	NP_525021			ATP-binding cassette, sub-family A, member 10						transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
KCNJ2	3759	broad.mit.edu	37	17	68171712	68171712	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68171712G>T	uc010dfg.2	+	2	933	c.532G>T	c.(532-534)GCA>TCA	p.A178S	KCNJ2_uc002jir.2_Missense_Mutation_p.A178S	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	178	Helical; Name=M2; (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)																	---	---	---	---
CD300LF	146722	broad.mit.edu	37	17	72700850	72700850	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72700850A>G	uc002jlg.2	-	2	252	c.149T>C	c.(148-150)TTG>TCG	p.L50S	RAB37_uc002jlc.2_Intron|RAB37_uc010dfu.2_Intron|RAB37_uc002jld.2_Intron|CD300LF_uc002jlf.2_Missense_Mutation_p.L53S|CD300LF_uc010dfw.2_RNA|CD300LF_uc002jlh.2_Missense_Mutation_p.L50S|CD300LF_uc002jli.2_Missense_Mutation_p.L53S|CD300LF_uc010wra.1_Missense_Mutation_p.L50S|CD300LF_uc002jlj.1_Missense_Mutation_p.L53S	NM_139018	NP_620587	Q8TDQ1	CLM1_HUMAN	NK inhibitory receptor precursor	50	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
SLC16A5	9121	broad.mit.edu	37	17	73094127	73094127	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73094127C>A	uc002jmr.2	+						SLC16A5_uc002jms.1_Intron|SLC16A5_uc002jmt.2_Intron|SLC16A5_uc002jmu.2_Intron|SLC16A5_uc010wrt.1_Intron	NM_004695	NP_004686			solute carrier family 16, member 5						organic anion transport	integral to plasma membrane|membrane fraction	secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)													---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73389634	73389634	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73389634T>C	uc002jnx.3	-	2	433	c.76A>G	c.(76-78)AAG>GAG	p.K26E	GRB2_uc002jny.3_Missense_Mutation_p.K26E	NM_002086	NP_002077	P62993	GRB2_HUMAN	growth factor receptor-bound protein 2 isoform	26	SH3 1.				axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation	cytosol|Golgi apparatus	epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity			ovary(3)	3	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)													---	---	---	---
EVPL	2125	broad.mit.edu	37	17	74004745	74004745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74004745G>A	uc002jqi.2	-	22	4769	c.4541C>T	c.(4540-4542)TCG>TTG	p.S1514L	EVPL_uc010wss.1_Missense_Mutation_p.S1536L|EVPL_uc010wst.1_Missense_Mutation_p.S984L	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1514	Central fibrous rod domain.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ST6GALNAC1	55808	broad.mit.edu	37	17	74625570	74625570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74625570C>T	uc002jsh.2	-	2	529	c.355G>A	c.(355-357)GCA>ACA	p.A119T	ST6GALNAC1_uc002jsi.2_5'UTR|ST6GALNAC1_uc002jsj.2_RNA	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	119	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0																		---	---	---	---
ENPP7	339221	broad.mit.edu	37	17	77705066	77705066	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77705066C>T	uc002jxa.2	+	1	185	c.165C>T	c.(163-165)GAC>GAT	p.D55D		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	55					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78865556	78865556	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78865556T>C	uc002jyt.1	+	18	2825	c.2020T>C	c.(2020-2022)TAT>CAT	p.Y674H	RPTOR_uc010wug.1_Missense_Mutation_p.Y516H	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	674					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78882649	78882649	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78882649G>T	uc002jyt.1	+	21	3245	c.2440G>T	c.(2440-2442)GTC>TTC	p.V814F	RPTOR_uc010wug.1_Missense_Mutation_p.V656F	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	814					cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78938131	78938131	+	3'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78938131C>T	uc002jyt.1	+	34					RPTOR_uc010wug.1_3'UTR|RPTOR_uc002jyu.1_3'UTR	NM_020761	NP_065812			raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79430712	79430712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79430712C>T	uc002kaf.2	+	26	7696	c.7696C>T	c.(7696-7698)CGC>TGC	p.R2566C		NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1	2566	BAH.						DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
LRRC45	201255	broad.mit.edu	37	17	79984832	79984832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79984832G>A	uc002kde.2	+	6	959	c.719G>A	c.(718-720)CGC>CAC	p.R240H		NM_144999	NP_659436	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	240						centrosome				pancreas(1)	1	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)															---	---	---	---
UTS2R	2837	broad.mit.edu	37	17	80332642	80332642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80332642C>T	uc010wvl.1	+	1	442	c.442C>T	c.(442-444)CGC>TGC	p.R148C		NM_018949	NP_061822	Q9UKP6	UR2R_HUMAN	urotensin 2 receptor	148	Cytoplasmic (Potential).					integral to membrane|plasma membrane				breast(1)	1	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.00928)|BRCA - Breast invasive adenocarcinoma(99;0.0833)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80529613	80529613	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80529613C>T	uc002kfn.2	+	4	947	c.776C>T	c.(775-777)CCG>CTG	p.P259L	FOXK2_uc002kfm.1_Missense_Mutation_p.P259L|FOXK2_uc010diu.2_Missense_Mutation_p.P259L	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2	259	Fork-head.				embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80851515	80851515	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80851515C>A	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_5'Flank	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5396200	5396200	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5396200C>A	uc002kmt.1	-	19	3059	c.2973G>T	c.(2971-2973)CAG>CAT	p.Q991H	EPB41L3_uc010wzh.1_Missense_Mutation_p.Q822H|EPB41L3_uc002kmu.1_Missense_Mutation_p.Q769H|EPB41L3_uc010dkq.1_Missense_Mutation_p.Q660H|EPB41L3_uc002kms.1_Missense_Mutation_p.Q226H|EPB41L3_uc010wze.1_Missense_Mutation_p.Q296H|EPB41L3_uc010wzf.1_Missense_Mutation_p.Q288H|EPB41L3_uc010wzg.1_Missense_Mutation_p.Q263H|EPB41L3_uc010dkr.2_Missense_Mutation_p.Q383H	NM_012307	NP_036439	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	991	Carboxyl-terminal (CTD).				cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
CIDEA	1149	broad.mit.edu	37	18	12274164	12274164	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12274164A>G	uc002kqt.3	+	4	468	c.403A>G	c.(403-405)AGG>GGG	p.R135G	CIDEA_uc002kqu.3_Missense_Mutation_p.R169G|CIDEA_uc010dlc.2_RNA	NM_001279	NP_001270	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a isoform	135					DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change|lipid metabolic process|lipid storage|negative regulation of apoptosis|negative regulation of cytokine secretion|negative regulation of lipid catabolic process|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of sequestering of triglyceride|temperature homeostasis	mitochondrial envelope|nucleus	protein homodimerization activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TUBB6	84617	broad.mit.edu	37	18	12325150	12325150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12325150G>A	uc002kqw.2	+	4	407	c.362G>A	c.(361-363)CGG>CAG	p.R121Q	TUBB6_uc002kqv.2_Missense_Mutation_p.R49Q|TUBB6_uc010dld.2_RNA|TUBB6_uc002kqx.2_Missense_Mutation_p.R84Q|TUBB6_uc002kqy.2_Intron	NM_032525	NP_115914	Q9BUF5	TBB6_HUMAN	tubulin, beta 6	121					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0				READ - Rectum adenocarcinoma(1;0.0649)														---	---	---	---
C18orf8	29919	broad.mit.edu	37	18	21109596	21109596	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21109596T>C	uc010xax.1	+						C18orf8_uc002kul.2_Intron|C18orf8_uc010xay.1_Intron|NPC1_uc010dlu.1_RNA	NM_013326	NP_037458			colon cancer-associated protein Mic1											ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
DSG3	1830	broad.mit.edu	37	18	29044085	29044085	+	Silent	SNP	T	C	C	rs113083364		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29044085T>C	uc002kws.2	+	9	1120	c.1011T>C	c.(1009-1011)TAT>TAC	p.Y337Y		NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	337	Cadherin 3.|Extracellular (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			skin(4)|ovary(3)|lung(1)|central_nervous_system(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
MIR924	100126323	broad.mit.edu	37	18	37202099	37202099	+	RNA	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37202099A>G	hsa-mir-924|MI0005716	-			c.41A>G			LOC647946_uc010xcj.1_Intron|LOC647946_uc002lal.1_Intron																	0																		---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42281525	42281525	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42281525A>C	uc010dni.2	+	2	510	c.214A>C	c.(214-216)AAC>CAC	p.N72H	SETBP1_uc002lay.2_Missense_Mutation_p.N72H	NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	72						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43253755	43253755	+	Nonsense_Mutation	SNP	C	T	T	rs151319242		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43253755C>T	uc010dnj.2	+	19	2806	c.2485C>T	c.(2485-2487)CAG>TAG	p.Q829*	SLC14A2_uc002lbe.2_Nonsense_Mutation_p.Q829*	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	829						apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
TCEB3B	51224	broad.mit.edu	37	18	44561289	44561289	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44561289G>T	uc002lcr.1	-	1	700	c.347C>A	c.(346-348)GCG>GAG	p.A116E	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	116					regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
HDHD2	84064	broad.mit.edu	37	18	44656702	44656702	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44656702G>T	uc002lcs.2	-						HDHD2_uc002lct.2_Intron	NM_032124	NP_115500			haloacid dehalogenase-like hydrolase domain								hydrolase activity				0																		---	---	---	---
HDHD2	84064	broad.mit.edu	37	18	44662713	44662713	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44662713T>A	uc002lcs.2	-	2	231	c.98A>T	c.(97-99)AAA>ATA	p.K33I	HDHD2_uc002lct.2_5'UTR	NM_032124	NP_115500	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain	33							hydrolase activity				0																		---	---	---	---
DYM	54808	broad.mit.edu	37	18	46956658	46956658	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46956658A>C	uc002ldi.1	-	2	472	c.107T>G	c.(106-108)CTT>CGT	p.L36R	DYM_uc010xdf.1_Missense_Mutation_p.L36R	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin	36						Golgi apparatus					0																		---	---	---	---
CXXC1	30827	broad.mit.edu	37	18	47811481	47811481	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47811481T>C	uc002leq.3	-	7	1536	c.803A>G	c.(802-804)GAG>GGG	p.E268G	CXXC1_uc002lep.3_Missense_Mutation_p.E125G|CXXC1_uc002ler.3_Missense_Mutation_p.E268G|CXXC1_uc010doy.2_Missense_Mutation_p.E268G|CXXC1_uc002les.2_Missense_Mutation_p.E268G	NM_014593	NP_055408	Q9P0U4	CXXC1_HUMAN	CXXC finger 1 (PHD domain) isoform 2	268	Asp/Glu-rich (acidic).				histone H3-K4 methylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|Set1C/COMPASS complex	protein binding|unmethylated CpG binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48241512	48241512	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48241512A>G	uc002lev.2	+	3	1610	c.610A>G	c.(610-612)AAT>GAT	p.N204D	MAPK4_uc010xdm.1_5'UTR|MAPK4_uc010doz.2_Missense_Mutation_p.N204D	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	204	Protein kinase.				cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48604840	48604840	+	3'UTR	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48604840T>C	uc010xdp.1	+	12					SMAD4_uc002lfb.3_3'UTR	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	p.?(1)		pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
FECH	2235	broad.mit.edu	37	18	55233706	55233706	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55233706A>G	uc002lgq.3	-	5	688	c.571T>C	c.(571-573)TAT>CAT	p.Y191H	FECH_uc002lgp.3_Missense_Mutation_p.Y197H|FECH_uc002lgr.3_Missense_Mutation_p.Y49H	NM_000140	NP_000131	P22830	HEMH_HUMAN	ferrochelatase isoform b precursor	191			Y -> H (in EPP; enzyme retains 72% of activity).		generation of precursor metabolites and energy|heme biosynthetic process|protoporphyrinogen IX metabolic process|response to light stimulus	mitochondrial inner membrane|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferrochelatase activity|ferrous iron binding|protein binding			central_nervous_system(1)	1		Colorectal(73;0.227)																---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55335683	55335683	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55335683C>G	uc002lgw.2	-	18	2187	c.2187G>C	c.(2185-2187)TGG>TGC	p.W729C	uc002lgu.1_RNA|uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	729	Cytoplasmic (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)												Byler_disease				---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55862926	55862926	+	Intron	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55862926C>A	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_5'UTR	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59221533	59221533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59221533G>A	uc010dps.1	+	11	2023	c.2011G>A	c.(2011-2013)GGC>AGC	p.G671S	CDH20_uc002lif.2_Missense_Mutation_p.G665S	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	671	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
KDSR	2531	broad.mit.edu	37	18	61018111	61018111	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61018111C>T	uc010dpw.2	-						KDSR_uc010xem.1_Intron	NM_002035	NP_002026			3-ketodihydrosphingosine reductase precursor						3-keto-sphinganine metabolic process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding			skin(1)	1																		---	---	---	---
SERPINB5	5268	broad.mit.edu	37	18	61154235	61154235	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61154235G>A	uc002liz.3	+	3	367	c.225G>A	c.(223-225)TCG>TCA	p.S75S	SERPINB5_uc002liy.2_Silent_p.S75S	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	75					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
SERPINB13	5275	broad.mit.edu	37	18	61260166	61260166	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61260166C>T	uc002ljc.2	+	5	601	c.433C>T	c.(433-435)CGA>TGA	p.R145*	SERPINB13_uc002ljd.2_5'UTR|SERPINB13_uc010xep.1_Nonsense_Mutation_p.R154*|SERPINB13_uc010xeq.1_Intron|SERPINB13_uc010xer.1_Intron	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	145					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67806936	67806936	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67806936A>G	uc002lkp.2	-	21	2755	c.2687T>C	c.(2686-2688)GTA>GCA	p.V896A	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_5'UTR	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	896							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
CNDP2	55748	broad.mit.edu	37	18	72178084	72178084	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72178084A>G	uc002llm.1	+	6	655	c.493A>G	c.(493-495)ATG>GTG	p.M165V	CNDP2_uc002lln.1_Missense_Mutation_p.M81V|CNDP2_uc010dqs.2_Missense_Mutation_p.M1V	NM_018235	NP_060705	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2	165						cytoplasm	carboxypeptidase activity|metal ion binding|metallopeptidase activity|protein binding|tripeptidase activity			ovary(2)|skin(1)	3		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72998529	72998529	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72998529C>T	uc002lly.2	+	2	1595	c.1032C>T	c.(1030-1032)TAC>TAT	p.Y344Y		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	389						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	73000349	73000349	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73000349G>A	uc002lly.2	+	2	3415	c.2852G>A	c.(2851-2853)AGC>AAC	p.S951N		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	996						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74563868	74563868	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74563868G>A	uc002lmi.2	+	3	528	c.330G>A	c.(328-330)GCG>GCA	p.A110A	ZNF236_uc002lmj.2_RNA|ZNF236_uc002lmk.1_Silent_p.A110A	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	110	C2H2-type 3.				cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77475147	77475147	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77475147C>T	uc002lnh.1	+	8	1834	c.1687C>T	c.(1687-1689)CTG>TTG	p.L563L	CTDP1_uc002lni.1_Silent_p.L563L|CTDP1_uc010drd.1_Silent_p.L563L	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	563					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77513792	77513792	+	3'UTR	SNP	C	T	T	rs140149044		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77513792C>T	uc002lnh.1	+	13					CTDP1_uc002lni.1_3'UTR|CTDP1_uc010drd.1_3'UTR	NM_004715	NP_004706			CTD (carboxy-terminal domain, RNA polymerase II,						positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)														---	---	---	---
ADNP2	22850	broad.mit.edu	37	18	77894088	77894088	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77894088G>A	uc002lnw.2	+	4	1247	c.792G>A	c.(790-792)ACG>ACA	p.T264T		NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	264					cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)														---	---	---	---
ADNP2	22850	broad.mit.edu	37	18	77894778	77894778	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77894778G>A	uc002lnw.2	+	4	1937	c.1482G>A	c.(1480-1482)CCG>CCA	p.P494P		NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	494					cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)														---	---	---	---
CFD	1675	broad.mit.edu	37	19	861776	861776	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:861776A>G	uc002lqc.2	+	4	460	c.435A>G	c.(433-435)GGA>GGG	p.G145G	CFD_uc010drv.2_Silent_p.G152G	NM_001928	NP_001919	P00746	CFAD_HUMAN	complement factor D preproprotein	145	Peptidase S1.				complement activation, alternative pathway|platelet activation|platelet degranulation|proteolysis	platelet alpha granule lumen	serine-type endopeptidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
JSRP1	126306	broad.mit.edu	37	19	2254215	2254215	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2254215G>A	uc002lvi.1	-	3	268	c.233C>T	c.(232-234)ACG>ATG	p.T78M	JSRP1_uc002lvj.1_Missense_Mutation_p.T78M	NM_144616	NP_653217	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	78						sarcoplasmic reticulum membrane				pancreas(1)	1				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)												OREG0025137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC39A3	29985	broad.mit.edu	37	19	2737214	2737214	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2737214G>A	uc002lwg.2	-	2	296	c.42C>T	c.(40-42)GGC>GGT	p.G14G	SLC39A3_uc010xgy.1_Silent_p.G14G|SLC39A3_uc002lwh.2_Silent_p.G14G	NM_144564	NP_653165	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter),	14	Helical; (Potential).					integral to membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF554	115196	broad.mit.edu	37	19	2833886	2833886	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2833886C>T	uc002lwm.2	+	5	851	c.653C>T	c.(652-654)GCA>GTA	p.A218V	ZNF554_uc002lwl.2_Missense_Mutation_p.A167V	NM_001102651	NP_001096121	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	218					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		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)														---	---	---	---
ZNF556	80032	broad.mit.edu	37	19	2877814	2877814	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2877814G>A	uc002lwp.1	+	4	945	c.858G>A	c.(856-858)CCG>CCA	p.P286P	ZNF556_uc002lwq.2_Silent_p.P285P	NM_024967	NP_079243	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	286					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)	3				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)														---	---	---	---
ZNF57	126295	broad.mit.edu	37	19	2917901	2917901	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2917901A>G	uc002lwr.2	+	4	1430	c.1282A>G	c.(1282-1284)ACC>GCC	p.T428A	ZNF57_uc010xha.1_Missense_Mutation_p.T396A	NM_173480	NP_775751	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	428	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
CREB3L3	84699	broad.mit.edu	37	19	4164623	4164623	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4164623C>T	uc002lzl.2	+	5	816	c.700C>T	c.(700-702)CTG>TTG	p.L234L	CREB3L3_uc002lzm.2_Silent_p.L224L|CREB3L3_uc010xib.1_Silent_p.L223L|CREB3L3_uc010xic.1_Silent_p.L225L	NM_032607	NP_115996	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like	234	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ANKRD24	170961	broad.mit.edu	37	19	4216540	4216540	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4216540T>C	uc010dtt.1	+						ANKRD24_uc002lzs.2_Intron|ANKRD24_uc002lzt.2_Intron	NM_133475	NP_597732			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)														---	---	---	---
TMIGD2	126259	broad.mit.edu	37	19	4292680	4292680	+	Silent	SNP	G	A	A	rs148804982	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4292680G>A	uc002lzx.1	-	5	811	c.765C>T	c.(763-765)CCC>CCT	p.P255P	TMIGD2_uc010dtv.1_Silent_p.P251P	NM_144615	NP_653216	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain	255	Pro-rich.|Cytoplasmic (Potential).					integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
LONP1	9361	broad.mit.edu	37	19	5693672	5693672	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5693672A>G	uc002mcx.2	-	16	2462	c.2429T>C	c.(2428-2430)ATG>ACG	p.M810T	LONP1_uc002mcy.2_Missense_Mutation_p.M746T|LONP1_uc010duh.2_Missense_Mutation_p.M551T|LONP1_uc010dui.2_Missense_Mutation_p.M794T|LONP1_uc002mcz.2_Missense_Mutation_p.M614T	NM_004793	NP_004784	P36776	LONM_HUMAN	mitochondrial lon peptidase 1 precursor	810					cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding				0																		---	---	---	---
LONP1	9361	broad.mit.edu	37	19	5700863	5700863	+	Silent	SNP	C	T	T	rs146759309	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5700863C>T	uc002mcx.2	-	9	1476	c.1443G>A	c.(1441-1443)GCG>GCA	p.A481A	LONP1_uc002mcy.2_Silent_p.A417A|LONP1_uc010duh.2_Silent_p.A222A|LONP1_uc010dui.2_Silent_p.A465A|LONP1_uc002mcz.2_Silent_p.A285A	NM_004793	NP_004784	P36776	LONM_HUMAN	mitochondrial lon peptidase 1 precursor	481					cellular chaperone-mediated protein complex assembly|cellular response to oxidative stress|misfolded or incompletely synthesized protein catabolic process|mitochondrial DNA metabolic process|oxidation-dependent protein catabolic process|protein homooligomerization|response to hypoxia	mitochondrial nucleoid	ADP binding|ATP binding|ATP-dependent peptidase activity|DNA polymerase binding|G-quadruplex DNA binding|mitochondrial heavy strand promoter anti-sense binding|mitochondrial light strand promoter anti-sense binding|sequence-specific DNA binding|serine-type endopeptidase activity|single-stranded DNA binding|single-stranded RNA binding				0																		---	---	---	---
MLLT1	4298	broad.mit.edu	37	19	6230733	6230733	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6230733G>T	uc002mek.2	-							NM_005934	NP_005925			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|protein binding			skin(1)	1								T	MLL	AL								---	---	---	---
DENND1C	79958	broad.mit.edu	37	19	6471311	6471311	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6471311G>T	uc002mfe.2	-	17	1347	c.1255C>A	c.(1255-1257)CTT>ATT	p.L419I	DENND1C_uc002mfb.2_5'UTR|DENND1C_uc002mfc.2_5'UTR|DENND1C_uc002mfd.2_5'UTR|DENND1C_uc010xje.1_Missense_Mutation_p.L375I	NM_024898	NP_079174	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	419						clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1																		---	---	---	---
SH2D3A	10045	broad.mit.edu	37	19	6760727	6760727	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6760727A>C	uc002mft.2	-	3	535	c.341T>G	c.(340-342)GTG>GGG	p.V114G	SH2D3A_uc010xjg.1_Intron	NM_005490	NP_005481	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	114	SH2.				JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			breast(2)	2																		---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7685435	7685435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7685435G>A	uc002mgx.2	-	15	2118	c.2092C>T	c.(2092-2094)CGG>TGG	p.R698W		NM_020196	NP_064581	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	698	HAT 14.				transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4													Direct_reversal_of_damage|NER					---	---	---	---
CD320	51293	broad.mit.edu	37	19	8367483	8367483	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8367483A>G	uc002mjj.1	-	5	778	c.713T>C	c.(712-714)CTC>CCC	p.L238P	CD320_uc002mjk.1_RNA|CD320_uc002mjl.1_Missense_Mutation_p.L196P	NM_016579	NP_057663	Q9NPF0	CD320_HUMAN	8D6 antigen isoform 1 precursor	238	Helical; (Potential).				regulation of cell growth	endoplasmic reticulum|integral to membrane	growth factor activity				0																		---	---	---	---
ZNF558	148156	broad.mit.edu	37	19	8932736	8932736	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8932736T>C	uc002mkn.1	-	2	293	c.63A>G	c.(61-63)CAA>CAG	p.Q21Q	ZNF558_uc010xkh.1_5'Flank|ZNF558_uc010dwg.1_Silent_p.Q21Q	NM_144693	NP_653294	Q96NG5	ZN558_HUMAN	zinc finger protein 558	21					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9077103	9077103	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9077103T>C	uc002mkp.2	-	3	10547	c.10343A>G	c.(10342-10344)AAC>AGC	p.N3448S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3449	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9087343	9087343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9087343G>A	uc002mkp.2	-	1	4676	c.4472C>T	c.(4471-4473)CCT>CTT	p.P1491L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	1491	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
ZNF266	10781	broad.mit.edu	37	19	9524026	9524026	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9524026G>A	uc002mll.2	-	4	1841	c.1575C>T	c.(1573-1575)TGC>TGT	p.C525C	ZNF266_uc002mlm.2_Silent_p.C525C|ZNF266_uc002mln.2_Silent_p.C525C|ZNF266_uc002mlo.2_Silent_p.C525C|ZNF266_uc010dwp.2_Silent_p.C525C|ZNF266_uc010dwq.2_Silent_p.C525C	NM_198058	NP_932175	Q14584	ZN266_HUMAN	zinc finger protein 266	525	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	9968487	9968487	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9968487G>A	uc002mmp.2	-	3	292	c.264C>T	c.(262-264)CGC>CGT	p.R88R	OLFM2_uc002mmo.2_Silent_p.R10R	NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor	88						extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
ZGLP1	100125288	broad.mit.edu	37	19	10419251	10419251	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10419251C>T	uc002mnw.3	-	1	983	c.107G>A	c.(106-108)CGT>CAT	p.R36H	FDX1L_uc002mnx.1_Intron	NM_001103167	NP_001096637	P0C6A0	ZGLP1_HUMAN	GATA like protein-1	36					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
CDC37	11140	broad.mit.edu	37	19	10506695	10506695	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10506695C>T	uc002mof.1	-	2	403	c.287G>A	c.(286-288)CGG>CAG	p.R96Q	CDC37_uc002moe.1_5'Flank|CDC37_uc010dxf.1_5'UTR|CDC37_uc002mog.1_Missense_Mutation_p.R96Q|CDC37_uc002moh.2_Missense_Mutation_p.R96Q	NM_007065	NP_008996	Q16543	CDC37_HUMAN	cell division cycle 37 protein	96					protein targeting|regulation of cyclin-dependent protein kinase activity|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway		unfolded protein binding				0			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)														---	---	---	---
KEAP1	9817	broad.mit.edu	37	19	10610092	10610092	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10610092G>A	uc002moq.1	-	2	774	c.618C>T	c.(616-618)TAC>TAT	p.Y206Y	KEAP1_uc002mor.1_Silent_p.Y206Y	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	206	BACK.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)															---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11565601	11565601	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11565601C>T	uc002mry.1	-	7	1224	c.844G>A	c.(844-846)GCC>ACC	p.A282T	ELAVL3_uc002mrx.1_Missense_Mutation_p.A275T	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1	282				Missing (in Ref. 1; AAA58677 and 4; BAA21838).	cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ELOF1	84337	broad.mit.edu	37	19	11664600	11664600	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11664600G>A	uc002mse.1	-	4	277	c.213C>T	c.(211-213)TAC>TAT	p.Y71Y	ELOF1_uc002msd.1_Silent_p.Y92Y	NM_032377	NP_115753	P60002	ELOF1_HUMAN	elongation factor 1 homolog (ELF1, S.	71					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding				0																		---	---	---	---
ZNF564	163050	broad.mit.edu	37	19	12638137	12638137	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12638137A>G	uc002mty.2	-	4	995	c.785T>C	c.(784-786)TTT>TCT	p.F262S	ZNF709_uc002mtx.3_Intron	NM_144976	NP_659413	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	262	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14574680	14574680	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14574680C>T	uc002myp.2	+	11	1704	c.1536C>T	c.(1534-1536)GTC>GTT	p.V512V	PKN1_uc002myq.2_Silent_p.V518V	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2	512					activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
HSH2D	84941	broad.mit.edu	37	19	16268222	16268222	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16268222G>A	uc002ndp.3	+	9	1207	c.676G>A	c.(676-678)GCC>ACC	p.A226T	HSH2D_uc002ndr.2_Missense_Mutation_p.R169H|HSH2D_uc010ead.2_RNA	NM_032855	NP_116244	Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	226						cytoplasm|nucleus					0																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16918704	16918704	+	Silent	SNP	C	T	T	rs61735363	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16918704C>T	uc002neu.3	+	18	4466	c.4044C>T	c.(4042-4044)CCC>CCT	p.P1348P	NWD1_uc002net.3_Silent_p.P1213P|NWD1_uc002nev.3_Silent_p.P1142P			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;	1348							ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17298808	17298808	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17298808C>T	uc010eak.2	+	19	2794	c.2642C>T	c.(2641-2643)ACC>ATC	p.T881I	MYO9B_uc002nfi.2_Missense_Mutation_p.T881I|MYO9B_uc002nfj.1_Missense_Mutation_p.T881I	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	881	Myosin head-like.				actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1																		---	---	---	---
GTPBP3	84705	broad.mit.edu	37	19	17452410	17452410	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17452410G>T	uc010eas.2	+	9	1442	c.1377G>T	c.(1375-1377)GAG>GAT	p.E459D	GTPBP3_uc010xpo.1_Missense_Mutation_p.E481D|GTPBP3_uc002ngh.3_Missense_Mutation_p.E438D|GTPBP3_uc002ngg.3_Missense_Mutation_p.E491D|GTPBP3_uc002ngi.3_Missense_Mutation_p.E125D	NM_032620	NP_116009	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial) isoform V	459					tRNA modification	mitochondrion	GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
LPAR2	9170	broad.mit.edu	37	19	19735185	19735185	+	Silent	SNP	G	A	A	rs144833106		TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19735185G>A	uc002nnb.3	-	3	1075	c.936C>T	c.(934-936)TGC>TGT	p.C312C	LPAR2_uc002nna.3_Silent_p.C312C|LPAR2_uc002nnc.3_Silent_p.C312C	NM_004720	NP_004711	Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	312	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration	cell surface|integral to plasma membrane	LIM domain binding|lipid binding			ovary(1)|breast(1)	2																		---	---	---	---
ZNF506	440515	broad.mit.edu	37	19	19906095	19906095	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19906095A>G	uc010eci.2	-	4	749	c.601T>C	c.(601-603)TAT>CAT	p.Y201H	ZNF506_uc002nog.2_Intron|ZNF506_uc002noh.3_Missense_Mutation_p.Y169H	NM_001099269	NP_001092739	Q5JVG8	ZN506_HUMAN	zinc finger protein 506 isoform 1	201	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF708	7562	broad.mit.edu	37	19	21477541	21477541	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21477541G>A	uc002npq.1	-	4	425	c.227C>T	c.(226-228)GCT>GTT	p.A76V	ZNF708_uc002npr.1_Missense_Mutation_p.A12V|ZNF708_uc010ecs.1_Missense_Mutation_p.A12V	NM_021269	NP_067092	P17019	ZN708_HUMAN	zinc finger protein 708	76					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(4)|skin(2)	6																		---	---	---	---
ZNF254	9534	broad.mit.edu	37	19	24309052	24309052	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24309052T>C	uc002nru.2	+						ZNF254_uc010xrk.1_Intron	NM_203282	NP_975011			zinc finger protein 254						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)																---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31039376	31039376	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039376C>T	uc002nsu.1	+	4	2988	c.2850C>T	c.(2848-2850)CAC>CAT	p.H950H	ZNF536_uc010edd.1_Silent_p.H950H	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	950					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31039865	31039865	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039865G>T	uc002nsu.1	+	4	3477	c.3339G>T	c.(3337-3339)AAG>AAT	p.K1113N	ZNF536_uc010edd.1_Missense_Mutation_p.K1113N	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1113					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
LSM14A	26065	broad.mit.edu	37	19	34687605	34687605	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34687605C>T	uc002nvb.3	+	3	548	c.352C>T	c.(352-354)CCC>TCC	p.P118S	LSM14A_uc002nva.3_Missense_Mutation_p.P118S|LSM14A_uc010xru.1_Missense_Mutation_p.P118S	NM_001114093	NP_001107565	Q8ND56	LS14A_HUMAN	LSM14 homolog A isoform a	118					cytoplasmic mRNA processing body assembly|multicellular organismal development|regulation of translation	cytoplasmic mRNA processing body|intracellular membrane-bounded organelle|stress granule				skin(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34921570	34921570	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34921570T>C	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490			SUMO-1 activating enzyme subunit 2						protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
ZNF302	55900	broad.mit.edu	37	19	35174067	35174067	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35174067C>T	uc002nvr.1	+	5	533	c.270C>T	c.(268-270)TCC>TCT	p.S90S	ZNF302_uc010xrz.1_Silent_p.S47S|ZNF302_uc002nvp.1_Silent_p.S46S|ZNF302_uc002nvq.1_Silent_p.S46S|ZNF302_uc002nvs.1_Silent_p.S46S	NM_018443	NP_060913	Q9NR11	ZN302_HUMAN	zinc finger protein 302	Error:Variant_position_missing_in_Q9NR11_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
ATP4A	495	broad.mit.edu	37	19	36051500	36051500	+	Silent	SNP	G	A	A	rs149907700	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36051500G>A	uc002oal.1	-	6	581	c.552C>T	c.(550-552)CGC>CGT	p.R184R	ATP4A_uc010eee.1_5'Flank	NM_000704	NP_000695	P20648	ATP4A_HUMAN	hydrogen/potassium-exchanging ATPase 4A	184	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport	integral to plasma membrane	ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding			ovary(1)	1	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831)													---	---	---	---
ZNF567	163081	broad.mit.edu	37	19	37210721	37210721	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37210721T>A	uc010xtl.1	+	6	1317	c.1095T>A	c.(1093-1095)TAT>TAA	p.Y365*	ZNF567_uc002oeo.1_Nonsense_Mutation_p.Y365*|ZNF567_uc010xtk.1_Nonsense_Mutation_p.Y365*|ZNF567_uc002oep.3_Nonsense_Mutation_p.Y334*|ZNF567_uc002oeq.1_Nonsense_Mutation_p.Y334*	NM_152603	NP_689816	Q8N184	ZN567_HUMAN	zinc finger protein 567	365	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
ZNF607	84775	broad.mit.edu	37	19	38189172	38189172	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38189172T>C	uc002ohc.1	-	5	2456	c.1860A>G	c.(1858-1860)AAA>AAG	p.K620K	ZNF607_uc002ohb.1_Silent_p.K619K	NM_032689	NP_116078	Q96SK3	ZN607_HUMAN	zinc finger protein 607	620	C2H2-type 18.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38572895	38572895	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38572895C>T	uc002ohk.2	+	3	1199	c.690C>T	c.(688-690)CCC>CCT	p.P230P		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	230					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38573583	38573583	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38573583G>A	uc002ohk.2	+	3	1887	c.1378G>A	c.(1378-1380)GCA>ACA	p.A460T		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	460					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
DPF1	8193	broad.mit.edu	37	19	38706879	38706879	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38706879T>C	uc002ohl.2	-	8	775	c.748A>G	c.(748-750)ACT>GCT	p.T250A	DPF1_uc002ohm.2_Missense_Mutation_p.T294A|DPF1_uc002ohn.2_Missense_Mutation_p.T212A|DPF1_uc010xtu.1_Missense_Mutation_p.T268A|DPF1_uc010xtv.1_Missense_Mutation_p.T268A	NM_004647	NP_004638	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1 isoform	250					induction of apoptosis|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nBAF complex	zinc ion binding				0	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39018367	39018367	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39018367C>T	uc002oit.2	+	73	10897	c.10767C>T	c.(10765-10767)CCC>CCT	p.P3589P	RYR1_uc002oiu.2_Silent_p.P3584P|RYR1_uc002oiv.1_Silent_p.P504P|RYR1_uc010xuf.1_Silent_p.P509P	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3589					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
CAPN12	147968	broad.mit.edu	37	19	39221806	39221806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39221806C>T	uc002ojd.1	-	19	2324	c.2015G>A	c.(2014-2016)CGT>CAT	p.R672H	CAPN12_uc010egd.1_Missense_Mutation_p.R33H|CAPN12_uc002ojc.1_Missense_Mutation_p.R126H	NM_144691	NP_653292	Q6ZSI9	CAN12_HUMAN	calpain 12	672	Domain IV.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			central_nervous_system(1)|pancreas(1)	2	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
NFKBIB	4793	broad.mit.edu	37	19	39399383	39399383	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39399383G>A	uc002ojw.2	+	6	1040	c.982G>A	c.(982-984)GAC>AAC	p.D328N	NFKBIB_uc002ojx.2_3'UTR|NFKBIB_uc002ojy.2_3'UTR	NM_002503	NP_002494	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene	328					innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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|transcription, DNA-dependent	cytosol|nucleus	protein binding|signal transducer activity|transcription coactivator activity			lung(1)|kidney(1)	2	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
FBXO17	115290	broad.mit.edu	37	19	39443215	39443215	+	Intron	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39443215T>C	uc002okg.1	-						SARS2_uc010xuq.1_5'Flank|FBXO17_uc002okf.1_Missense_Mutation_p.Q3R	NM_024907	NP_079183			F-box protein FBG4 isoform 2						protein catabolic process	SCF ubiquitin ligase complex	glycoprotein binding				0	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
IL28B	282617	broad.mit.edu	37	19	39735101	39735101	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39735101G>A	uc010xut.1	-	2	218	c.214C>T	c.(214-216)CGC>TGC	p.R72C	IL28B_uc010xuu.1_Missense_Mutation_p.R72C	NM_172139	NP_742151	Q8IZI9	IL28B_HUMAN	interleukin 28B	72					response to virus	extracellular space	cytokine activity				0	all_cancers(60;2.81e-07)|all_lung(34;7.81e-08)|Lung NSC(34;9.29e-08)|all_epithelial(25;3.9e-07)|Ovarian(47;0.0315)		Epithelial(26;1.55e-27)|all cancers(26;1.41e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)															---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39860437	39860437	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39860437C>T	uc002olb.2	+	6	1374	c.339C>T	c.(337-339)ATC>ATT	p.I113I	SAMD4B_uc002ola.2_Silent_p.I113I	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	113							protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
ZNF546	339327	broad.mit.edu	37	19	40520949	40520949	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40520949G>C	uc002oms.2	+	7	2028	c.1772G>C	c.(1771-1773)AGT>ACT	p.S591T	ZNF546_uc002omt.2_Missense_Mutation_p.S565T	NM_178544	NP_848639	Q86UE3	ZN546_HUMAN	zinc finger protein 546	591	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)																	---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41265406	41265406	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41265406G>A	uc002ooz.2	+	3	852	c.317G>A	c.(316-318)CGC>CAC	p.R106H	SNRPA_uc002opa.2_Missense_Mutation_p.R56H	NM_004596	NP_004587	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	106						nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding			skin(2)|ovary(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41388023	41388023	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41388023C>T	uc002opm.2	-	1	635	c.93G>A	c.(91-93)GGG>GGA	p.G31G	CYP2A7_uc002opo.2_Intron|CYP2A7_uc002opn.2_Silent_p.G31G	NM_000764	NP_000755	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A,	31						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42839311	42839311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42839311G>A	uc002otl.3	+	4	1318	c.683G>A	c.(682-684)CGT>CAT	p.R228H	MEGF8_uc002otm.3_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	228	Extracellular (Potential).					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
LIPE	3991	broad.mit.edu	37	19	42912224	42912224	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42912224G>T	uc002otr.2	-	4	1837	c.1560C>A	c.(1558-1560)CCC>CCA	p.P520P	uc010eif.1_Intron|LIPE_uc002ots.1_Silent_p.P265P	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	520					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)																---	---	---	---
CXCL17	284340	broad.mit.edu	37	19	42937210	42937210	+	Silent	SNP	C	T	T	rs151260095	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42937210C>T	uc002otu.2	-	3	332	c.180G>A	c.(178-180)CCG>CCA	p.P60P	uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron	NM_198477	NP_940879	Q6UXB2	VCC1_HUMAN	chemokine (C-X-C motif) ligand 17 precursor	60					angiogenesis|cell differentiation|chemotaxis	extracellular region					0		Prostate(69;0.00899)																---	---	---	---
CEACAM1	634	broad.mit.edu	37	19	43015774	43015774	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43015774G>A	uc002otv.2	-	7	1496	c.1383C>T	c.(1381-1383)AGC>AGT	p.S461S	uc010eif.1_Intron|uc002ott.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron|CEACAM1_uc010eii.2_Intron|CEACAM1_uc002otw.2_Intron|CEACAM1_uc010eij.2_Intron|CEACAM1_uc002otx.2_Silent_p.S396S|CEACAM1_uc002oty.2_Silent_p.S365S|CEACAM1_uc002otz.2_Intron|CEACAM1_uc010eik.2_Silent_p.S187S	NM_001712	NP_001703	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion	461	Cytoplasmic (Potential).				angiogenesis|cell migration|homophilic cell adhesion|integrin-mediated signaling pathway	extracellular region|integral to plasma membrane|membrane fraction				ovary(1)|central_nervous_system(1)	2		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)													---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43689024	43689024	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43689024G>T	uc002ovu.2	-	2	471	c.340C>A	c.(340-342)CGG>AGG	p.R114R	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Silent_p.R42R|PSG5_uc002ovx.2_Silent_p.R114R|PSG5_uc002ovv.2_Silent_p.R114R|PSG5_uc002ovw.2_Silent_p.R114R	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	114	Ig-like V-type.				female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43690566	43690566	+	5'UTR	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43690566C>T	uc002ovu.2	-	1					PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovx.2_5'UTR|PSG5_uc002ovv.2_5'UTR|PSG5_uc002ovw.2_5'UTR	NM_002781	NP_002772			pregnancy specific beta-1-glycoprotein 5						female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
ZNF224	7767	broad.mit.edu	37	19	44611163	44611163	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44611163G>T	uc002oyh.1	+	6	1152	c.850G>T	c.(850-852)GGG>TGG	p.G284W	uc002oyi.2_RNA	NM_013398	NP_037530	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	284					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	DNA binding|protein binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)																---	---	---	---
ZNF227	7770	broad.mit.edu	37	19	44739572	44739572	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44739572G>T	uc002oyu.2	+	6	1194	c.989G>T	c.(988-990)GGC>GTC	p.G330V	ZNF227_uc010xwu.1_Missense_Mutation_p.G279V|ZNF227_uc002oyv.2_Missense_Mutation_p.G330V|ZNF227_uc010xwv.1_Missense_Mutation_p.G279V|ZNF227_uc010xww.1_Missense_Mutation_p.G251V|ZNF227_uc002oyw.2_Missense_Mutation_p.G302V|ZNF227_uc010ejh.2_Missense_Mutation_p.G323V|ZNF235_uc002oyx.1_Intron	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	330	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)																---	---	---	---
ZNF296	162979	broad.mit.edu	37	19	45574990	45574990	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45574990G>A	uc002pao.2	-	3	1354	c.1297C>T	c.(1297-1299)CGC>TGC	p.R433C		NM_145288	NP_660331	Q8WUU4	ZN296_HUMAN	zinc finger protein 296	433	C2H2-type 5.				regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
FOSB	2354	broad.mit.edu	37	19	45974040	45974040	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45974040G>A	uc002pbx.3	+	2	872	c.280G>A	c.(280-282)GTC>ATC	p.V94I	ERCC1_uc002pbu.1_Intron|FOSB_uc002pbw.2_Missense_Mutation_p.V94I|FOSB_uc010eke.2_Missense_Mutation_p.V55I|FOSB_uc002pby.3_Missense_Mutation_p.V94I|FOSB_uc010eka.1_Missense_Mutation_p.V55I|FOSB_uc010ekb.1_Missense_Mutation_p.V94I|FOSB_uc010ekc.1_Intron|FOSB_uc010ekf.2_Missense_Mutation_p.V55I|FOSB_uc010ekd.1_Missense_Mutation_p.V94I|FOSB_uc010ekg.2_Intron|FOSB_uc002pca.3_Missense_Mutation_p.V45I	NM_006732	NP_006723	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	94					behavior|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|lung(1)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)														---	---	---	---
DMPK	1760	broad.mit.edu	37	19	46278263	46278263	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46278263C>T	uc002pdd.1	-	8	1750	c.1206G>A	c.(1204-1206)GCG>GCA	p.A402A	DMPK_uc010xxs.1_Silent_p.A303A|DMPK_uc002pde.1_Silent_p.A397A|DMPK_uc002pdf.1_Silent_p.A392A|DMPK_uc002pdg.1_Silent_p.A387A|DMPK_uc002pdh.1_Silent_p.A387A|DMPK_uc002pdi.1_Silent_p.A418A|DMPK_uc010xxt.1_Silent_p.A387A	NM_001081563	NP_001075032	Q09013	DMPK_HUMAN	myotonic dystrophy protein kinase isoform 1	402	AGC-kinase C-terminal.				regulation of heart contraction		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)	3		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)														---	---	---	---
KPTN	11133	broad.mit.edu	37	19	47984241	47984241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47984241C>T	uc002pgy.2	-	5	603	c.499G>A	c.(499-501)GAC>AAC	p.D167N	KPTN_uc010xys.1_RNA	NM_007059	NP_008990	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	167					actin filament organization|cellular component movement|sensory perception of sound	actin cytoskeleton|growth cone|microtubule organizing center|nucleus|perinuclear region of cytoplasm|stereocilium	actin binding			ovary(1)	1		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)														---	---	---	---
CRX	1406	broad.mit.edu	37	19	48343102	48343102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48343102G>A	uc002phq.3	+	4	982	c.778G>A	c.(778-780)GCC>ACC	p.A260T		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	260					organ morphogenesis|response to stimulus|visual perception		leucine zipper domain binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48647224	48647224	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48647224C>T	uc002pia.1	-						LIG1_uc010xze.1_Intron|LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225			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)								NER					---	---	---	---
TMEM143	55260	broad.mit.edu	37	19	48845798	48845798	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48845798G>A	uc002pix.1	-	6	973	c.964C>T	c.(964-966)CGG>TGG	p.R322W	TMEM143_uc002piw.1_Intron|TMEM143_uc002piy.1_Missense_Mutation_p.R287W|TMEM143_uc010xzn.1_Missense_Mutation_p.R257W|TMEM143_uc010elw.1_Missense_Mutation_p.R222W|TMEM143_uc010xzo.1_Missense_Mutation_p.R112W	NM_018273	NP_060743	Q96AN5	TM143_HUMAN	transmembrane protein 143	322						integral to membrane|mitochondrion					0		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)														---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49863216	49863216	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49863216C>T	uc002pnj.2	-	2	208	c.117G>A	c.(115-117)CCG>CCA	p.P39P	TEAD2_uc002png.2_Silent_p.P39P|TEAD2_uc002pnh.2_Silent_p.P39P|TEAD2_uc002pni.2_Silent_p.P39P|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Silent_p.P39P	NM_003598	NP_003589	Q15562	TEAD2_HUMAN	TEA domain family member 2	39					hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50812440	50812440	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50812440G>A	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
SPIB	6689	broad.mit.edu	37	19	50926110	50926110	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50926110C>A	uc002psd.2	+	4	180	c.155C>A	c.(154-156)CCT>CAT	p.P52H	SPIB_uc002pse.2_Missense_Mutation_p.P52H|SPIB_uc010ycc.1_Intron	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	52	TAD2.				regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	sequence-specific DNA binding			lung(1)|kidney(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
SIGLEC9	27180	broad.mit.edu	37	19	51631709	51631709	+	Missense_Mutation	SNP	C	T	T	rs61739656	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51631709C>T	uc002pvu.2	+	6	1212	c.1145C>T	c.(1144-1146)GCG>GTG	p.A382V	SIGLEC9_uc010yct.1_Missense_Mutation_p.A382V	NM_014441	NP_055256	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9 precursor	382	Cytoplasmic (Potential).				cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)														---	---	---	---
ZNF600	162966	broad.mit.edu	37	19	53269380	53269380	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53269380G>A	uc002qab.3	-	3	1915	c.1629C>T	c.(1627-1629)TGC>TGT	p.C543C		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	543	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)														---	---	---	---
CACNG6	59285	broad.mit.edu	37	19	54515275	54515275	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54515275G>A	uc002qct.2	+	4	1205	c.615G>A	c.(613-615)CCG>CCA	p.P205P	CACNG6_uc002qcu.2_Silent_p.P159P|CACNG6_uc002qcv.2_Silent_p.P134P	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN	voltage-dependent calcium channel gamma-6	205						voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(2)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)														---	---	---	---
NLRP7	199713	broad.mit.edu	37	19	55450708	55450708	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55450708G>A	uc002qih.3	-	4	1555	c.1479C>T	c.(1477-1479)CAC>CAT	p.H493H	NLRP7_uc002qig.3_Silent_p.H493H|NLRP7_uc002qii.3_Silent_p.H493H|NLRP7_uc010esk.2_Silent_p.H493H|NLRP7_uc010esl.2_Silent_p.H521H	NM_206828	NP_996611	Q8WX94	NALP7_HUMAN	NACHT, leucine rich repeat and PYD containing 7	493							ATP binding			large_intestine(1)|breast(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(193;0.0325)														---	---	---	---
ZNF628	89887	broad.mit.edu	37	19	55994085	55994085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55994085G>A	uc002qld.2	+	3	2078	c.1513G>A	c.(1513-1515)GCC>ACC	p.A505T	NAT14_uc002qle.1_5'Flank	NM_033113	NP_149104	Q5EBL2	ZN628_HUMAN	zinc finger protein 628	505						nucleus	DNA binding|zinc ion binding				0	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)														---	---	---	---
NLRP4	147945	broad.mit.edu	37	19	56392902	56392902	+	Silent	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56392902T>G	uc002qmd.3	+	10	3356	c.2934T>G	c.(2932-2934)CCT>CCG	p.P978P	NLRP4_uc002qmf.2_Silent_p.P903P|NLRP4_uc010etf.2_Silent_p.P753P	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	978							ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)														---	---	---	---
ANGPT4	51378	broad.mit.edu	37	20	870947	870947	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:870947T>C	uc002wei.2	-	2	477	c.374A>G	c.(373-375)CAG>CGG	p.Q125R	ANGPT4_uc010zpn.1_Missense_Mutation_p.Q119R	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	125	Potential.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2																		---	---	---	---
SIRPA	140885	broad.mit.edu	37	20	1902206	1902206	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1902206T>C	uc002wfq.2	+	4	962	c.602T>C	c.(601-603)GTA>GCA	p.V201A	SIRPA_uc010zps.1_Missense_Mutation_p.V181A|SIRPA_uc002wfr.2_Missense_Mutation_p.V201A|SIRPA_uc002wfs.2_Missense_Mutation_p.V201A|SIRPA_uc002wft.2_Missense_Mutation_p.V201A	NM_001040022	NP_001035111	P78324	SHPS1_HUMAN	signal-regulatory protein alpha precursor	201	Ig-like C1-type 1.|Extracellular (Potential).		VG -> AR.		blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)														---	---	---	---
TGM6	343641	broad.mit.edu	37	20	2384384	2384384	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2384384G>A	uc002wfy.1	+	9	1312	c.1251G>A	c.(1249-1251)ACG>ACA	p.T417T	TGM6_uc010gal.1_Silent_p.T417T	NM_198994	NP_945345	O95932	TGM3L_HUMAN	transglutaminase 6	417					cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)													---	---	---	---
GNRH2	2797	broad.mit.edu	37	20	3025077	3025077	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3025077G>A	uc002whr.1	+	2	68	c.17G>A	c.(16-18)CGA>CAA	p.R6Q	GNRH2_uc002whp.1_Missense_Mutation_p.R6Q|GNRH2_uc002whq.1_Missense_Mutation_p.R6Q|GNRH2_uc010gau.1_Missense_Mutation_p.R6Q|MRPS26_uc002whs.2_5'Flank	NM_001501	NP_001492	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2 isoform a	6					multicellular organismal development|signal transduction	extracellular region|soluble fraction	hormone activity				0																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3145701	3145701	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3145701C>T	uc002wia.1	-	3	2819	c.1421G>A	c.(1420-1422)CGC>CAC	p.R474H	ProSAPiP1_uc002wib.1_Missense_Mutation_p.R428H	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	474	Potential.					cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
ADAM33	80332	broad.mit.edu	37	20	3652952	3652952	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3652952G>A	uc002wit.2	-	14	1513	c.1426C>T	c.(1426-1428)CGC>TGC	p.R476C	ADAM33_uc002wiq.1_5'Flank|ADAM33_uc002wir.1_Missense_Mutation_p.R476C|ADAM33_uc002wis.2_5'UTR|ADAM33_uc002wiu.2_Missense_Mutation_p.R476C|uc002wiv.1_5'Flank|ADAM33_uc002wiw.1_Intron|ADAM33_uc010gba.1_Intron|ADAM33_uc010gbb.1_Intron	NM_025220	NP_079496	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33 isoform alpha	476	Extracellular (Potential).|Disintegrin.				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4																		---	---	---	---
ADRA1D	146	broad.mit.edu	37	20	4202257	4202257	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4202257T>C	uc002wkr.2	-	2	1687	c.1632A>G	c.(1630-1632)CTA>CTG	p.L544L		NM_000678	NP_000669	P25100	ADA1D_HUMAN	alpha-1D-adrenergic receptor	544	Cytoplasmic (By similarity).			KPPSAFREWRLLGPFRRPTTQLRAKVSSLSHKIRAGGAQRA EAACAQRSEVEAVSLGVPHEVAEGATCQAYELADYSNLRET DI -> SHPAPSASGGCWGRSGDPRPSCAPKSPACRTRSPP GARSAQRQRAPSAQRWRLCP (in Ref. 1).	cell proliferation|cell-cell signaling|DNA metabolic process|G-protein signaling, coupled to cAMP nucleotide second messenger|multicellular organismal development|positive regulation of cell proliferation	integral to plasma membrane	alpha1-adrenergic receptor activity				0					Alfuzosin(DB00346)|Bethanidine(DB00217)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Doxazosin(DB00590)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Methotrimeprazine(DB01403)|Norepinephrine(DB00368)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)													---	---	---	---
MCM8	84515	broad.mit.edu	37	20	5933111	5933111	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5933111T>C	uc002wmi.2	+	3	567	c.190T>C	c.(190-192)TCA>CCA	p.S64P	TRMT6_uc002wmh.1_5'Flank|TRMT6_uc010zra.1_5'Flank|TRMT6_uc010gbn.1_5'Flank|TRMT6_uc010gbo.1_5'Flank|MCM8_uc002wmj.2_Missense_Mutation_p.S64P|MCM8_uc002wmk.2_Missense_Mutation_p.S64P|MCM8_uc002wml.2_Missense_Mutation_p.S64P|MCM8_uc010gbp.2_Missense_Mutation_p.S64P	NM_032485	NP_115874	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	64					cell cycle checkpoint|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of transcription, DNA-dependent|S phase of mitotic cell cycle|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|nucleoside-triphosphatase activity			skin(1)	1																		---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14307651	14307651	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14307651T>C	uc002wov.1	-	3	969	c.502A>G	c.(502-504)ACA>GCA	p.T168A	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Missense_Mutation_p.T168A	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	168	Extracellular (Potential).|LRR 5.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)														---	---	---	---
THBD	7056	broad.mit.edu	37	20	23028798	23028798	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23028798G>A	uc002wss.2	-	1	1504	c.1344C>T	c.(1342-1344)GGC>GGT	p.G448G	THBD_uc002wst.1_5'Flank|THBD_uc002wsu.1_Silent_p.G389G	NM_000361	NP_000352	P07204	TRBM_HUMAN	thrombomodulin precursor	448	EGF-like 6; calcium-binding (Potential).|Extracellular (Potential).				blood coagulation|leukocyte migration|negative regulation of fibrinolysis|negative regulation of platelet activation	cell surface|integral to plasma membrane	calcium ion binding|protein binding|transmembrane receptor activity				0	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)													---	---	---	---
CST11	140880	broad.mit.edu	37	20	23433415	23433415	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23433415G>T	uc002wtf.1	-	1	68	c.34C>A	c.(34-36)CTG>ATG	p.L12M	CST11_uc002wtg.1_Missense_Mutation_p.L12M	NM_130794	NP_570612	Q9H112	CST11_HUMAN	cystatin 11 isoform 1 precursor	12					defense response to bacterium	cytoplasm|nucleus	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)																	---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24524119	24524119	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24524119C>T	uc002wtw.1	+	2	1019	c.386C>T	c.(385-387)CCG>CTG	p.P129L		NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B	129	Cytoplasmic (Potential).				response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0																		---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	25004171	25004171	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25004171C>T	uc002wub.2	-	4	1616	c.738G>A	c.(736-738)CAG>CAA	p.Q246Q	ACSS1_uc002wuc.2_Silent_p.Q246Q|ACSS1_uc010gdc.2_Intron|ACSS1_uc002wud.1_5'Flank|ACSS1_uc002wua.2_Silent_p.Q163Q	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	246					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
NINL	22981	broad.mit.edu	37	20	25493618	25493618	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25493618T>G	uc002wux.1	-	4	376	c.302A>C	c.(301-303)AAG>ACG	p.K101T	NINL_uc010gdn.1_Missense_Mutation_p.K101T|NINL_uc010gdo.1_5'UTR|NINL_uc010ztf.1_Missense_Mutation_p.K117T	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	101					G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
DEFB119	245932	broad.mit.edu	37	20	29965051	29965051	+	Nonstop_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29965051A>G	uc002wvt.2	-	2	373	c.253T>C	c.(253-255)TGA>CGA	p.*85R	DEFB119_uc002wvs.2_3'UTR	NM_153289	NP_695021	Q8N690	DB119_HUMAN	defensin, beta 119 isoform a precursor	85					defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30904405	30904405	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30904405A>C	uc002wxq.2	+	4	1749	c.1582A>C	c.(1582-1584)AGC>CGC	p.S528R	KIF3B_uc010ztw.1_Missense_Mutation_p.S466R	NM_004798	NP_004789	O15066	KIF3B_HUMAN	kinesin family member 3B	528	Potential.				anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
PXMP4	11264	broad.mit.edu	37	20	32307891	32307891	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32307891C>T	uc002wzv.2	-						PXMP4_uc002wzw.2_Intron|PXMP4_uc010zuh.1_Intron	NM_007238	NP_009169			peroxisomal membrane protein 4 isoform a							integral to membrane|membrane fraction|mitochondrial inner membrane|peroxisomal membrane	protein transporter activity				0																		---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33577633	33577633	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33577633G>A	uc002xbi.1	+	18	1896	c.1804G>A	c.(1804-1806)GCG>ACG	p.A602T	MIR499_hsa-mir-499|MI0003183_5'Flank	NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	560	Myosin head-like.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35125326	35125326	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35125326C>T	uc002xff.2	+	8	2302	c.1867C>T	c.(1867-1869)CGG>TGG	p.R623W	DLGAP4_uc010zvp.1_Missense_Mutation_p.R623W|DLGAP4_uc002xfg.2_Translation_Start_Site|DLGAP4_uc002xfh.2_Missense_Mutation_p.R84W|DLGAP4_uc002xfi.2_Translation_Start_Site|DLGAP4_uc002xfj.2_5'Flank	NM_014902	NP_055717	Q9Y2H0	DLGP4_HUMAN	disks large-associated protein 4 isoform a	623					cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
NNAT	4826	broad.mit.edu	37	20	36149740	36149740	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36149740G>A	uc002xhd.2	+	1	134	c.7G>A	c.(7-9)GCA>ACA	p.A3T	BLCAP_uc002xha.2_5'UTR|BLCAP_uc002xhb.2_Intron|BLCAP_uc002xhc.2_Intron|NNAT_uc002xhe.2_Missense_Mutation_p.A3T	NM_005386	NP_005377	Q16517	NNAT_HUMAN	neuronatin isoform alpha	3					brain development|protein lipoylation|transport						0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PPP1R16B	26051	broad.mit.edu	37	20	37536802	37536802	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37536802G>T	uc002xje.2	+	10	1349	c.1160G>T	c.(1159-1161)AGG>ATG	p.R387M	PPP1R16B_uc010ggc.2_Missense_Mutation_p.R345M	NM_015568	NP_056383	Q96T49	PP16B_HUMAN	protein phosphatase 1 regulatory inhibitor	387					regulation of filopodium assembly|signal transduction	nucleus|plasma membrane	protein phosphatase binding			upper_aerodigestive_tract(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
FAM83D	81610	broad.mit.edu	37	20	37570621	37570621	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37570621A>G	uc002xjg.2	+	2	634	c.593A>G	c.(592-594)GAC>GGC	p.D198G	FAM83D_uc002xjf.2_Missense_Mutation_p.D198G	NM_030919	NP_112181	Q9H4H8	FA83D_HUMAN	hypothetical protein LOC81610	168					cell division|mitosis	cytoplasm|spindle pole				ovary(3)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
DHX35	60625	broad.mit.edu	37	20	37647462	37647462	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37647462G>A	uc002xjh.2	+	15	1429	c.1418G>A	c.(1417-1419)TGT>TAT	p.C473Y	DHX35_uc010zwa.1_Missense_Mutation_p.C318Y|DHX35_uc010zwb.1_Missense_Mutation_p.C318Y|DHX35_uc010zwc.1_Missense_Mutation_p.C442Y	NM_021931	NP_068750	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	473						catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|nucleic acid binding			lung(1)|kidney(1)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40126803	40126803	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40126803C>T	uc002xka.1	-						CHD6_uc002xkd.2_Intron|CHD6_uc002xkc.2_Missense_Mutation_p.V362I	NM_032221	NP_115597			chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
YWHAB	7529	broad.mit.edu	37	20	43535058	43535058	+	Silent	SNP	C	T	T	rs150381005	by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43535058C>T	uc002xmt.2	+	7	1002	c.720C>T	c.(718-720)GAC>GAT	p.D240D	YWHAB_uc002xmu.2_Silent_p.D240D	NM_003404	NP_003395	P31946	1433B_HUMAN	tyrosine 3-monooxygenase/tryptophan	240					activation of MAPKK activity|activation of pro-apoptotic gene products|axon guidance|cytoplasmic sequestering of protein|epidermal growth factor receptor signaling pathway|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|mRNA metabolic process|negative regulation of protein dephosphorylation|nerve growth factor receptor signaling pathway|Ras protein signal transduction	centrosome|cytosol|melanosome|perinuclear region of cytoplasm	histone deacetylase binding|phosphoserine binding|protein domain specific binding			kidney(2)|ovary(1)|breast(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SYS1	90196	broad.mit.edu	37	20	43995543	43995543	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43995543C>T	uc002xnv.2	+	4	517	c.259C>T	c.(259-261)CGA>TGA	p.R87*	SYS1_uc010gha.2_RNA|SYS1_uc002xnw.1_Intron|SYS1-DBNDD2_uc002xnx.2_Intron	NM_033542	NP_291020	Q8N2H4	SYS1_HUMAN	SYS1 Golgi-localized integral membrane protein	87					protein transport	Golgi membrane|integral to membrane				skin(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
KCNB1	3745	broad.mit.edu	37	20	48098564	48098564	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48098564C>T	uc002xur.1	-	1	618	c.454G>A	c.(454-456)GCC>ACC	p.A152T	KCNB1_uc002xus.1_Missense_Mutation_p.A152T	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	152	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48164538	48164538	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48164538A>G	uc002xut.2	-	3	271	c.217T>C	c.(217-219)TAT>CAT	p.Y73H	PTGIS_uc010zyi.1_Intron	NM_000961	NP_000952	Q16647	PTGIS_HUMAN	prostaglandin I2 synthase	73					hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
PARD6B	84612	broad.mit.edu	37	20	49366959	49366959	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49366959G>A	uc002xvo.2	+	3	1296	c.1053G>A	c.(1051-1053)ACG>ACA	p.T351T		NM_032521	NP_115910	Q9BYG5	PAR6B_HUMAN	PAR-6 beta	351					axonogenesis|cell cycle|cell division|establishment or maintenance of cell polarity|protein complex assembly|regulation of cell migration|tight junction assembly	cytosol|tight junction	protein binding			kidney(1)	1																		---	---	---	---
SALL4	57167	broad.mit.edu	37	20	50408031	50408031	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50408031G>T	uc002xwh.3	-	2	1092	c.991C>A	c.(991-993)CCG>ACG	p.P331T	SALL4_uc010gii.2_Missense_Mutation_p.P331T|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	331					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60737894	60737894	+	Missense_Mutation	SNP	G	A	A	rs146049243	byFrequency	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60737894G>A	uc002ycb.2	+	5	518	c.463G>A	c.(463-465)GCG>ACG	p.A155T	SS18L1_uc011aaa.1_Missense_Mutation_p.A155T|SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1	155	Methionine-rich intra-molecular domain (By similarity).				chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
COL9A3	1299	broad.mit.edu	37	20	61467685	61467685	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61467685G>T	uc002ydm.2	+	28	1551	c.1548G>T	c.(1546-1548)CCG>CCT	p.P516P	COL9A3_uc002ydn.2_5'Flank	NM_001853	NP_001844	Q14050	CO9A3_HUMAN	alpha 3 type IX collagen precursor	516	Triple-helical region 3 (COL3).				axon guidance	collagen type IX					0	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61511012	61511012	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61511012G>T	uc002ydr.1	-	16	6560	c.6296C>A	c.(6295-6297)CCG>CAG	p.P2099Q	DIDO1_uc002yds.1_Missense_Mutation_p.P2099Q	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	2099					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61528048	61528048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61528048C>T	uc002ydr.1	-	7	2153	c.1889G>A	c.(1888-1890)GGC>GAC	p.G630D	DIDO1_uc002yds.1_Missense_Mutation_p.G630D|DIDO1_uc002ydt.1_Missense_Mutation_p.G630D|DIDO1_uc002ydu.1_Missense_Mutation_p.G630D	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	630					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62421833	62421833	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62421833G>A	uc002ygv.1	-	2	479	c.278C>T	c.(277-279)GCG>GTG	p.A93V	ZBTB46_uc002ygu.2_RNA	NM_025224	NP_079500	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	93	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62838958	62838958	+	Missense_Mutation	SNP	G	A	A	rs117661126	byFrequency;by1000genomes	TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62838958G>A	uc002yii.2	+	7	773	c.409G>A	c.(409-411)GTC>ATC	p.V137I	MYT1_uc002yih.2_Intron|MYT1_uc002yij.2_5'UTR	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	137					cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62858781	62858781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62858781G>A	uc002yii.2	+	17	2906	c.2542G>A	c.(2542-2544)GGC>AGC	p.G848S	MYT1_uc002yih.2_Missense_Mutation_p.G527S|MYT1_uc002yij.2_Missense_Mutation_p.G507S	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	848	C2HC-type 5.				cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
TMPRSS15	5651	broad.mit.edu	37	21	19737461	19737461	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19737461T>C	uc002ykw.2	-	7	800	c.769A>G	c.(769-771)ATA>GTA	p.I257V		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	257	Extracellular (Potential).|CUB 1.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8																		---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22849745	22849745	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22849745C>T	uc002yld.1	+	15	2279	c.2030C>T	c.(2029-2031)CCG>CTG	p.P677L	NCAM2_uc011acb.1_Missense_Mutation_p.P535L	NM_004540	NP_004531	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2 precursor	677	Fibronectin type-III 2.|Extracellular (Potential).				neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27136926	27136926	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27136926C>T	uc002ylx.3	+	9	1491	c.964C>T	c.(964-966)CTA>TTA	p.L322L	GABPA_uc002yly.3_Silent_p.L322L	NM_002040	NP_002031	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha	322	ETS.				positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28212698	28212698	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28212698C>T	uc002ymf.2	-	5	2017	c.1562G>A	c.(1561-1563)TGT>TAT	p.C521Y		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	521	Disintegrin.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)														---	---	---	---
ADAMTS1	9510	broad.mit.edu	37	21	28214961	28214961	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28214961G>A	uc002ymf.2	-	2	1229	c.774C>T	c.(772-774)CGC>CGT	p.R258R		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	258	Peptidase M12B.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	40250561	40250561	+	IGR	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40250561G>T								ETS2 (53685 upstream) : PSMG1 (296829 downstream)																																			---	---	---	---
LCA5L	150082	broad.mit.edu	37	21	40778104	40778104	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40778104C>A	uc002yxu.2	-	10	2030	c.1717G>T	c.(1717-1719)GGG>TGG	p.G573W	LCA5L_uc002yxv.2_Missense_Mutation_p.G573W	NM_152505	NP_689718	O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	573											0		Prostate(19;1.2e-06)																---	---	---	---
ZNF295	49854	broad.mit.edu	37	21	43412000	43412000	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43412000T>C	uc002zab.3	-	3	2419	c.2205A>G	c.(2203-2205)CTA>CTG	p.L735L	ZNF295_uc002yzz.3_Intron|ZNF295_uc002yzy.3_Silent_p.L735L|ZNF295_uc002zaa.3_Silent_p.L735L	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	735					negative regulation of transcription, DNA-dependent|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|nucleus	methyl-CpG binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43508533	43508533	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43508533A>G	uc002zaf.1	+	5	733	c.733A>G	c.(733-735)ACC>GCC	p.T245A	UMODL1_uc002zad.1_Missense_Mutation_p.T173A|UMODL1_uc002zae.1_Missense_Mutation_p.T173A|UMODL1_uc002zag.1_Missense_Mutation_p.T245A|UMODL1_uc010gow.1_Missense_Mutation_p.T37A|UMODL1_uc002zai.1_5'UTR|UMODL1_uc010gox.1_RNA|UMODL1_uc010goy.1_Intron|UMODL1_uc002zaj.1_RNA|UMODL1_uc010goz.1_Missense_Mutation_p.T37A	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	245	Extracellular (Potential).					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
TMPRSS3	64699	broad.mit.edu	37	21	43810131	43810131	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43810131G>A	uc002zbb.2	-	3	311	c.110C>T	c.(109-111)GCT>GTT	p.A37V	TMPRSS3_uc002zaz.2_5'Flank|TMPRSS3_uc002zba.2_5'UTR|TMPRSS3_uc002zbc.2_Missense_Mutation_p.A37V|TMPRSS3_uc002zbd.2_Missense_Mutation_p.A37V	NM_024022	NP_076927	P57727	TMPS3_HUMAN	transmembrane protease, serine 3 isoform 1	37	Cytoplasmic (Potential).				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3																		---	---	---	---
NDUFV3	4731	broad.mit.edu	37	21	44324217	44324217	+	Intron	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44324217G>T	uc002zcn.2	+						NDUFV3_uc002zcm.2_Missense_Mutation_p.K365N	NM_001001503	NP_001001503			NADH-ubiquinone oxidoreductase flavoprotein 3						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I|nucleus	NADH dehydrogenase (ubiquinone) activity			ovary(2)	2				STAD - Stomach adenocarcinoma(101;0.0606)	NADH(DB00157)													---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45168941	45168941	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45168941G>A	uc002zdm.3	+	6	642	c.444G>A	c.(442-444)ACG>ACA	p.T148T	PDXK_uc010gpj.2_Silent_p.T148T|PDXK_uc002zdn.3_Silent_p.T120T|PDXK_uc002zdq.3_Silent_p.T75T	NM_003681	NP_003672	O00764	PDXK_HUMAN	pyridoxal kinase	148					cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45741668	45741668	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45741668G>A	uc002zel.2	+	13	1307	c.1248G>A	c.(1246-1248)GCG>GCA	p.A416A	PFKL_uc002zek.2_Silent_p.A463A|PFKL_uc002zem.2_Silent_p.A3A|PFKL_uc002zen.2_Silent_p.A3A	NM_002626	NP_002617	P17858	K6PL_HUMAN	liver phosphofructokinase	416					fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)														---	---	---	---
GAB4	128954	broad.mit.edu	37	22	17468910	17468910	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17468910G>T	uc002zlw.2	-	3	734	c.626C>A	c.(625-627)CCT>CAT	p.P209H	GAB4_uc010gqs.1_Missense_Mutation_p.P192H	NM_001037814	NP_001032903	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member	209										large_intestine(1)|ovary(1)	2		all_epithelial(15;0.112)|Lung NSC(13;0.248)																---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17585611	17585611	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17585611C>T	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154			interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)														---	---	---	---
CECR2	27443	broad.mit.edu	37	22	17978463	17978463	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17978463C>T	uc010gqw.1	+	3	427	c.301C>T	c.(301-303)CGT>TGT	p.R101C	CECR2_uc010gqv.1_5'UTR|CECR2_uc002zml.2_5'UTR|CECR2_uc002zmm.1_5'UTR	NM_031413	NP_113601	Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	143					chromatin modification|cytokinesis|cytoskeleton organization|DNA fragmentation involved in apoptotic nuclear change|vesicle-mediated transport		protein binding			ovary(1)|skin(1)	2		all_epithelial(15;0.139)		Lung(27;0.146)														---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20761010	20761010	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20761010G>T	uc010gsm.2	+	6	1899	c.1687G>T	c.(1687-1689)GAG>TAG	p.E563*	ZNF74_uc002zsg.2_Nonsense_Mutation_p.E492*|ZNF74_uc002zsh.2_Nonsense_Mutation_p.E563*|ZNF74_uc002zsi.2_Nonsense_Mutation_p.E492*|ZNF74_uc010gsn.2_Nonsense_Mutation_p.E492*	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	563	C2H2-type 12.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|nucleus	DNA binding|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
RTDR1	27156	broad.mit.edu	37	22	23404006	23404006	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23404006G>A	uc002zwt.2	-	6	929	c.771C>T	c.(769-771)TTC>TTT	p.F257F		NM_014433	NP_055248	Q9UHP6	RTDR1_HUMAN	rhabdoid tumor deletion region protein 1	257							binding			ovary(1)	1	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)														---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24717611	24717611	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24717611G>T	uc002zzw.2	+	5	970	c.663G>T	c.(661-663)GAG>GAT	p.E221D	CYTSA_uc002zzv.3_Missense_Mutation_p.E221D|CYTSA_uc011ajq.1_Missense_Mutation_p.E221D	NM_015330	NP_056145	Q69YQ0	CYTSA_HUMAN	cytospin A	221	Potential.				cell cycle|cell division						0																		---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25294421	25294421	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25294421G>A	uc003abg.2	+	20	2827	c.2670G>A	c.(2668-2670)TCG>TCA	p.S890S	SGSM1_uc003abh.2_Silent_p.S829S|SGSM1_uc010guu.1_Silent_p.S835S|SGSM1_uc003abj.2_Silent_p.S774S|SGSM1_uc003abi.1_Silent_p.S810S	NM_001039948	NP_001035037	Q2NKQ1	SGSM1_HUMAN	RUN and TBC1 domain containing 2 isoform 1	890	Rab-GAP TBC.					Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																		---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26086188	26086188	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26086188C>T	uc003abx.3	+	12	1137	c.990C>T	c.(988-990)CAC>CAT	p.H330H	ADRBK2_uc010gux.2_Silent_p.H330H|ADRBK2_uc003abw.2_Silent_p.H217H|ADRBK2_uc003aby.3_RNA	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2	330	Protein kinase.						ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26895229	26895229	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26895229G>A	uc003acr.2	-	8	1544	c.1170C>T	c.(1168-1170)GAC>GAT	p.D390D	TFIP11_uc003acs.2_Silent_p.D390D|TFIP11_uc003act.2_Silent_p.D390D	NM_012143	NP_036275	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	390					biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29120963	29120963	+	Splice_Site	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29120963A>G	uc003adu.1	-	4	664	c.592_splice	c.e4+1	p.V198_splice	CHEK2_uc003ads.1_Intron|CHEK2_uc010gvh.1_Intron|CHEK2_uc010gvi.1_Splice_Site_p.V198_splice|CHEK2_uc010gvj.1_Intron|CHEK2_uc003adr.1_Splice_Site|CHEK2_uc010gvk.1_Splice_Site|CHEK2_uc003adt.1_Splice_Site_p.V241_splice|CHEK2_uc003adv.1_Splice_Site_p.V198_splice|CHEK2_uc003adw.1_Splice_Site_p.V198_splice|CHEK2_uc003adx.1_Splice_Site|CHEK2_uc003ady.1_Splice_Site_p.V198_splice|CHEK2_uc003adz.1_Intron	NM_007194	NP_009125			protein kinase CHK2 isoform a						cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20								F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				---	---	---	---
EWSR1	2130	broad.mit.edu	37	22	29695771	29695771	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29695771C>G	uc003aet.2	+	16	2189	c.1861C>G	c.(1861-1863)CCC>GCC	p.P621A	EWSR1_uc003aev.2_Missense_Mutation_p.P626A|EWSR1_uc003aew.2_Missense_Mutation_p.P565A|EWSR1_uc003aex.2_Missense_Mutation_p.P620A|EWSR1_uc003aey.2_Missense_Mutation_p.P416A|EWSR1_uc003aez.2_Missense_Mutation_p.P282A	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2	621	Arg/Gly/Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254								T	FLI1|ERG|ZNF278|NR4A3|FEV|ATF1|ETV1|ETV4|WT1|ZNF384|CREB1|POU5F1| PBX1	Ewing sarcoma| desmoplastic small round cell tumor |ALL|clear cell sarcoma|sarcoma|myoepithelioma								---	---	---	---
RNF215	200312	broad.mit.edu	37	22	30780336	30780336	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30780336G>T	uc003ahp.2	-	5	736	c.736C>A	c.(736-738)CAG>AAG	p.Q246K	RNF215_uc011akw.1_Missense_Mutation_p.Q151K	NM_001017981	NP_001017981	Q9Y6U7	RN215_HUMAN	ring finger protein 215	246	Extracellular (Potential).					integral to membrane	zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32239152	32239152	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32239152G>A	uc003als.2	+	28	2702	c.2560G>A	c.(2560-2562)GTG>ATG	p.V854M	DEPDC5_uc011als.1_Missense_Mutation_p.V785M|DEPDC5_uc011alu.1_Missense_Mutation_p.V863M|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Missense_Mutation_p.V854M|DEPDC5_uc003alu.2_Missense_Mutation_p.V303M|DEPDC5_uc003alv.2_RNA|DEPDC5_uc011alw.1_Missense_Mutation_p.V184M|DEPDC5_uc003alw.2_Missense_Mutation_p.V152M|DEPDC5_uc011alx.1_Intron|DEPDC5_uc010gwk.2_5'Flank	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	854					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33327401	33327401	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33327401G>A	uc003amx.2	-	3	594	c.435C>T	c.(433-435)GTC>GTT	p.V145V	SYN3_uc003amy.2_Silent_p.V145V|SYN3_uc003amz.2_Silent_p.V145V	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa	145	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37914112	37914112	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37914112C>T	uc003asx.1	-	2	242	c.239G>A	c.(238-240)CGC>CAC	p.R80H	CARD10_uc003ast.1_RNA|CARD10_uc003asy.1_Missense_Mutation_p.R80H	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	80	CARD.				activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
SUN2	25777	broad.mit.edu	37	22	39141791	39141791	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39141791C>T	uc003awh.1	-	9	995	c.711G>A	c.(709-711)GGG>GGA	p.G237G	SUN2_uc011anz.1_Silent_p.G272G|SUN2_uc011aoa.1_Silent_p.G226G|SUN2_uc003awi.1_Silent_p.G237G|SUN2_uc010gxq.1_Silent_p.G258G|SUN2_uc010gxr.1_Silent_p.G237G|SUN2_uc010gxs.1_Silent_p.G237G	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B	237	Perinuclear space.				centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)|skin(1)	2																		---	---	---	---
CBX6	23466	broad.mit.edu	37	22	39262866	39262866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39262866G>A	uc003awl.2	-	5	650	c.587C>T	c.(586-588)GCG>GTG	p.A196V		NM_014292	NP_055107	O95503	CBX6_HUMAN	chromobox homolog 6	196					chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	PcG protein complex					0	Melanoma(58;0.04)																	---	---	---	---
FAM83F	113828	broad.mit.edu	37	22	40415244	40415244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40415244C>T	uc003ayk.1	+	2	656	c.562C>T	c.(562-564)CGC>TGC	p.R188C		NM_138435	NP_612444	Q8NEG4	FA83F_HUMAN	hypothetical protein LOC113828	188										breast(1)	1																		---	---	---	---
SLC25A17	10478	broad.mit.edu	37	22	41173356	41173356	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41173356C>T	uc003azc.2	-	6	613	c.473G>A	c.(472-474)CGC>CAC	p.R158H	SLC25A17_uc010gyg.2_RNA|SLC25A17_uc011aou.1_Missense_Mutation_p.R121H|SLC25A17_uc003azd.2_RNA|SLC25A17_uc011aov.1_Missense_Mutation_p.R85H	NM_006358	NP_006349	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier;	158	Lumenal (Potential).|Solcar 2.				fatty acid alpha-oxidation	integral to plasma membrane|mitochondrial inner membrane|peroxisomal membrane	adenine nucleotide transmembrane transporter activity|protein binding				0																		---	---	---	---
XRCC6	2547	broad.mit.edu	37	22	42032527	42032527	+	Silent	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42032527A>G	uc003bao.1	+	5	412	c.342A>G	c.(340-342)AAA>AAG	p.K114K	XRCC6_uc003bap.1_Silent_p.K73K|XRCC6_uc011apc.1_Silent_p.K64K|XRCC6_uc003baq.1_Silent_p.K114K|XRCC6_uc003bar.1_Silent_p.K114K|XRCC6_uc003bas.1_Silent_p.K64K	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	114					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5													Direct_reversal_of_damage|NHEJ					---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42125712	42125712	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42125712A>G	uc003baz.1	+	8	933	c.908A>G	c.(907-909)CAC>CGC	p.H303R	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc003bay.3_Missense_Mutation_p.H303R|MEI1_uc011apd.1_RNA	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	303							binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42191805	42191805	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42191805C>A	uc003baz.1	+	30	3758	c.3733C>A	c.(3733-3735)CTT>ATT	p.L1245I	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_RNA|MEI1_uc003bbb.1_Missense_Mutation_p.L631I|MEI1_uc003bbc.1_Missense_Mutation_p.L613I|MEI1_uc010gym.1_Missense_Mutation_p.L578I|MEI1_uc003bbd.1_Missense_Mutation_p.L458I|MEI1_uc010gyn.1_RNA|MEI1_uc003bbe.1_RNA|MEI1_uc003bbf.2_Missense_Mutation_p.L259I|MEI1_uc003bbg.2_Missense_Mutation_p.L215I	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	1245							binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43616498	43616498	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43616498T>C	uc003bdt.1	-	14	1733	c.1645A>G	c.(1645-1647)ACA>GCA	p.T549A		NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	549					adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)																---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47073062	47073062	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47073062A>G	uc003bhx.2	+	18	1690	c.1651A>G	c.(1651-1653)ATG>GTG	p.M551V	GRAMD4_uc010had.2_Missense_Mutation_p.M467V|GRAMD4_uc003bhy.2_Missense_Mutation_p.M74V	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein	551					apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50667976	50667976	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50667976C>T	uc003bkb.1	-	4	1659	c.1147G>A	c.(1147-1149)GTC>ATC	p.V383I	TUBGCP6_uc010har.1_Missense_Mutation_p.V383I|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	383					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
PPP2R3B	28227	broad.mit.edu	37	X	299553	299553	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:299553T>C	uc004cpg.2	-	11	1631	c.1430A>G	c.(1429-1431)TAC>TGC	p.Y477C	PPP2R3B_uc004cpf.2_Missense_Mutation_p.Y78C	NM_013239	NP_037371	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'',	477					cell cycle arrest|protein dephosphorylation	nucleus|protein phosphatase type 2A complex	calcium ion binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase 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)																---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	5821797	5821797	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5821797T>C	uc010ndh.2	-	5	1423	c.922A>G	c.(922-924)ATG>GTG	p.M308V	NLGN4X_uc004crp.2_Missense_Mutation_p.M328V|NLGN4X_uc004crq.2_Missense_Mutation_p.M308V|NLGN4X_uc010ndi.2_Missense_Mutation_p.M345V|NLGN4X_uc004crr.2_Missense_Mutation_p.M308V|NLGN4X_uc010ndj.2_Missense_Mutation_p.M308V	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor	308	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
GPR143	4935	broad.mit.edu	37	X	9716622	9716622	+	Silent	SNP	G	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9716622G>T	uc004cst.1	-	4	600	c.600C>A	c.(598-600)TCC>TCA	p.S200S		NM_000273	NP_000264	P51810	GP143_HUMAN	G protein-coupled receptor 143	180	Extracellular (Potential).				calcium-mediated signaling using intracellular calcium source|eye pigment biosynthetic process|melanosome organization|melanosome transport|phosphatidylinositol-mediated signaling|regulation of calcium-mediated signaling|visual perception	apical plasma membrane|Golgi apparatus|integral to membrane|lysosomal membrane|melanosome membrane|membrane fraction	dopamine binding|L-DOPA receptor activity|protein binding|tyrosine binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14027111	14027111	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14027111G>A	uc004cwb.2	-	5	993	c.650C>T	c.(649-651)GCC>GTC	p.A217V	GEMIN8_uc004cwc.2_Missense_Mutation_p.A217V|GEMIN8_uc004cwd.2_Missense_Mutation_p.A217V	NM_017856	NP_060326	Q9NWZ8	GEMI8_HUMAN	gem (nuclear organelle) associated protein 8	217					spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0																		---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18622050	18622050	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18622050C>T	uc004cym.2	+	12	1259	c.1006C>T	c.(1006-1008)CAG>TAG	p.Q336*	CDKL5_uc004cyn.2_Nonsense_Mutation_p.Q336*	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	336					neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29301049	29301049	+	Intron	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29301049C>T	uc004dby.2	+							NM_014271	NP_055086			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																		---	---	---	---
SUV39H1	6839	broad.mit.edu	37	X	48558962	48558962	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48558962G>A	uc004dkn.2	+	3	691	c.646G>A	c.(646-648)GGG>AGG	p.G216R	SUV39H1_uc011mmf.1_Missense_Mutation_p.G227R|SUV39H1_uc011mmg.1_RNA	NM_003173	NP_003164	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1	216	Pre-SET.				cell cycle|cell differentiation|chromatin silencing at rDNA|interspecies interaction between organisms|rRNA processing|transcription, DNA-dependent	chromatin silencing complex|chromosome, centromeric region|condensed nuclear chromosome|rDNA heterochromatin	chromatin binding|histone methyltransferase activity (H3-K9 specific)|protein N-terminus binding|zinc ion binding				0																		---	---	---	---
MED12	9968	broad.mit.edu	37	X	70348474	70348474	+	Silent	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70348474G>A	uc004dyy.2	+	24	3580	c.3381G>A	c.(3379-3381)TCG>TCA	p.S1127S	MED12_uc011mpq.1_Silent_p.S1127S|MED12_uc004dyz.2_Silent_p.S1127S|MED12_uc004dza.2_Silent_p.S974S|MED12_uc010nla.2_5'Flank	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1127					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)															OREG0019857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70353001	70353001	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70353001A>G	uc004dyy.2	+	33	4755	c.4556A>G	c.(4555-4557)TAC>TGC	p.Y1519C	MED12_uc011mpq.1_Missense_Mutation_p.Y1519C|MED12_uc004dyz.2_Missense_Mutation_p.Y1519C|MED12_uc004dza.2_Missense_Mutation_p.Y1366C|MED12_uc010nla.2_Missense_Mutation_p.Y145C	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1519					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73047637	73047637	+	RNA	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73047637C>T	uc004ebn.2	+	1		c.35598C>T			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0																		---	---	---	---
SATL1	340562	broad.mit.edu	37	X	84363304	84363304	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84363304C>T	uc011mqx.1	-	1	671	c.671G>A	c.(670-672)AGC>AAC	p.S224N	SATL1_uc004een.2_Missense_Mutation_p.S224N	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	37	Gln-rich.						N-acetyltransferase activity			breast(2)	2																		---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122616765	122616765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122616765C>T	uc004etq.3	+	16	2848	c.2555C>T	c.(2554-2556)GCA>GTA	p.A852V	GRIA3_uc004etr.3_Missense_Mutation_p.A852V|GRIA3_uc004ets.3_RNA	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	852	Cytoplasmic (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
ACTRT1	139741	broad.mit.edu	37	X	127185298	127185298	+	Silent	SNP	T	C	C			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127185298T>C	uc004eum.2	-	1	1085	c.888A>G	c.(886-888)GCA>GCG	p.A296A		NM_138289	NP_612146	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	296						cytoplasm|cytoskeleton				ovary(2)|central_nervous_system(2)|skin(1)	5																		---	---	---	---
F9	2158	broad.mit.edu	37	X	138644004	138644004	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138644004A>G	uc004fas.1	+	8	1189	c.1160A>G	c.(1159-1161)AAG>AGG	p.K387R	F9_uc004fat.1_Missense_Mutation_p.K349R	NM_000133	NP_000124	P00740	FA9_HUMAN	coagulation factor IX preproprotein	387	Peptidase S1.		K -> E (in HEMB; mild).		blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)													---	---	---	---
CD99L2	83692	broad.mit.edu	37	X	149983362	149983362	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149983362G>A	uc004fel.2	-	4	368	c.250C>T	c.(250-252)CGC>TGC	p.R84C	CD99L2_uc004fek.2_RNA|CD99L2_uc004fem.2_Intron|CD99L2_uc004fen.2_Intron|CD99L2_uc004feo.2_RNA|CD99L2_uc011myb.1_Missense_Mutation_p.R84C	NM_031462	NP_113650	Q8TCZ2	C99L2_HUMAN	CD99 antigen-like 2 isoform E3'-E4'-E3-E4	84	Extracellular (Potential).				cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PLXNB3	5365	broad.mit.edu	37	X	153040420	153040420	+	Silent	SNP	C	T	T			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153040420C>T	uc004fii.2	+	24	4191	c.4017C>T	c.(4015-4017)CGC>CGT	p.R1339R	PLXNB3_uc010nuk.2_Silent_p.R1362R|PLXNB3_uc011mzd.1_Silent_p.R978R|PLXNB3_uc004fij.1_RNA|SRPK3_uc004fik.2_5'Flank	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3 isoform 1	1339	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153699670	153699670	+	Intron	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153699670G>A	uc004flm.2	+							NM_017514	NP_059984			plexin A3 precursor						axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
SPRY3	10251	broad.mit.edu	37	X	155003589	155003589	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4257-01A-01D-1126-08	TCGA-BR-4257-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155003589G>A	uc004fnq.1	+	2	510	c.56G>A	c.(55-57)CGC>CAC	p.R19H	SPRY3_uc010nvl.1_Missense_Mutation_p.R19H	NM_005840	NP_005831	O43610	SPY3_HUMAN	sprouty homolog 3	19					multicellular organismal development|regulation of signal transduction	cytoplasm|membrane					0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
