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	797377	797380	+	IGR	DEL	GATA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:797377_797380delGATA								LOC643837 (7637 upstream) : FAM41C (6073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	821363	821363	+	IGR	DEL	C	-	-	rs80242220		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:821363delC								FAM41C (9181 upstream) : FLJ39609 (31590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	952495	952495	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:952495delT								ISG15 (2580 upstream) : AGRN (3008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4945838	4945838	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4945838delA								AJAP1 (101988 upstream) : NPHP4 (977032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5276779	5276780	+	IGR	DEL	AC	-	-	rs35543009		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5276779_5276780delAC								AJAP1 (432929 upstream) : NPHP4 (646090 downstream)																																			---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	6020801	6020801	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6020801delA	uc001alq.1	-						NPHP4_uc001als.1_Intron|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron	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)														---	---	---	---
ICMT	23463	broad.mit.edu	37	1	6289817	6289817	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6289817delA	uc001amk.2	-						ICMT_uc001aml.2_Intron	NM_012405	NP_036537			isoprenylcysteine carboxyl methyltransferase						protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|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;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	6977623	6977623	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6977623delG	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)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7688048	7688048	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7688048delT	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)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7719873	7719873	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7719873delT	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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8515069	8515069	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8515069delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8568551	8568551	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8568551delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_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)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8806936	8806937	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8806936_8806937delAG	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)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9144201	9144201	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9144201delA	uc010oab.1	-							NM_003039	NP_003030			solute carrier family 2 (facilitated						carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9494300	9494301	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9494300_9494301delTT								SPSB1 (64712 upstream) : SLC25A33 (105227 downstream)																																			---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10132438	10132438	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10132438delT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-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;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10132494	10132494	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10132494delT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-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;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10369954	10369954	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10369954delT	uc001aqx.3	+						KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-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;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PEX14	5195	broad.mit.edu	37	1	10658935	10658937	+	Intron	DEL	TCT	-	-	rs35822240	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10658935_10658937delTCT	uc001arn.2	+						PEX14_uc009vmu.1_Intron|PEX14_uc009vmv.2_Intron|PEX14_uc010oam.1_Intron|PEX14_uc010oan.1_Intron|PEX14_uc009vmw.2_Intron	NM_004565	NP_004556			peroxisomal biogenesis factor 14						negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10985539	10985539	+	IGR	DEL	A	-	-	rs75700579		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10985539delA								CASZ1 (128832 upstream) : C1orf127 (20994 downstream)																																			---	---	---	---
MTHFR	4524	broad.mit.edu	37	1	11847334	11847335	+	3'UTR	INS	-	GAA	GAA	rs149602082	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11847334_11847335insGAA	uc001atc.1	-	12					uc001asz.2_Intron|uc001ata.2_Intron|MTHFR_uc001atb.1_3'UTR	NM_005957	NP_005948			5,10-methylenetetrahydrofolate reductase						blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				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)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|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)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	13137052	13137052	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13137052delC								PRAMEF5 (19301 upstream) : LOC440563 (45909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	13143166	13143166	+	IGR	DEL	T	-	-	rs112205639		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13143166delT								PRAMEF5 (25415 upstream) : LOC440563 (39795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	13385686	13385686	+	IGR	DEL	A	-	-	rs9438815	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13385686delA								PRAMEF3 (54015 upstream) : PRAMEF9 (35490 downstream)																																			---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13941794	13941794	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13941794delT	uc001avd.2	+						PDPN_uc001avc.2_Intron|PDPN_uc009vob.2_Intron|PDPN_uc009voc.2_Intron|PDPN_uc001ave.2_Intron|PDPN_uc001avf.2_Intron	NM_006474	NP_006465			lung type-I cell membrane-associated						cell morphogenesis|lymphangiogenesis|regulation of cell shape	filopodium membrane|integral to plasma membrane|lamellipodium membrane|microvillus membrane|ruffle membrane				ovary(2)	2	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14248128	14248128	+	IGR	DEL	T	-	-	rs74848873		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14248128delT								PRDM2 (96556 upstream) : KAZ (677085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14765855	14765855	+	IGR	DEL	C	-	-	rs74795530		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14765855delC								PRDM2 (614283 upstream) : KAZ (159358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	15928917	15928918	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15928917_15928918insA								DNAJC16 (10045 upstream) : DDI2 (15152 downstream)																																			---	---	---	---
TMEM82	388595	broad.mit.edu	37	1	16073788	16073788	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16073788delA	uc001axc.2	+							NM_001013641	NP_001013663			transmembrane protein 82							integral to membrane				breast(1)|central_nervous_system(1)	2		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16856184	16856184	+	IGR	DEL	T	-	-	rs76459018		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16856184delT								CROCCL2 (36988 upstream) : NBPF1 (34228 downstream)																																			---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16912836	16912840	+	Intron	DEL	TTTTT	-	-	rs72068639		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16912836_16912840delTTTTT	uc009vos.1	-						NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17185383	17185384	+	Intron	INS	-	C	C	rs143082557	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17185383_17185384insC	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	17254992	17254992	+	Intron	DEL	T	-	-	rs113967647		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17254992delT	uc001azt.2	+						CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						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	17274341	17274342	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17274341_17274342insT	uc001azt.2	+						CROCC_uc009voz.1_Intron|CROCC_uc001azu.2_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						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	17624904	17624910	+	IGR	DEL	TTTGCAA	-	-	rs55782094		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17624904_17624910delTTTGCAA								PADI3 (14179 upstream) : PADI4 (9780 downstream)																																			---	---	---	---
PADI4	23569	broad.mit.edu	37	1	17680744	17680744	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17680744delA	uc001baj.2	+							NM_012387	NP_036519			peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)													---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17744396	17744396	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17744396delA	uc001bal.2	-						RCC2_uc001bam.2_Intron	NM_001136204	NP_001129676			regulator of chromosome condensation 2						cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	17860461	17860461	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17860461delT								RCC2 (94241 upstream) : ARHGEF10L (5869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18935998	18935998	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18935998delT								KLHDC7A (123459 upstream) : PAX7 (21502 downstream)																																			---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19519282	19519283	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19519282_19519283delTT	uc001bbi.2	-							NM_020765	NP_065816			retinoblastoma-associated factor 600						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19894700	19894702	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19894700_19894702delTTT								CAPZB (82708 upstream) : C1orf151 (28765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20346865	20346866	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20346865_20346866insT								PLA2G2A (39933 upstream) : PLA2G5 (7806 downstream)																																			---	---	---	---
PLA2G2D	26279	broad.mit.edu	37	1	20442544	20442544	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20442544delA	uc001bcz.2	-						PLA2G2D_uc009vpo.2_Intron	NM_012400	NP_036532			phospholipase A2, group IID precursor						inflammatory response|lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)											Multiple Myeloma(11;0.12)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	20479436	20479436	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20479436delG								PLA2G2F (2557 upstream) : PLA2G2C (11048 downstream)																																	OREG0013186	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	20708961	20708962	+	Intron	INS	-	TGG	TGG	rs75116840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20708961_20708962insTGG	uc009vpu.1	-						uc001bdf.1_Intron					Homo sapiens cDNA clone IMAGE:5269505.																														---	---	---	---
HP1BP3	50809	broad.mit.edu	37	1	21091729	21091729	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21091729delA	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc010odf.1_Intron|HP1BP3_uc010odg.1_Intron	NM_016287	NP_057371			HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21406744	21406744	+	Intron	DEL	G	-	-	rs79537206		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21406744delG	uc001bec.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc010odk.1_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21955383	21955383	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21955383delA	uc001bex.2	-						RAP1GAP_uc001bew.2_Intron|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876			RAP1 GTPase activating protein isoform c						regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22125053	22125053	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22125053delT								USP48 (15365 upstream) : LDLRAD2 (13705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22269339	22269339	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22269339delT								HSPG2 (5589 upstream) : CELA3B (34079 downstream)																																			---	---	---	---
CELA3A	10136	broad.mit.edu	37	1	22335254	22335254	+	Intron	DEL	A	-	-	rs34410812		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22335254delA	uc001bfl.2	+							NM_005747	NP_005738			elastase 3A, pancreatic preproprotein						cholesterol metabolic process|digestion|proteolysis		serine-type endopeptidase activity			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	22424834	22424834	+	IGR	DEL	A	-	-	rs34637390		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22424834delA								CDC42 (5399 upstream) : WNT4 (18966 downstream)																																			---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22928009	22928009	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22928009delG	uc001bfx.1	+							NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23503567	23503567	+	Intron	DEL	G	-	-	rs143901252		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23503567delG	uc001bgm.1	-							NM_033631	NP_361013			leucine zipper protein 1							nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	23524563	23524565	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23524563_23524565delAAA								HTR1D (3341 upstream) : HNRNPR (111712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	23879053	23879055	+	IGR	DEL	TTT	-	-	rs113017925		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23879053_23879055delTTT								E2F2 (21340 upstream) : ID3 (5355 downstream)																																			---	---	---	---
NIPAL3	57185	broad.mit.edu	37	1	24765379	24765379	+	Intron	DEL	A	-	-	rs35844987		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24765379delA	uc001bjh.2	+						NIPAL3_uc010oek.1_Intron|NIPAL3_uc001bjg.2_Intron|NIPAL3_uc009vrc.2_Intron	NM_020448	NP_065181			NIPA-like domain containing 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	25212338	25212339	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25212338_25212339insT								CLIC4 (41523 upstream) : RUNX3 (13664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25432071	25432071	+	IGR	DEL	T	-	-	rs111771528		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25432071delT								RUNX3 (140459 upstream) : SYF2 (116696 downstream)																																			---	---	---	---
RHD	6007	broad.mit.edu	37	1	25645077	25645078	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25645077_25645078delAA	uc001bjz.2	+						RHD_uc001bkc.2_Intron|RHD_uc009vrm.2_Intron|RHD_uc001bka.2_Intron|RHD_uc001bkb.2_Intron|RHD_uc009vrn.2_Intron|RHD_uc009vro.2_Intron|RHD_uc009vrp.2_Intron	NM_016124	NP_057208			Rh blood group D antigen isoform 1							integral to plasma membrane				breast(1)	1		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;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
TMEM57	55219	broad.mit.edu	37	1	25826647	25826647	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25826647delT	uc001bkk.2	+	11					TMEM57_uc009vru.2_3'UTR|TMEM57_uc009vrv.2_3'UTR	NM_018202	NP_060672			transmembrane protein 57							axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26897613	26897613	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26897613delA	uc001bmr.1	+						RPS6KA1_uc010ofe.1_Intron|RPS6KA1_uc010off.1_Intron|RPS6KA1_uc001bms.1_Intron|RPS6KA1_uc009vsl.1_Intron	NM_002953	NP_002944			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|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
SMPDL3B	27293	broad.mit.edu	37	1	28259560	28259561	+	5'Flank	INS	-	T	T	rs138518649	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28259560_28259561insT	uc001bpg.2	+						SMPDL3B_uc001bpf.2_5'Flank|SMPDL3B_uc010ofq.1_5'Flank|SMPDL3B_uc010ofr.1_5'Flank	NM_014474	NP_055289			acid sphingomyelinase-like phosphodiesterase 3B						sphingomyelin catabolic process	extracellular space	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity			ovary(3)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)														---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28415822	28415823	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28415822_28415823insT	uc001bpi.1	-						EYA3_uc010ofs.1_5'Flank|EYA3_uc010oft.1_5'Flank|EYA3_uc001bpj.2_5'Flank|EYA3_uc001bpk.1_5'Flank|EYA3_uc010ofu.1_5'Flank	NM_001990	NP_001981			eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
SNHG3-RCC1	751867	broad.mit.edu	37	1	28841274	28841274	+	Intron	DEL	A	-	-	rs139010543		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28841274delA	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)														---	---	---	---
TAF12	6883	broad.mit.edu	37	1	28963317	28963318	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28963317_28963318delAA	uc009vti.2	-						TAF12_uc001bqx.2_Intron|TAF12_uc001bqy.2_Intron	NM_005644	NP_005635			TAF12 RNA polymerase II, TATA box binding						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	PCAF complex|STAGA complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
GMEB1	10691	broad.mit.edu	37	1	29025949	29025949	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29025949delT	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573			glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
YTHDF2	51441	broad.mit.edu	37	1	29074640	29074641	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29074640_29074641delAA	uc001brc.2	+						YTHDF2_uc001brd.2_Intron|YTHDF2_uc010ofx.1_Intron|YTHDF2_uc001bre.2_Intron	NM_016258	NP_057342			high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29223898	29223898	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29223898delA	uc001bri.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001brj.1_Intron	NM_203343	NP_976218			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29446106	29446106	+	3'UTR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29446106delC	uc001brl.1	+	19					EPB41_uc001brg.1_3'UTR|EPB41_uc001brh.1_3'UTR|EPB41_uc001bri.1_3'UTR|EPB41_uc001brj.1_3'UTR|EPB41_uc009vtl.1_3'UTR|EPB41_uc009vtm.1_3'UTR|EPB41_uc009vtn.1_RNA|TMEM200B_uc001brn.1_3'UTR	NM_004437	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
SFRS4	6429	broad.mit.edu	37	1	29505558	29505558	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29505558delA	uc001bro.2	-						SFRS4_uc010ofy.1_Intron|SFRS4_uc009vtp.2_Intron	NM_005626	NP_005617			splicing factor, arginine/serine-rich 4						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|RNA binding				0		Colorectal(325;0.00161)|Breast(348;0.0364)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0529)|Lung NSC(340;0.0654)|all_lung(284;0.074)|Ovarian(437;0.104)|Medulloblastoma(700;0.151)		Colorectal(126;1.01e-07)|COAD - Colon adenocarcinoma(152;6.21e-06)|STAD - Stomach adenocarcinoma(196;0.0196)|BRCA - Breast invasive adenocarcinoma(304;0.0531)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.138)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	31032077	31032077	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31032077delA								None (None upstream) : MATN1 (152049 downstream)																																			---	---	---	---
MATN1	4146	broad.mit.edu	37	1	31186225	31186226	+	3'UTR	DEL	CA	-	-	rs71794590		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31186225_31186226delCA	uc001brz.2	-	8						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)														---	---	---	---
NKAIN1	79570	broad.mit.edu	37	1	31700494	31700497	+	Intron	DEL	CCAA	-	-	rs71675172		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31700494_31700497delCCAA	uc010ogd.1	-							NM_024522	NP_078798			Na+/K+ transporting ATPase interacting 1							integral to membrane|plasma membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31789773	31789773	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31789773delC	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
EIF3I	8668	broad.mit.edu	37	1	32693980	32693980	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32693980delG	uc001bur.3	+						EIF3I_uc009vuc.2_Intron|EIF3I_uc001bus.2_Intron	NM_003757	NP_003748			eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)																---	---	---	---
TSSK3	81629	broad.mit.edu	37	1	32825184	32825185	+	5'Flank	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32825184_32825185delTT	uc001bvf.2	+							NM_052841	NP_443073			testis-specific serine kinase 3						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			stomach(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)																---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	32973368	32973369	+	Intron	INS	-	T	T	rs72444124		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32973368_32973369insT	uc001bvk.2	+							NM_001145720				zinc finger and BTB domain containing 8B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
S100PBP	64766	broad.mit.edu	37	1	33302053	33302053	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33302053delT	uc001bvz.2	+						S100PBP_uc001bwc.2_Intron|S100PBP_uc001bwd.2_Intron	NM_022753	NP_073590			S100P binding protein isoform a							nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33344923	33344924	+	IGR	DEL	TT	-	-	rs113176350		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33344923_33344924delTT								FNDC5 (6841 upstream) : HPCA (7174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33519967	33519967	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33519967delA								AK2 (17475 upstream) : ADC (26747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33539244	33539244	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33539244delT								AK2 (36752 upstream) : ADC (7470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	34774266	34774266	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34774266delA								C1orf94 (89537 upstream) : MIR552 (360934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	34818276	34818276	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34818276delA								C1orf94 (133547 upstream) : MIR552 (316924 downstream)																																			---	---	---	---
ZMYM6	9204	broad.mit.edu	37	1	35462464	35462464	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35462464delT	uc001byh.2	-						ZMYM6_uc001byf.1_Intron|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Intron	NM_007167	NP_009098			zinc finger protein 258						multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	36683134	36683135	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36683134_36683135delTT								MAP7D1 (36698 upstream) : THRAP3 (6882 downstream)																																			---	---	---	---
STK40	83931	broad.mit.edu	37	1	36853370	36853371	+	5'Flank	DEL	AC	-	-	rs113801278		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36853370_36853371delAC	uc001cak.1	-						STK40_uc001cal.1_5'Flank|STK40_uc001cam.1_5'Flank|STK40_uc009vva.1_5'Flank	NM_032017	NP_114406			serine/threonine kinase 40							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1		Myeloproliferative disorder(586;0.0393)																---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37482816	37482818	+	Intron	DEL	AAA	-	-	rs112000328		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37482816_37482818delAAA	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822			glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	37568453	37568458	+	IGR	DEL	AGGAGG	-	-	rs71053960		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37568453_37568458delAGGAGG								GRIK3 (68609 upstream) : ZC3H12A (371661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37664333	37664334	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37664333_37664334delAA								GRIK3 (164489 upstream) : ZC3H12A (275785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37733798	37733799	+	IGR	DEL	TT	-	-	rs67205097		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37733798_37733799delTT								GRIK3 (233954 upstream) : ZC3H12A (206320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37813786	37813787	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37813786_37813787delAA								GRIK3 (313942 upstream) : ZC3H12A (126332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38122123	38122123	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38122123delT								RSPO1 (21632 upstream) : C1orf109 (25127 downstream)																																			---	---	---	---
C1orf109	54955	broad.mit.edu	37	1	38153550	38153551	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38153550_38153551delTT	uc001cbp.2	-						C1orf109_uc010oig.1_Intron|C1orf109_uc001cbo.2_Intron|C1orf109_uc001cbq.1_Intron	NM_017850	NP_060320			hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	40170559	40170560	+	IGR	INS	-	A	A	rs147111693	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40170559_40170560insA								HPCAL4 (13470 upstream) : PPIE (33970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40411075	40411075	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40411075delT								MYCL1 (43388 upstream) : MFSD2A (9709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40572191	40572191	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40572191delG								PPT1 (9049 upstream) : RLF (54850 downstream)																																			---	---	---	---
ZNF643	65243	broad.mit.edu	37	1	40921142	40921142	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40921142delA	uc001cfn.1	+						ZNF643_uc001cfl.1_Intron|ZNF643_uc001cfm.1_Intron	NM_023070	NP_075558			zinc finger protein 643						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.25e-18)															---	---	---	---
ZNF684	127396	broad.mit.edu	37	1	40996567	40996567	+	5'Flank	DEL	A	-	-	rs2184876	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40996567delA	uc001cft.1	+							NM_152373	NP_689586			zinc finger protein 684						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)															---	---	---	---
RIMS3	9783	broad.mit.edu	37	1	41091998	41091999	+	3'UTR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41091998_41091999delAC	uc001cfu.1	-	8					RIMS3_uc001cfv.1_3'UTR	NM_014747	NP_055562			regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)															---	---	---	---
RIMS3	9783	broad.mit.edu	37	1	41106439	41106439	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41106439delA	uc001cfu.1	-						RIMS3_uc001cfv.1_Intron	NM_014747	NP_055562			regulating synaptic membrane exocytosis 3						neurotransmitter transport	cell junction|synapse					0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)															---	---	---	---
NFYC	4802	broad.mit.edu	37	1	41195351	41195352	+	Intron	INS	-	T	T	rs72659572	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41195351_41195352insT	uc001cgb.2	+						NFYC_uc010ojm.1_Intron|NFYC_uc001cfx.3_Intron|NFYC_uc009vwd.2_Intron|NFYC_uc001cfz.2_Intron|NFYC_uc010ojn.1_Intron|NFYC_uc001cfy.3_Intron|NFYC_uc001cgc.2_Intron	NM_014223	NP_055038			nuclear transcription factor Y, gamma isoform 2						protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)															---	---	---	---
KCNQ4	9132	broad.mit.edu	37	1	41271517	41271519	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41271517_41271519delTTT	uc001cgh.1	+						KCNQ4_uc001cgi.1_Intron	NM_004700	NP_004691			potassium voltage-gated channel KQT-like protein						sensory perception of sound	basal plasma membrane|voltage-gated potassium channel complex				central_nervous_system(1)	1	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41909105	41909106	+	IGR	INS	-	T	T	rs147533070	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41909105_41909106insT								SCMH1 (201317 upstream) : EDN2 (35343 downstream)																																			---	---	---	---
WDR65	149465	broad.mit.edu	37	1	43651750	43651750	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43651750delA	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)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43862179	43862179	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43862179delA	uc009vws.1	+						C1orf84_uc001cjh.2_Intron|C1orf84_uc001cji.1_Intron					Homo sapiens mRNA for KIAA0467 protein, partial cds.							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43911163	43911164	+	Intron	DEL	CC	-	-	rs71943751		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43911163_43911164delCC	uc001cjk.1	+						KIAA0467_uc001cjl.1_5'UTR	NM_015284	NP_056099			hypothetical protein LOC23334							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44216554	44216554	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44216554delA	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	44360318	44360318	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44360318delT	uc001ckc.2	+						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)																---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44459116	44459117	+	Intron	DEL	AA	-	-	rs35911583		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44459116_44459117delAA	uc010okm.1	-						SLC6A9_uc009vxe.2_Intron|CCDC24_uc001clj.2_Intron|CCDC24_uc001clk.2_Intron|CCDC24_uc009vxc.2_Intron					RecName: Full=Transporter;							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)													---	---	---	---
ERI3	79033	broad.mit.edu	37	1	44776623	44776624	+	Intron	INS	-	CGCGCG	CGCGCG	rs141114785	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44776623_44776624insCGCGCG	uc001clt.2	-						ERI3_uc010okv.1_Intron|ERI3_uc009vxg.2_Intron|ERI3_uc010okw.1_Intron|ERI3_uc001clu.2_Intron	NM_024066	NP_076971			prion protein interacting protein							intracellular	exonuclease activity|metal ion binding|nucleic acid binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44957335	44957336	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44957335_44957336delTT	uc001clv.1	+						RNF220_uc001clw.1_Intron|RNF220_uc010okx.1_Intron|RNF220_uc010oky.1_Intron	NM_018150	NP_060620			ring finger protein 220						protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45952670	45952670	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45952670delT	uc001cns.1	-						TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron|TESK2_uc010olp.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46909044	46909044	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46909044delT								FAAH (29524 upstream) : DMBX1 (63624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	47952570	47952570	+	IGR	DEL	A	-	-	rs11362633		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47952570delA								FOXD2 (46208 upstream) : SKINTL (614817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	48197870	48197870	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48197870delG								FOXD2 (291508 upstream) : SKINTL (369517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	48382399	48382399	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48382399delG								FOXD2 (476037 upstream) : SKINTL (184988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	48478000	48478001	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48478000_48478001delCT								FOXD2 (571638 upstream) : SKINTL (89386 downstream)																																			---	---	---	---
SKINTL	391037	broad.mit.edu	37	1	48569479	48569480	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48569479_48569480delTG	uc010omr.1	-							NR_026749				Homo sapiens Skint-like (pseudogene) (SKINTL), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	48677603	48677603	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48677603delT								SKINTL (29503 upstream) : SLC5A9 (10754 downstream)																																			---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48782169	48782170	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48782169_48782170insG	uc001crr.1	-						SPATA6_uc001crs.1_Intron|SPATA6_uc010omv.1_Intron	NM_019073	NP_061946			spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49218432	49218432	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49218432delT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron|BEND5_uc001crx.3_Intron|BEND5_uc001crw.3_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49344945	49344946	+	Intron	DEL	GT	-	-	rs71672631		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49344945_49344946delGT	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49702944	49702944	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49702944delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	50429615	50429615	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50429615delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	50463795	50463795	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50463795delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
RNF11	26994	broad.mit.edu	37	1	51716222	51716222	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51716222delT	uc001csi.3	+							NM_014372	NP_055187			ring finger protein 11						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	DNA binding|protein binding|zinc ion binding				0																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52345490	52345490	+	5'Flank	DEL	T	-	-	rs36080456		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52345490delT	uc001ctc.3	-						NRD1_uc001ctd.3_5'Flank|NRD1_uc001cte.2_5'Flank|NRD1_uc001ctf.2_5'Flank|NRD1_uc010ong.1_5'Flank|NRD1_uc009vzc.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																		---	---	---	---
TXNDC12	51060	broad.mit.edu	37	1	52510647	52510647	+	Intron	DEL	A	-	-	rs78675272		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52510647delA	uc001cti.2	-							NM_015913	NP_056997			thioredoxin domain containing 12 precursor						activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(1)	1																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53287007	53287007	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53287007delA	uc001cuj.2	+						ZYG11B_uc010onj.1_Intron|ZYG11B_uc009vzh.2_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53829460	53829460	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53829460delA								LRP8 (35639 upstream) : FLJ40434 (74584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	54933309	54933311	+	IGR	DEL	TTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54933309_54933311delTTG								SSBP3 (61217 upstream) : ACOT11 (74619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55216469	55216470	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55216469_55216470insG								C1orf175 (8489 upstream) : PARS2 (6103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55313815	55313816	+	IGR	INS	-	TGTGTG	TGTGTG	rs139125598	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55313815_55313816insTGTGTG								C1orf177 (5879 upstream) : DHCR24 (1484 downstream)																																			---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58356128	58356129	+	Intron	INS	-	T	T	rs71670200		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58356128_58356129insT	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	59012351	59012351	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59012351delA	uc001cyt.1	-						OMA1_uc001cyy.2_Intron|OMA1_uc009vzz.2_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																OREG0013516	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	61072907	61072907	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61072907delG								C1orf87 (533481 upstream) : NFIA (470039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61130778	61130778	+	Intron	DEL	T	-	-	rs67802708		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61130778delT	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																														---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61543525	61543526	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61543525_61543526delTT	uc001czy.2	+							NM_001145511	NP_001138983			nuclear factor I/A isoform 3						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61606019	61606019	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61606019delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61785783	61785784	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61785783_61785784delTT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61850909	61850909	+	Intron	DEL	A	-	-	rs33952551		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61850909delA	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	62882830	62882830	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62882830delA								KANK4 (97747 upstream) : USP1 (19145 downstream)																																			---	---	---	---
DNAJC6	9829	broad.mit.edu	37	1	65796143	65796143	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65796143delT	uc001dcd.1	+						DNAJC6_uc001dcc.1_Intron|DNAJC6_uc010opc.1_Intron|DNAJC6_uc001dce.1_Intron	NM_014787	NP_055602			DnaJ (Hsp40) homolog, subfamily C, member 6						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																		---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66281660	66281660	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66281660delA	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron	NM_001037341	NP_001032418			phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	68012802	68012806	+	IGR	DEL	TAGAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68012802_68012806delTAGAT								SERBP1 (116679 upstream) : GADD45A (138077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68111326	68111327	+	IGR	INS	-	T	T	rs147608521	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68111326_68111327insT								SERBP1 (215203 upstream) : GADD45A (39556 downstream)																																			---	---	---	---
WLS	79971	broad.mit.edu	37	1	68573317	68573317	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68573317delA	uc001dee.2	-						uc001deb.1_Intron|uc001dec.1_Intron	NM_001002292	NP_001002292			G protein-coupled receptor 177 isoform 2						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	69015795	69015795	+	IGR	DEL	A	-	-	rs147974333		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69015795delA								DEPDC1 (52996 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69297422	69297433	+	IGR	DEL	TAAGCTCTTAGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69297422_69297433delTAAGCTCTTAGT								DEPDC1 (334623 upstream) : LRRC7 (735435 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70165220	70165220	+	Intron	DEL	A	-	-	rs142899292	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70165220delA	uc001deo.1	+											SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 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	71153444	71153444	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71153444delT								CTH (248192 upstream) : PTGER3 (164592 downstream)																																			---	---	---	---
PTGER3	5733	broad.mit.edu	37	1	71386558	71386567	+	Intron	DEL	TTGTATGTTG	-	-	rs36204308		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71386558_71386567delTTGTATGTTG	uc001dfg.1	-						PTGER3_uc001dfh.1_Intron|PTGER3_uc001dfi.1_Intron|PTGER3_uc001dfj.1_Intron|PTGER3_uc001dfk.1_Intron|PTGER3_uc001dfl.1_Intron|PTGER3_uc009wbm.1_Intron|PTGER3_uc001dfm.1_Intron|PTGER3_uc001dfn.2_Intron|PTGER3_uc009wbn.1_Intron	NM_198714	NP_942007			prostaglandin E receptor 3, subtype EP3 isoform						cell death|positive regulation of fever generation|transcription, DNA-dependent	integral to plasma membrane|nuclear envelope	ligand-dependent nuclear receptor activity|prostaglandin E receptor activity			pancreas(1)|lung(1)|skin(1)	3					Bimatoprost(DB00905)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	71730059	71730060	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71730059_71730060delTT								ZRANB2 (183314 upstream) : NEGR1 (138566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	71766993	71766993	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71766993delT								ZRANB2 (220248 upstream) : NEGR1 (101633 downstream)																																			---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72318475	72318475	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72318475delA	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	73626498	73626499	+	IGR	INS	-	T	T	rs146317157	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73626498_73626499insT								NEGR1 (878093 upstream) : LRRIQ3 (865205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74029645	74029645	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74029645delT								None (None upstream) : LRRIQ3 (462059 downstream)																																			---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74534514	74534515	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74534514_74534515delAA	uc001dfy.3	-						LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129			leucine-rich repeats and IQ motif containing 3											ovary(2)	2																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75963165	75963165	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75963165delG	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	76062001	76062001	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76062001delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76579186	76579187	+	Intron	INS	-	T	T	rs145078243	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76579186_76579187insT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76999021	76999024	+	Intron	DEL	ACAA	-	-	rs147723240		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76999021_76999024delACAA	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	80078453	80078453	+	IGR	DEL	A	-	-	rs72043738		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80078453delA								ELTD1 (605958 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80688082	80688082	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80688082delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80723943	80723946	+	IGR	DEL	TATC	-	-	rs72433239		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80723943_80723946delTATC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83225700	83225700	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83225700delA								LPHN2 (767594 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84133149	84133150	+	Intron	INS	-	ACACAGACAC	ACACAGACAC	rs75131513		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84133149_84133150insACACAGACAC	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	84500557	84500558	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84500557_84500558delAC								TTLL7 (35724 upstream) : PRKACB (43078 downstream)																																			---	---	---	---
PRKACB	5567	broad.mit.edu	37	1	84639049	84639049	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84639049delT	uc001djj.2	+						PRKACB_uc001djl.2_Intron|PRKACB_uc010ort.1_Intron|PRKACB_uc001djn.2_Intron|PRKACB_uc010oru.1_Intron|PRKACB_uc001djp.2_Intron|PRKACB_uc001djq.2_Intron|PRKACB_uc001dji.2_Intron|PRKACB_uc001djk.2_Intron|PRKACB_uc001djo.1_Intron|PRKACB_uc009wcf.1_Intron	NM_002731	NP_002722			cAMP-dependent protein kinase catalytic subunit						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)														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85965733	85965736	+	Intron	DEL	TCTC	-	-	rs142961084		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85965733_85965736delTCTC	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)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85989831	85989832	+	Intron	INS	-	G	G	rs139714427	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85989831_85989832insG	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)													---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86259141	86259142	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86259141_86259142delAG	uc001dlj.2	-						COL24A1_uc001dli.2_Intron|COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86563061	86563065	+	Intron	DEL	TCTTC	-	-	rs72085934		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86563061_86563065delTCTTC	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron|COL24A1_uc009wcq.2_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87157952	87157953	+	IGR	INS	-	TCTC	TCTC	rs72722211		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87157952_87157953insTCTC								CLCA3P (36894 upstream) : SH3GLB1 (12304 downstream)																																			---	---	---	---
SH3GLB1	51100	broad.mit.edu	37	1	87181251	87181251	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87181251delA	uc001dlw.2	+						SH3GLB1_uc001dlx.2_Intron|SH3GLB1_uc001dly.2_Intron|SH3GLB1_uc001dlz.2_Intron	NM_016009	NP_057093			SH3-containing protein SH3GLB1						anti-apoptosis|filopodium assembly|signal transduction	Golgi membrane|mitochondrial outer membrane	cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding				0		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	88094174	88094174	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88094174delA								LMO4 (279571 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88303590	88303591	+	IGR	INS	-	T	T	rs72510720	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88303590_88303591insT								LMO4 (488987 upstream) : PKN2 (846331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88308562	88308564	+	IGR	DEL	TTC	-	-	rs34452400		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88308562_88308564delTTC								LMO4 (493959 upstream) : PKN2 (841358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	89119768	89119768	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89119768delA								None (None upstream) : PKN2 (30154 downstream)																																			---	---	---	---
GTF2B	2959	broad.mit.edu	37	1	89335315	89335315	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89335315delT	uc001dmo.3	-						GTF2B_uc009wcw.1_Intron	NM_001514	NP_001505			general transcription factor IIB						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	thyroid hormone receptor binding|translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	89552434	89552434	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89552434delT								GBP1 (21391 upstream) : GBP2 (19409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	89774097	89774097	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89774097delA								GBP5 (35553 upstream) : GBP6 (55339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91630339	91630339	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91630339delG								ZNF644 (142668 upstream) : HFM1 (95985 downstream)																																			---	---	---	---
TGFBR3	7049	broad.mit.edu	37	1	92373638	92373638	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92373638delA	uc001doj.2	-							NM_003243	NP_003234			transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)														---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92568324	92568325	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92568324_92568325delTT	uc001doo.2	+						BTBD8_uc010otc.1_Intron	NM_183242	NP_899065			BTB (POZ) domain containing 8							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)														---	---	---	---
KIAA1107	23285	broad.mit.edu	37	1	92646877	92646877	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92646877delA	uc010otd.1	+	8	2421	c.2323delA	c.(2323-2325)AAAfs	p.K775fs	KIAA1107_uc001dop.2_Frame_Shift_Del_p.K700fs	NM_015237	NP_056052	Q9UPP5	K1107_HUMAN	hypothetical protein LOC23285	830											0																		---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93208909	93208909	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93208909delA	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)														---	---	---	---
RPL5	6125	broad.mit.edu	37	1	93301569	93301569	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93301569delT	uc001doz.2	+						FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_Intron|RPL5_uc001dpd.2_5'Flank|SNORD21_uc001dpe.2_5'Flank	NM_000969	NP_000960			ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93489783	93489783	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93489783delT								FAM69A (62704 upstream) : MTF2 (55009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	93744310	93744310	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93744310delT	uc001dps.2	-											Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	94025117	94025118	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94025117_94025118delTT								FNBP1L (4901 upstream) : BCAR3 (2233 downstream)																																			---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94505150	94505150	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94505150delA	uc001dqh.2	-							NM_000350	NP_000341			ATP-binding cassette, sub-family A member 4						phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)												OREG0013610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ABCD3	5825	broad.mit.edu	37	1	94962008	94962009	+	Intron	DEL	TG	-	-	rs147383585		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94962008_94962009delTG	uc001dqn.3	+						ABCD3_uc010oto.1_Intron|ABCD3_uc010otp.1_Intron|ABCD3_uc009wdr.2_Intron|ABCD3_uc001dqo.3_Intron	NM_002858	NP_002849			ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	96589574	96589574	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96589574delT								RWDD3 (876801 upstream) : PTBP2 (597601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	98759356	98759356	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98759356delA								MIR137 (247629 upstream) : SNX7 (367880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	100088781	100088781	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100088781delA								LPPR4 (313645 upstream) : PALMD (22650 downstream)																																			---	---	---	---
DPH5	51611	broad.mit.edu	37	1	101460111	101460111	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101460111delC	uc001dts.2	-						DPH5_uc001dtr.2_Intron|DPH5_uc001dtq.2_Intron|DPH5_uc001dtt.2_Intron|DPH5_uc001dtu.2_Intron|DPH5_uc001dtv.2_Intron|DPH5_uc001dtw.2_Intron|DPH5_uc001dtx.2_Intron|DPH5_uc001dty.2_Intron|DPH5_uc001dtz.2_Intron	NM_015958	NP_057042			diphthine synthase isoform a						peptidyl-diphthamide biosynthetic process from peptidyl-histidine		diphthine synthase activity				0		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103074554	103074554	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103074554delA								OLFM3 (611764 upstream) : COL11A1 (267470 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103376228	103376228	+	Intron	DEL	T	-	-	rs78943090		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103376228delT	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	104936373	104936374	+	IGR	INS	-	A	A	rs143370387	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104936373_104936374insA								AMY1A (729201 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105443516	105443516	+	IGR	DEL	A	-	-	rs34951494		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105443516delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105969977	105969978	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105969977_105969978insA								None (None upstream) : None (None downstream)																																			---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108188719	108188719	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108188719delA	uc001dvk.1	-						VAV3_uc010ouu.1_Intron|VAV3_uc001dvj.1_Intron|VAV3_uc010ouv.1_Intron|VAV3_uc010ouw.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108491464	108491464	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108491464delA	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	109053976	109053977	+	IGR	INS	-	C	C	rs148257461	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109053976_109053977insC								NBPF6 (40717 upstream) : FAM102B (48994 downstream)																																			---	---	---	---
FAM102B	284611	broad.mit.edu	37	1	109122287	109122287	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109122287delT	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)														---	---	---	---
AKNAD1	254268	broad.mit.edu	37	1	109391940	109391940	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109391940delA	uc001dwa.2	-						AKNAD1_uc010ovb.1_Intron|AKNAD1_uc001dwb.2_Intron	NM_152763	NP_689976			hypothetical protein LOC254268											ovary(3)	3																		---	---	---	---
CLCC1	23155	broad.mit.edu	37	1	109495100	109495100	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109495100delT	uc001dwe.1	-						AKNAD1_uc010ovb.1_Intron|CLCC1_uc001dwf.1_Intron|CLCC1_uc001dwg.1_Intron|CLCC1_uc009wes.1_5'Flank|CLCC1_uc009wet.1_5'Flank|CLCC1_uc001dwh.1_Intron	NM_001048210	NP_001041675			Mid-1-related chloride channel 1 isoform 1							endoplasmic reticulum|Golgi apparatus|integral to membrane|nucleus				liver(1)	1		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)														---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110119900	110119901	+	Intron	INS	-	TTTTTTTT	TTTTTTTT	rs9728726		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110119900_110119901insTTTTTTTT	uc001dxz.2	+							NM_006496	NP_006487			guanine nucleotide binding protein (G protein),						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110504746	110504748	+	IGR	DEL	AAA	-	-	rs11809936		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110504746_110504748delAAA								CSF1 (32392 upstream) : AHCYL1 (22560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	110833896	110833896	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110833896delG	uc001dzj.2	-											Homo sapiens cDNA clone IMAGE:5166911.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	111065230	111065233	+	IGR	DEL	AAAA	-	-	rs146296248		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111065230_111065233delAAAA								KCNA10 (3433 upstream) : KCNA2 (70970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	112006173	112006174	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112006173_112006174delAG								ATP5F1 (1650 upstream) : C1orf162 (10430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	112257708	112257708	+	RNA	DEL	T	-	-	rs72222174		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112257708delT	uc001ebn.1	+	1		c.879delT								Homo sapiens cDNA FLJ13395 fis, clone PLACE1001311.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112659196	112659196	+	IGR	DEL	T	-	-	rs5777093		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112659196delT								KCND3 (127419 upstream) : CTTNBP2NL (279604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	112722211	112722211	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112722211delT								KCND3 (190434 upstream) : CTTNBP2NL (216589 downstream)																																			---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114242393	114242393	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114242393delT	uc009wgp.1	-	16	2527	c.2075delA	c.(2074-2076)AAGfs	p.K692fs	PHTF1_uc001edm.2_Frame_Shift_Del_p.K449fs	NM_006608	NP_006599	Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	692						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	114839653	114839653	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114839653delA								SYT6 (143181 upstream) : TRIM33 (95748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	115344127	115344127	+	IGR	DEL	G	-	-	rs34791119		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115344127delG								SIKE1 (20819 upstream) : SYCP1 (53328 downstream)																																			---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115456687	115456687	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115456687delT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167			synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116891725	116891725	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116891725delA								C1orf161 (213864 upstream) : ATP1A1 (23279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117374968	117374968	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117374968delA								CD2 (63118 upstream) : PTGFRN (77721 downstream)																																			---	---	---	---
TRIM45	80263	broad.mit.edu	37	1	117659023	117659023	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117659023delT	uc001egz.2	-						TRIM45_uc009whe.2_Intron|TRIM45_uc001eha.2_Intron	NM_025188	NP_079464			tripartite motif-containing 45 isoform 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)														---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118513676	118513676	+	Intron	DEL	T	-	-	rs11361620		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118513676delT	uc001ehk.2	-							NM_206996	NP_996879			sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	118856232	118856233	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118856232_118856233delAC								SPAG17 (128384 upstream) : TBX15 (569433 downstream)																																			---	---	---	---
TBX15	6913	broad.mit.edu	37	1	119519265	119519266	+	Intron	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119519265_119519266delCT	uc001ehl.1	-							NM_152380	NP_689593			T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	120006520	120006520	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120006520delA								HSD3B2 (17400 upstream) : HSD3B1 (43306 downstream)																																			---	---	---	---
ZNF697	90874	broad.mit.edu	37	1	120185496	120185497	+	Intron	INS	-	GATT	GATT	rs145493171	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120185496_120185497insGATT	uc001ehy.1	-							NM_001080470	NP_001073939			zinc finger protein 697						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	120206565	120206566	+	IGR	INS	-	GCAG	GCAG	rs148623840	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120206565_120206566insGCAG								ZNF697 (16175 upstream) : PHGDH (47853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	120218950	120218950	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120218950delT								ZNF697 (28560 upstream) : PHGDH (35469 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120501337	120501338	+	Intron	INS	-	TG	TG	rs138391538	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120501337_120501338insTG	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				---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120516073	120516073	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120516073delA	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	120810321	120810322	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120810321_120810322insA								NOTCH2 (198045 upstream) : FAM72B (28683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142557979	142557979	+	IGR	DEL	C	-	-	rs140910928		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142557979delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142578027	142578027	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142578027delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142593372	142593372	+	IGR	DEL	G	-	-	rs149569221		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142593372delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143142555	143142555	+	Intron	DEL	T	-	-	rs111246166		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143142555delT	uc001eiw.1	+						uc001ejf.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143174696	143174696	+	Intron	DEL	C	-	-	rs112579256		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143174696delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143285690	143285690	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143285690delT								None (None upstream) : LOC100286793 (361949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	144014490	144014499	+	Intron	DEL	TCTCTCTCTC	-	-	rs72117340		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144014490_144014499delTCTCTCTCTC	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	144590644	144590644	+	Intron	DEL	A	-	-	rs139951242		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144590644delA	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144678541	144678541	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144678541delT	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144966673	144966673	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144966673delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_Intron|PDE4DIP_uc001emh.2_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								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145029115	145029115	+	Intron	DEL	C	-	-	rs10717150		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145029115delC	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	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	145106432	145106439	+	Intron	DEL	TGTGTGTA	-	-	rs3977180		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145106432_145106439delTGTGTGTA	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	145199586	145199586	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145199586delA	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	145368208	145368213	+	Intron	DEL	TCTCTG	-	-	rs72354261		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145368208_145368213delTCTCTG	uc001end.3	+						NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792			hypothetical protein LOC100132406												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	145733851	145733851	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145733851delT	uc001emp.3	+						PDZK1_uc001eon.1_Intron|PDZK1_uc001eoo.1_Intron|PDZK1_uc010oza.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146476728	146476729	+	IGR	DEL	AT	-	-	rs67696815		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146476728_146476729delAT								NBPF10 (52633 upstream) : LOC728989 (14166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	147318806	147318808	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147318806_147318808delAAA								GJA5 (73322 upstream) : GJA8 (56128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	147345651	147345651	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147345651delG								GJA5 (100167 upstream) : GJA8 (29285 downstream)																																			---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	147720385	147720386	+	Intron	DEL	TT	-	-	rs111322116		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147720385_147720386delTT	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148556366	148556367	+	5'Flank	INS	-	G	G	rs151071059		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148556366_148556367insG	uc001esb.1	+							NM_001102663	NP_001096133			hypothetical protein LOC728936							cytoplasm					0	all_hematologic(923;0.032)																	---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148934313	148934313	+	Intron	DEL	T	-	-	rs71220700		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148934313delT	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
LOC728855	728855	broad.mit.edu	37	1	149601954	149601957	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149601954_149601957delTTTT	uc001esk.3	+						LOC728855_uc001esl.3_Intron|LOC728855_uc009wlc.2_Intron|LOC728855_uc009wld.2_Intron	NR_024510				Homo sapiens mRNA, chromosome 1 specific transcript KIAA0493.												0																		---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149977611	149977611	+	Intron	DEL	T	-	-	rs76018516		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149977611delT	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	150060017	150060018	+	Intron	INS	-	T	T	rs144960753	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150060017_150060018insT	uc001etp.2	+						VPS45_uc010pbp.1_Intron|VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron|VPS45_uc009wlm.1_Intron	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150331592	150331593	+	IGR	DEL	AG	-	-	rs1260374	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150331592_150331593delAG								PRPF3 (5889 upstream) : RPRD2 (5397 downstream)																																			---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150381476	150381477	+	Intron	INS	-	TA	TA	rs5777726		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150381476_150381477insTA	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
MCL1	4170	broad.mit.edu	37	1	150550659	150550659	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150550659delA	uc001euz.2	-						MCL1_uc010pch.1_Intron|MCL1_uc001eva.2_Intron	NM_021960	NP_068779			myeloid cell leukemia sequence 1 isoform 1						anti-apoptosis|apoptosis|cell fate determination|cellular homeostasis|multicellular organismal development|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nucleoplasm	BH3 domain binding|protein binding|protein channel activity|protein heterodimerization activity				0	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-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;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150592893	150592893	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150592893delA								MCL1 (40757 upstream) : ENSA (1711 downstream)																																			---	---	---	---
CTSK	1513	broad.mit.edu	37	1	150779544	150779545	+	Intron	DEL	TC	-	-	rs72340399		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150779544_150779545delTC	uc001evp.1	-						CTSK_uc001evq.1_Intron|CTSK_uc009wma.1_Intron	NM_000396	NP_000387			cathepsin K preproprotein						proteolysis	lysosome	cysteine-type endopeptidase activity|protein binding			skin(1)	1	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
GABPB2	126626	broad.mit.edu	37	1	151058722	151058723	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151058722_151058723delAA	uc001ewr.2	+						GABPB2_uc010pcp.1_Intron|GABPB2_uc001ews.2_Intron	NM_144618	NP_653219			GA repeat binding protein, beta 2						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)														---	---	---	---
VPS72	6944	broad.mit.edu	37	1	151164462	151164463	+	5'Flank	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151164462_151164463delAA	uc001exe.1	-						VPS72_uc001exf.1_5'Flank	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)															---	---	---	---
SELENBP1	8991	broad.mit.edu	37	1	151345907	151345908	+	5'Flank	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151345907_151345908delTG	uc001exx.2	-						SELENBP1_uc010pcy.1_5'Flank|SELENBP1_uc001exy.2_5'Flank|SELENBP1_uc001exz.2_5'Flank|SELENBP1_uc010pcz.1_5'Flank|SELENBP1_uc009wms.2_5'Flank|SELENBP1_uc009wmt.2_5'Flank|SELENBP1_uc001eya.2_5'Flank|SELENBP1_uc009wmu.2_5'Flank	NM_003944	NP_003935			selenium binding protein 1						protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|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)															---	---	---	---
IL6R	3570	broad.mit.edu	37	1	154398259	154398260	+	Intron	DEL	AA	-	-	rs112621723		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154398259_154398260delAA	uc001fez.1	+						IL6R_uc001ffa.1_Intron	NM_000565	NP_000556			interleukin 6 receptor isoform 1 precursor						acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity			ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155466596	155466596	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155466596delT	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)															---	---	---	---
RIT1	6016	broad.mit.edu	37	1	155870617	155870617	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155870617delT	uc001fmh.1	-						RIT1_uc010pgr.1_Intron	NM_006912	NP_008843			Ras-like without CAAX 1						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)															---	---	---	---
RIT1	6016	broad.mit.edu	37	1	155875311	155875311	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155875311delA	uc001fmh.1	-						RIT1_uc010pgr.1_Intron	NM_006912	NP_008843			Ras-like without CAAX 1						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)															---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156083859	156083860	+	5'Flank	INS	-	C	C	rs140490020	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156083859_156083860insC	uc001fni.2	+						LMNA_uc001fnf.1_Intron|LMNA_uc001fng.2_5'Flank|LMNA_uc001fnh.2_5'Flank|LMNA_uc009wro.1_5'Flank	NM_170707	NP_733821			lamin A/C isoform 1 precursor						cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration	cytoplasm|lamin filament|nuclear envelope|nuclear envelope|perinuclear region of cytoplasm	protein binding|structural molecule activity|structural molecule activity			ovary(2)	2	Hepatocellular(266;0.158)													Werner_syndrome|Hutchinson-Gilford_Progeria_Syndrome				---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156146087	156146087	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156146087delA	uc001fnl.2	+						SEMA4A_uc009wrq.2_Intron|SEMA4A_uc001fnm.2_Intron|SEMA4A_uc001fnn.2_Intron|SEMA4A_uc001fno.2_Intron	NM_022367	NP_071762			semaphorin B precursor						axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
CCT3	7203	broad.mit.edu	37	1	156306596	156306596	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156306596delA	uc001fol.1	-						CCT3_uc001fom.1_Intron|CCT3_uc001fon.1_Intron|CCT3_uc010phj.1_Intron|CCT3_uc010phk.1_Intron|CCT3_uc010phl.1_Intron|C1orf182_uc001foo.2_5'Flank|C1orf182_uc009wry.2_5'Flank|C1orf182_uc001fop.3_5'Flank	NM_005998	NP_005989			chaperonin containing TCP1, subunit 3 isoform a						'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156414120	156414120	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156414120delT								C1orf61 (13627 upstream) : MEF2D (19400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157360369	157360370	+	IGR	INS	-	TTG	TTG	rs140547676	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157360369_157360370insTTG								ETV3 (251986 upstream) : FCRL5 (122798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157604146	157604146	+	IGR	DEL	T	-	-	rs11317296		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157604146delT								FCRL4 (36276 upstream) : FCRL3 (42132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157947532	157947532	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157947532delA								CD5L (135898 upstream) : KIRREL (15531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158112010	158112010	+	5'Flank	DEL	T	-	-	rs113022942		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158112010delT	uc001frq.2	-											Homo sapiens cDNA clone IMAGE:5295410.																														---	---	---	---
CD1A	909	broad.mit.edu	37	1	158221651	158221651	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158221651delT	uc001frt.2	+							NM_001763	NP_001754			CD1A antigen precursor						antigen processing and presentation|immune response	endosome membrane|integral to plasma membrane|MHC class I protein complex				pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)													---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158969660	158969660	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158969660delA	uc001ftf.1	+							NM_005531	NP_005522			interferon, gamma-inducible protein 16						cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	159089587	159089588	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159089587_159089588delTG								AIM2 (42940 upstream) : CADM3 (51789 downstream)																																			---	---	---	---
FCRL6	343413	broad.mit.edu	37	1	159775154	159775154	+	Intron	DEL	T	-	-	rs10616063		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159775154delT	uc001fud.3	+						FCRL6_uc010pix.1_Intron|FCRL6_uc001fuc.2_Intron|FCRL6_uc009wsz.1_Intron|FCRL6_uc009wta.2_Intron	NM_001004310	NP_001004310			Fc receptor-like 6 precursor							integral to membrane				ovary(2)|skin(1)	3	all_hematologic(112;0.0597)																	---	---	---	---
PEA15	8682	broad.mit.edu	37	1	160179301	160179302	+	Intron	DEL	AC	-	-	rs111598251		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160179301_160179302delAC	uc001fvk.2	+						uc001fvj.1_5'Flank|PEA15_uc001fvl.2_Intron|PEA15_uc001fvm.2_Intron	NM_003768	NP_003759			phosphoprotein enriched in astrocytes 15						anti-apoptosis|apoptosis|carbohydrate transport|negative regulation of glucose import	cytoplasm|microtubule associated complex	protein binding				0	all_cancers(52;3.11e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
NHLH1	4807	broad.mit.edu	37	1	160334426	160334427	+	5'Flank	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160334426_160334427delTT	uc001fwa.2	+							NM_005598	NP_005589			nescient helix loop helix 1						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160362366	160362366	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160362366delC								NHLH1 (19728 upstream) : VANGL2 (7865 downstream)																																			---	---	---	---
ITLN1	55600	broad.mit.edu	37	1	160847959	160847959	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160847959delA	uc001fxc.2	-							NM_017625	NP_060095			intelectin precursor						positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction	anchored to membrane|brush border membrane|extracellular region|membrane raft	receptor binding|sugar binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)	7	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160896614	160896614	+	IGR	DEL	C	-	-	rs59558686		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160896614delC								ITLN1 (41654 upstream) : ITLN2 (18203 downstream)																																			---	---	---	---
PFDN2	5202	broad.mit.edu	37	1	161074238	161074239	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161074238_161074239delTT	uc001fxu.2	-							NM_012394	NP_036526			prefoldin subunit 2						'de novo' posttranslational protein folding	prefoldin complex	unfolded protein binding				0	all_cancers(52;1.84e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
PCP4L1	654790	broad.mit.edu	37	1	161242811	161242811	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161242811delA	uc001gad.2	+							NM_001102566	NP_001096036			Purkinje cell protein 4 like 1												0	all_cancers(52;4.16e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
ATF6	22926	broad.mit.edu	37	1	161824662	161824662	+	Intron	DEL	A	-	-	rs75254377		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161824662delA	uc001gbr.2	+						ATF6_uc001gbq.1_Intron	NM_007348	NP_031374			activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)															---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162117723	162117723	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162117723delG	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)															---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162215719	162215719	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162215719delC	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)															---	---	---	---
SH2D1B	117157	broad.mit.edu	37	1	162382645	162382646	+	5'Flank	INS	-	G	G	rs138069521	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162382645_162382646insG	uc001gbz.1	-						SH2D1B_uc001gca.1_5'Flank	NM_053282	NP_444512			SH2 domain containing 1B											pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	164866401	164866402	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164866401_164866402insT								PBX1 (12101 upstream) : LMX1A (304703 downstream)																																			---	---	---	---
MGST3	4259	broad.mit.edu	37	1	165619919	165619920	+	Intron	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165619919_165619920insC	uc001gdf.2	+						MGST3_uc001gdg.2_Intron	NM_004528	NP_004519			microsomal glutathione S-transferase 3						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)													---	---	---	---
UCK2	7371	broad.mit.edu	37	1	165829674	165829675	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165829674_165829675delTT	uc001gdp.2	+						UCK2_uc010plb.1_Intron	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)																	---	---	---	---
GPA33	10223	broad.mit.edu	37	1	167025994	167025997	+	Intron	DEL	GCGT	-	-	rs138267814		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167025994_167025997delGCGT	uc001gea.1	-							NM_005814	NP_005805			transmembrane glycoprotein A33 precursor							integral to plasma membrane	receptor activity				0																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167328245	167328245	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167328245delT	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	167387896	167387896	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167387896delT								POU2F1 (2554 upstream) : CD247 (11982 downstream)																																			---	---	---	---
TBX19	9095	broad.mit.edu	37	1	168216312	168216312	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168216312delT	uc001gfj.3	+						ANKRD36BP1_uc010plo.1_RNA|uc001gfk.1_5'Flank	NM_005149	NP_005140			T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168865892	168865893	+	IGR	DEL	AG	-	-	rs149272258	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168865892_168865893delAG								MGC4473 (103772 upstream) : ATP1B1 (210054 downstream)																																			---	---	---	---
NME7	29922	broad.mit.edu	37	1	169266215	169266215	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169266215delT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron|NME7_uc001gfv.1_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
F5	2153	broad.mit.edu	37	1	169484915	169484915	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169484915delT	uc001ggg.1	-							NM_000130	NP_000121			coagulation factor V precursor						cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	170786037	170786037	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170786037delA								PRRX1 (77497 upstream) : C1orf129 (118575 downstream)																																			---	---	---	---
FMO1	2326	broad.mit.edu	37	1	171239244	171239244	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171239244delT	uc009wvz.2	+						FMO1_uc010pme.1_Intron|FMO1_uc001ghl.2_Intron|FMO1_uc001ghm.2_Intron|FMO1_uc001ghn.2_Intron	NM_002021	NP_002012			flavin containing monooxygenase 1						NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	171273928	171273936	+	IGR	DEL	AGGAGGAGG	-	-	rs111255926		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171273928_171273936delAGGAGGAGG								FMO1 (18817 upstream) : FMO4 (9550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	171579715	171579716	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171579715_171579716delAG								BAT2L2 (17066 upstream) : MYOC (24843 downstream)																																			---	---	---	---
MYOC	4653	broad.mit.edu	37	1	171623509	171623509	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171623509delT	uc001ghu.2	-						MYOC_uc010pmk.1_5'Flank	NM_000261	NP_000252			myocilin precursor						anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171819908	171819908	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171819908delT	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																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	172009618	172009619	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172009618_172009619insT	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	172984199	172984199	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172984199delT								FASLG (348189 upstream) : TNFSF18 (26161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	172997721	172997722	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172997721_172997722delTC								FASLG (361711 upstream) : TNFSF18 (12638 downstream)																																			---	---	---	---
DARS2	55157	broad.mit.edu	37	1	173819744	173819746	+	Intron	DEL	TTT	-	-	rs66665709		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173819744_173819746delTTT	uc001gjh.1	+							NM_018122	NP_060592			aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)													---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174201914	174201914	+	Intron	DEL	T	-	-	rs72711500	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174201914delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174501354	174501354	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174501354delT	uc001gjx.2	+						RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175418802	175418803	+	Intron	INS	-	CAA	CAA	rs142099980	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175418802_175418803insCAA	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)																	---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176525111	176525112	+	5'UTR	DEL	AA	-	-	rs2294653	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176525111_176525112delAA	uc001gkz.2	+	2					PAPPA2_uc001gky.1_5'UTR|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176798426	176798426	+	Intron	DEL	A	-	-	rs113825507		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176798426delA	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	176822782	176822782	+	IGR	DEL	A	-	-	rs5778916		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176822782delA								PAPPA2 (10814 upstream) : ASTN1 (3659 downstream)																																			---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176833843	176833844	+	Intron	INS	-	AATG	AATG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176833843_176833844insAATG	uc001glc.2	-						ASTN1_uc001glb.1_Intron	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	177724392	177724392	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177724392delA								FAM5B (472835 upstream) : SEC16B (173097 downstream)																																			---	---	---	---
C1orf49	84066	broad.mit.edu	37	1	178479880	178479880	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178479880delA	uc001glt.1	+						C1orf49_uc001glu.1_5'Flank|C1orf49_uc001glv.1_5'Flank|C1orf49_uc001glw.1_5'Flank	NM_032126	NP_115502			hypothetical protein LOC84066							microtubule cytoskeleton					0																		---	---	---	---
FAM20B	9917	broad.mit.edu	37	1	179025943	179025943	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179025943delT	uc001gmc.2	+							NM_014864	NP_055679			hypothetical protein LOC9917 precursor							Golgi membrane|integral to membrane	ATP binding|kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(3)	3																		---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179405990	179405990	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179405990delA	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180325008	180325008	+	Intron	DEL	T	-	-	rs34079820		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180325008delT	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	180483745	180483745	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180483745delG								ACBD6 (11723 upstream) : XPR1 (117401 downstream)																																			---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180636434	180636434	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180636434delT	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	181858612	181858613	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181858612_181858613delTT								CACNA1E (87899 upstream) : ZNF648 (165094 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182897317	182897318	+	Intron	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182897317_182897318delCT	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)														---	---	---	---
NMNAT2	23057	broad.mit.edu	37	1	183221068	183221069	+	3'UTR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183221068_183221069delGT	uc001gqc.1	-	11					NMNAT2_uc009wye.1_RNA|NMNAT2_uc001gqb.1_3'UTR	NM_015039	NP_055854			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	Golgi membrane|nucleus	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity			skin(1)	1																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183917327	183917327	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183917327delA	uc001gqr.2	-						GLT25D2_uc010poj.1_Intron|GLT25D2_uc001gqp.2_5'Flank|GLT25D2_uc001gqq.2_Intron|GLT25D2_uc001gqs.2_Intron	NM_015101	NP_055916			glycosyltransferase 25 domain containing 2						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184915131	184915131	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184915131delA	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																		---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185230806	185230808	+	Intron	DEL	TTT	-	-	rs71668785		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185230806_185230808delTTT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	187887550	187887559	+	IGR	DEL	ACACACACAC	-	-	rs72408476		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187887550_187887559delACACACACAC								PLA2G4A (929445 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188382347	188382348	+	IGR	DEL	TA	-	-	rs72286402		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188382347_188382348delTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189264295	189264296	+	IGR	INS	-	G	G	rs144871707	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189264295_189264296insG								None (None upstream) : FAM5C (802501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189763702	189763703	+	IGR	INS	-	T	T	rs139299409	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189763702_189763703insT								None (None upstream) : FAM5C (303094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192878270	192878271	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192878270_192878271insA								RGS2 (96864 upstream) : UCHL5 (106629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193665214	193665215	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193665214_193665215delTT								CDC73 (441274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194551747	194551747	+	IGR	DEL	T	-	-	rs66540332		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194551747delT								None (None upstream) : None (None downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196274286	196274286	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196526698	196526698	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196526698delA	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.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																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197670684	197670684	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197670684delT	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron	NM_144977	NP_659414			DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	197787018	197787018	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197787018delT								DENND1B (42395 upstream) : C1orf53 (84664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198308575	198308576	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198308575_198308576delCT								NEK7 (17029 upstream) : ATP6V1G3 (183780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198367585	198367585	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198367585delA								NEK7 (76039 upstream) : ATP6V1G3 (124771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198913273	198913273	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198913273delT								MIR181A1 (84991 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199108094	199108095	+	IGR	INS	-	TG	TG	rs144154758	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199108094_199108095insTG								MIR181A1 (279812 upstream) : NR5A2 (888675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199169734	199169734	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199169734delT								MIR181A1 (341452 upstream) : NR5A2 (827036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	200693097	200693097	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200693097delA								DDX59 (53971 upstream) : CAMSAP1L1 (15589 downstream)																																			---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200732032	200732033	+	Intron	INS	-	TT	TT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200732032_200732033insTT	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																		---	---	---	---
TMEM9	252839	broad.mit.edu	37	1	201106393	201106399	+	Intron	DEL	CAGCCTC	-	-	rs144642930		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201106393_201106399delCAGCCTC	uc001gvw.2	-						TMEM9_uc001gvx.2_Intron|TMEM9_uc001gvy.2_Intron|TMEM9_uc010ppo.1_Intron|TMEM9_uc001gvz.2_Intron|TMEM9_uc001gwa.2_Intron	NM_016456	NP_057540			transmembrane protein 9 precursor						transport	integral to membrane|late endosome membrane|lysosomal membrane					0		Breast(1374;0.000301)																---	---	---	---
TNNT2	7139	broad.mit.edu	37	1	201343155	201343156	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201343155_201343156delTG	uc001gwf.2	-						TNNT2_uc001gwg.2_Intron|TNNT2_uc001gwh.2_Intron|TNNT2_uc001gwi.2_Intron|TNNT2_uc009wzr.2_Intron|TNNT2_uc001gwk.1_5'Flank|TNNT2_uc009wzt.1_Intron|TNNT2_uc001gwl.1_5'Flank	NM_000364	NP_000355			troponin T type 2, cardiac isoform 1						ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	201416716	201416717	+	IGR	DEL	AA	-	-	rs66461244		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201416716_201416717delAA								TNNI1 (17722 upstream) : PHLDA3 (17906 downstream)																																			---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201656369	201656369	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201656369delT	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																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201675382	201675383	+	Intron	INS	-	GT	GT	rs150788509	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201675382_201675383insGT	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																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201680629	201680630	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201680629_201680630insA	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																		---	---	---	---
RNPEP	6051	broad.mit.edu	37	1	201966868	201966869	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201966868_201966869insA	uc001gxd.2	+						RNPEP_uc001gxe.2_Intron|RNPEP_uc001gxf.2_Intron	NM_020216	NP_064601			arginyl aminopeptidase						leukotriene biosynthetic process		epoxide hydrolase activity|zinc ion binding			upper_aerodigestive_tract(1)	1				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)														---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202213071	202213073	+	Intron	DEL	TTG	-	-	rs113039988		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202213071_202213073delTTG	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron|LGR6_uc009xac.1_Intron	NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202546698	202546700	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202546698_202546700delTTT	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)															---	---	---	---
PPFIA4	8497	broad.mit.edu	37	1	203023800	203023803	+	Intron	DEL	ACAC	-	-	rs5780136		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203023800_203023803delACAC	uc001gyz.2	+						PPFIA4_uc009xaj.2_Intron|PPFIA4_uc010pqf.1_Intron|PPFIA4_uc001gza.2_Intron|PPFIA4_uc001gzb.1_5'Flank	NM_015053	NP_055868			protein tyrosine phosphatase, receptor type, f						cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	203428159	203428162	+	IGR	DEL	TCTC	-	-	rs57884007	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203428159_203428162delTCTC								FMOD (107870 upstream) : PRELP (16721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203843403	203843403	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203843403delT								SNRPE (3125 upstream) : C1orf157 (158172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203878477	203878477	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203878477delT								SNRPE (38199 upstream) : C1orf157 (123098 downstream)																																			---	---	---	---
SOX13	9580	broad.mit.edu	37	1	204080031	204080032	+	Intron	DEL	AA	-	-	rs113294840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204080031_204080032delAA	uc001ham.2	+						SOX13_uc001hal.2_Intron|SOX13_uc010pqp.1_5'Flank	NM_005686	NP_005677			SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
KISS1	3814	broad.mit.edu	37	1	204162191	204162191	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204162191delA	uc001har.2	-							NM_002256	NP_002247			KiSS-1 metastasis-suppressor						cytoskeleton organization	extracellular region	protein binding			ovary(1)	1	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)														---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204491992	204491992	+	Intron	DEL	T	-	-	rs66900244		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204491992delT	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_5'Flank	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								---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204659149	204659149	+	Intron	DEL	T	-	-	rs72473521		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204659149delT	uc001hbd.1	+							NM_002393				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								---	---	---	---
DSTYK	25778	broad.mit.edu	37	1	205166267	205166269	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205166267_205166269delAAA	uc001hbw.2	-						DSTYK_uc001hbx.2_Intron	NM_015375	NP_056190			receptor interacting protein kinase 5 isoform 1							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1																		---	---	---	---
RAB7L1	8934	broad.mit.edu	37	1	205738328	205738330	+	3'UTR	DEL	GTT	-	-	rs147452045		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205738328_205738330delGTT	uc001hdf.3	-	6					RAB7L1_uc009xbp.2_3'UTR|RAB7L1_uc001hde.3_3'UTR|RAB7L1_uc010prr.1_3'UTR|RAB7L1_uc009xbq.2_RNA	NM_003929	NP_003920			RAB7, member RAS oncogene family-like 1 isoform						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding			ovary(1)	1	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)															---	---	---	---
SLC26A9	115019	broad.mit.edu	37	1	205909711	205909711	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205909711delT	uc001hdq.2	-						SLC26A9_uc001hdp.2_Intron	NM_052934	NP_443166			solute carrier family 26, member 9 isoform a							integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)|skin(1)	2	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)															---	---	---	---
AVPR1B	553	broad.mit.edu	37	1	206226085	206226085	+	Intron	DEL	T	-	-	rs80169095		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206226085delT	uc001hds.2	+							NM_000707	NP_000698			arginine vasopressin receptor 1B						activation of phospholipase C activity|elevation of cytosolic calcium ion concentration	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity			ovary(2)|large_intestine(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	206314451	206314451	+	IGR	DEL	T	-	-	rs112308639		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206314451delT								C1orf186 (25804 upstream) : CTSE (3008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	206486400	206486400	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206486400delT								CTSE (154297 upstream) : SRGAP2 (29800 downstream)																																			---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206566603	206566604	+	Intron	INS	-	GG	GG	rs148368773		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206566603_206566604insGG	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
LGTN	1939	broad.mit.edu	37	1	206766820	206766823	+	Intron	DEL	GAGC	-	-	rs141098886		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206766820_206766823delGAGC	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824			ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
IL24	11009	broad.mit.edu	37	1	207075912	207075912	+	Intron	DEL	T	-	-	rs71570048		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207075912delT	uc001hes.1	+						IL24_uc001het.1_Intron|IL24_uc001heu.1_Intron|IL24_uc001hev.1_Intron|IL24_uc001hew.1_Intron	NM_006850	NP_006841			interleukin 24 isoform 1 precursor						apoptosis	extracellular space	cytokine activity				0	Breast(84;0.201)																	---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208207008	208207008	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208207008delT	uc001hgz.2	-							NM_025179	NP_079455			plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208247112	208247113	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208247112_208247113delAA	uc001hgz.2	-							NM_025179	NP_079455			plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	208450679	208450679	+	IGR	DEL	A	-	-	rs67068293		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208450679delA								PLXNA2 (33014 upstream) : None (None downstream)																																			---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211099606	211099607	+	Intron	INS	-	AC	AC	rs141650911	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211099606_211099607insAC	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)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211164945	211164946	+	Intron	INS	-	CA	CA	rs143743489	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211164945_211164946insCA	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	211333722	211333722	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211333722delT								KCNH1 (26265 upstream) : RCOR3 (98986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	211814459	211814460	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211814459_211814460delAA	uc001hip.1	+											full-length cDNA clone CS0DK012YI08 of HeLa cells Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
NEK2	4751	broad.mit.edu	37	1	211843194	211843195	+	Intron	INS	-	C	C	rs72507788	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211843194_211843195insC	uc001hir.1	-						NEK2_uc001hiq.1_Intron|NEK2_uc001his.3_Intron|NEK2_uc001hit.1_Intron	NM_002497	NP_002488			NIMA-related kinase 2						cell division|centrosome separation|G2/M transition of mitotic cell cycle|meiosis|protein autophosphorylation|regulation of mitosis	centrosome|condensed chromosome kinetochore|cytosol|nucleolus	ATP binding|metal ion binding|protein binding|protein phosphatase binding|protein serine/threonine kinase activity			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	211883016	211883017	+	IGR	INS	-	CAA	CAA			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211883016_211883017insCAA								NEK2 (34049 upstream) : LPGAT1 (33783 downstream)																																			---	---	---	---
LPGAT1	9926	broad.mit.edu	37	1	211930218	211930220	+	Intron	DEL	TTT	-	-	rs75910223		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211930218_211930220delTTT	uc001hiu.2	-						LPGAT1_uc001hiv.2_Intron	NM_014873	NP_055688			lysophosphatidylglycerol acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214220820	214220821	+	IGR	DEL	CA	-	-	rs35961689		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214220820_214220821delCA								PROX1 (11060 upstream) : SMYD2 (233744 downstream)																																			---	---	---	---
SMYD2	56950	broad.mit.edu	37	1	214458534	214458534	+	Intron	DEL	T	-	-	rs34399812		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214458534delT	uc010ptx.1	+						SMYD2_uc009xdj.2_Intron|SMYD2_uc010ptw.1_Intron|SMYD2_uc009xdl.1_Intron	NM_020197	NP_064582			SET and MYND domain containing 2						negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of DNA damage response, signal transduction by p53 class mediator|transcription, DNA-dependent	cytosol|nucleus	histone methyltransferase activity (H3-K36 specific)|p53 binding|RNA polymerase II core binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	215424756	215424756	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215424756delT								KCNK2 (14321 upstream) : KCTD3 (315979 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216221040	216221041	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216221040_216221041delAG	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	216579700	216579700	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216579700delT	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)			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217078645	217078645	+	Intron	DEL	T	-	-	rs146844581		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217078645delT	uc001hky.1	-						ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain 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)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	217556994	217556994	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217556994delA								ESRRG (245897 upstream) : GPATCH2 (46840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218619927	218619928	+	IGR	DEL	AA	-	-	rs114954206	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218619927_218619928delAA								TGFB2 (1968 upstream) : LYPLAL1 (727264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218736116	218736116	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218736116delT								TGFB2 (118157 upstream) : LYPLAL1 (611076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219343142	219343142	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219343142delT	uc001hlp.2	-											Homo sapiens cDNA clone IMAGE:6189076.																														---	---	---	---
EPRS	2058	broad.mit.edu	37	1	220157325	220157325	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220157325delA	uc001hly.1	-							NM_004446	NP_004437			glutamyl-prolyl tRNA synthetase						glutamyl-tRNA aminoacylation|prolyl-tRNA aminoacylation|protein complex assembly	cytosol|soluble fraction	ATP binding|glutamate-tRNA ligase activity|proline-tRNA ligase activity|protein binding|RNA binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0735)	L-Glutamic Acid(DB00142)|L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	220517653	220517653	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220517653delG								RAB3GAP2 (71810 upstream) : MARK1 (183915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220843726	220843727	+	IGR	DEL	AA	-	-	rs10707161		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220843726_220843727delAA								MARK1 (5928 upstream) : C1orf115 (19901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221247392	221247392	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221247392delT								HLX (188994 upstream) : LOC400804 (255878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221307067	221307068	+	IGR	INS	-	A	A	rs140242409	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221307067_221307068insA								HLX (248669 upstream) : LOC400804 (196202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221693773	221693774	+	IGR	INS	-	TCCTTCCTTCCTTCCCTCCTTTCTTCTTTCC	TCCTTCCTTCCTTCCCTCCTTTCTTCTTTCC	rs143298242	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221693773_221693774insTCCTTCCTTCCTTCCCTCCTTTCTTCTTTCC								LOC400804 (184135 upstream) : DUSP10 (180992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221762870	221762870	+	IGR	DEL	A	-	-	rs11322106		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221762870delA								LOC400804 (253232 upstream) : DUSP10 (111896 downstream)																																			---	---	---	---
TLR5	7100	broad.mit.edu	37	1	223315962	223315962	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223315962delT	uc001hnw.1	-							NM_003268	NP_003259			toll-like receptor 5 precursor						cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)												OREG0026714	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	223334323	223334330	+	IGR	DEL	GTGTGTGT	-	-	rs72242877		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223334323_223334330delGTGTGTGT								TLR5 (17699 upstream) : SUSD4 (59833 downstream)																																			---	---	---	---
TP53BP2	7159	broad.mit.edu	37	1	223980974	223980974	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223980974delA	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron|TP53BP2_uc010puz.1_Intron|TP53BP2_uc010pva.1_Intron	NM_001031685	NP_001026855			tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224775647	224775647	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224775647delA								WDR26 (153915 upstream) : CNIH3 (28532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	225019236	225019241	+	IGR	DEL	CTCTCT	-	-	rs141585956		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225019236_225019241delCTCTCT								CNIH3 (90987 upstream) : DNAH14 (98115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	225851126	225851127	+	IGR	DEL	TA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225851126_225851127delTA								ENAH (10281 upstream) : SRP9 (114388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226220043	226220044	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226220043_226220044delAA								C1orf55 (32977 upstream) : H3F3A (30377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226599380	226599381	+	IGR	INS	-	T	T	rs146931416	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226599380_226599381insT								PARP1 (3579 upstream) : C1orf95 (137120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226937211	226937212	+	IGR	DEL	GG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226937211_226937212delGG								ITPKB (10335 upstream) : PSEN2 (121061 downstream)																																			---	---	---	---
GJC2	57165	broad.mit.edu	37	1	228345913	228345915	+	In_Frame_Del	DEL	GAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228345913_228345915delGAG	uc001hsk.2	+	2	629_631	c.454_456delGAG	c.(454-456)GAGdel	p.E158del		NM_020435	NP_065168	Q5T442	CXG2_HUMAN	gap junction protein, gamma 2, 47kDa	158	Cytoplasmic (Potential).|Glu-rich.				cell death	connexon complex|integral to membrane					0		Prostate(94;0.0405)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	228937526	228937527	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228937526_228937527delTG								RHOU (55117 upstream) : RAB4A (469352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229535368	229535368	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229535368delT								C1orf96 (56680 upstream) : ACTA1 (31627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229944404	229944404	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229944404delT								URB2 (148458 upstream) : GALNT2 (249132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230095539	230095539	+	IGR	DEL	A	-	-	rs61025707	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230095539delA								URB2 (299593 upstream) : GALNT2 (97997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230537867	230537867	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230537867delA								PGBD5 (24500 upstream) : COG2 (240335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230761278	230761278	+	IGR	DEL	T	-	-	rs5781592		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230761278delT								PGBD5 (247911 upstream) : COG2 (16924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231294188	231294188	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231294188delT								FAM89A (118193 upstream) : TRIM67 (4486 downstream)																																			---	---	---	---
GNPAT	8443	broad.mit.edu	37	1	231381157	231381157	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231381157delT	uc001hup.3	+						GNPAT_uc009xfo.1_Intron|GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051			glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	231588390	231588390	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231588390delA								EGLN1 (27600 upstream) : TSNAX-DISC1 (76009 downstream)																																			---	---	---	---
DISC1	27185	broad.mit.edu	37	1	232093117	232093117	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232093117delT	uc001huz.2	+						TSNAX-DISC1_uc010pwl.1_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)																---	---	---	---
DISC1	27185	broad.mit.edu	37	1	232167072	232167073	+	Intron	INS	-	AAAGGA	AAAGGA	rs147764269	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232167072_232167073insAAAGGA	uc001huz.2	+						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	232930971	232930971	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232930971delA								SIPA1L2 (279728 upstream) : KIAA1383 (9667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233593089	233593089	+	IGR	DEL	T	-	-	rs5781743		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233593089delT								KIAA1804 (72196 upstream) : KCNK1 (156661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233726256	233726256	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233726256delG								KIAA1804 (205363 upstream) : KCNK1 (23494 downstream)																																			---	---	---	---
RBM34	23029	broad.mit.edu	37	1	235295562	235295562	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235295562delT	uc001hwn.2	-						RBM34_uc001hwo.2_Intron|ARID4B_uc001hwp.2_Intron	NM_015014	NP_055829			RNA binding motif protein 34 isoform 1							nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235657766	235657766	+	Intron	DEL	T	-	-	rs34730227		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235657766delT	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	235747961	235747962	+	Intron	INS	-	CGG	CGG	rs72515924		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235747961_235747962insCGG	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)															---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236385071	236385072	+	Intron	INS	-	TTAATA	TTAATA	rs10647377		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236385071_236385072insTTAATA	uc001hxt.2	-							NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236411226	236411227	+	Intron	INS	-	TCACTTAGG	TCACTTAGG	rs140354272	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236411226_236411227insTCACTTAGG	uc001hxt.2	-						ERO1LB_uc010pxt.1_Intron	NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
MTR	4548	broad.mit.edu	37	1	236980549	236980550	+	Intron	INS	-	T	T	rs146881944	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236980549_236980550insT	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron|MTR_uc009xgj.1_Intron	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
MTR	4548	broad.mit.edu	37	1	237055314	237055314	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237055314delC	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	238474634	238474635	+	IGR	INS	-	A	A	rs141582613	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238474634_238474635insA								LOC100130331 (383017 upstream) : LOC339535 (169051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238817094	238817095	+	IGR	INS	-	T	T	rs116818565	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238817094_238817095insT								LOC339535 (167777 upstream) : CHRM3 (732770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238997101	238997102	+	IGR	DEL	CT	-	-	rs112382577		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238997101_238997102delCT								LOC339535 (347784 upstream) : CHRM3 (552763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239097260	239097260	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239097260delA								LOC339535 (447943 upstream) : CHRM3 (452605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239104071	239104071	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239104071delT								LOC339535 (454754 upstream) : CHRM3 (445794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239460630	239460630	+	IGR	DEL	C	-	-	rs75323604	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239460630delC								LOC339535 (811313 upstream) : CHRM3 (89235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	240120919	240120919	+	IGR	DEL	T	-	-	rs67712208		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240120919delT								CHRM3 (48204 upstream) : FMN2 (134266 downstream)																																			---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240614659	240614659	+	Intron	DEL	A	-	-	rs72063364		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240614659delA	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyg.1_Intron	NM_020066	NP_064450			formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	241646739	241646739	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241646739delA								RGS7 (126261 upstream) : FH (14167 downstream)																																			---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242278959	242278959	+	Intron	DEL	A	-	-	rs11311583		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242278959delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242855057	242855058	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242855057_242855058insA								PLD5 (167059 upstream) : CEP170 (432673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	243021842	243021845	+	IGR	DEL	TTTT	-	-	rs71978882		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243021842_243021845delTTTT								PLD5 (333844 upstream) : CEP170 (265886 downstream)																																			---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243650570	243650570	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243650570delC	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	244097599	244097599	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244097599delT	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	244383015	244383015	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244383015delC								ZNF238 (162239 upstream) : C1orf100 (132922 downstream)																																			---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245403465	245403465	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245403465delA	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	245488414	245488414	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245488414delG	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	245935738	245935738	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245935738delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	248357293	248357293	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248357293delA								OR2M2 (12964 upstream) : OR2M3 (9077 downstream)																																			---	---	---	---
OR2T35	403244	broad.mit.edu	37	1	248801602	248801603	+	Frame_Shift_Ins	INS	-	CA	CA			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248801602_248801603insCA	uc001ies.1	-	1	957_958	c.957_958insTG	c.(955-960)GTGATCfs	p.V319fs		NM_001001827	NP_001001827	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T,	319_320	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
SH3BP5L	80851	broad.mit.edu	37	1	249105582	249105582	+	3'UTR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249105582delG	uc001iew.1	-	7					SH3BP5L_uc010pzp.1_3'UTR|SH3BP5L_uc010pzq.1_3'UTR|SH3BP5L_uc001iev.1_3'UTR	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)															---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1179033	1179034	+	Intron	INS	-	T	T	rs149906361	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1179033_1179034insT	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1189931	1189932	+	Intron	INS	-	G	G	rs72768818	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1189931_1189932insG	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
TPO	7173	broad.mit.edu	37	2	1545135	1545136	+	Intron	DEL	TT	-	-	rs66592009		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1545135_1545136delTT	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron|TPO_uc002qwz.2_Intron	NM_000547	NP_000538			thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	1600894	1600895	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1600894_1600895delAC								TPO (54396 upstream) : PXDN (34765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	1601772	1601775	+	IGR	DEL	CGTA	-	-	rs78708182		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1601772_1601775delCGTA								TPO (55274 upstream) : PXDN (33885 downstream)																																			---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1890247	1890247	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1890247delT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1907719	1907722	+	Intron	DEL	GTGC	-	-	rs148268202	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1907719_1907722delGTGC	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2010661	2010662	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2010661_2010662delAA	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2095397	2095398	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2095397_2095398delTG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
TTC15	51112	broad.mit.edu	37	2	3461813	3461833	+	Intron	DEL	AGAGGCCTCTGCGTCGGGGAC	-	-	rs144042551	by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3461813_3461833delAGAGGCCTCTGCGTCGGGGAC	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114			tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	3836381	3836389	+	IGR	DEL	TCCCTTCCT	-	-	rs58922019		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3836381_3836389delTCCCTTCCT								ALLC (86123 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4001708	4001709	+	IGR	INS	-	CC	CC	rs149795661	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4001708_4001709insCC								ALLC (251450 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5255011	5255012	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5255011_5255012insT								None (None upstream) : SOX11 (577787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5284073	5284074	+	IGR	INS	-	TTTG	TTTG	rs3082621		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5284073_5284074insTTTG								None (None upstream) : SOX11 (548725 downstream)																																			---	---	---	---
LOC150622	150622	broad.mit.edu	37	2	6110049	6110050	+	RNA	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6110049_6110050insT	uc002qyk.2	+	2		c.1567_1568insT				NR_026832				Homo sapiens cDNA FLJ30594 fis, clone BRAWH2008903.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	6485020	6485021	+	IGR	DEL	TG	-	-	rs35752615		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6485020_6485021delTG								LOC400940 (356656 upstream) : CMPK2 (495482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6695317	6695317	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6695317delG								LOC400940 (566953 upstream) : CMPK2 (285186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6849677	6849677	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6849677delT								LOC400940 (721313 upstream) : CMPK2 (130826 downstream)																																			---	---	---	---
CMPK2	129607	broad.mit.edu	37	2	7001234	7001235	+	Intron	DEL	CG	-	-	rs3085147		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	7774979	7774979	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7774979delA								RNF144A (590672 upstream) : LOC339788 (287579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8018039	8018039	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8018039delT								RNF144A (833732 upstream) : LOC339788 (44519 downstream)																																			---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8887029	8887029	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8887029delA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron|KIDINS220_uc002qzb.2_Intron|KIDINS220_uc002qze.2_3'UTR	NM_020738	NP_065789			kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	8989778	8989778	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8989778delT								KIDINS220 (12023 upstream) : MBOAT2 (6923 downstream)																																			---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11399005	11399005	+	Intron	DEL	A	-	-	rs35749452		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11399005delA	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
LPIN1	23175	broad.mit.edu	37	2	11816482	11816485	+	5'Flank	DEL	GTGG	-	-	rs5829322		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11816482_11816485delGTGG	uc010yjm.1	+							NM_145693	NP_663731			lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12231235	12231239	+	Intron	DEL	TCTCC	-	-	rs72385544		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12231235_12231239delTCTCC	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12335875	12335875	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12335875delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12351052	12351053	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12351052_12351053insT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13697431	13697431	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13697431delT								TRIB2 (814575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14493527	14493527	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14493527delA	uc002rby.2	-											Homo sapiens cDNA clone IMAGE:5263003.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	15284802	15284802	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15284802delA								FAM84A (493869 upstream) : NBAS (22230 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15534569	15534569	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15534569delA	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	15882499	15882499	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15882499delT								DDX1 (111275 upstream) : MYCNOS (197521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15966040	15966040	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15966040delG								DDX1 (194816 upstream) : MYCNOS (113980 downstream)																																			---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17860044	17860044	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17860044delA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron	NM_001142286	NP_001135758			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)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17959666	17959667	+	Intron	DEL	TA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17959666_17959667delTA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18561650	18561651	+	IGR	INS	-	C	C	rs114285414	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18561650_18561651insC								KCNS3 (447426 upstream) : NT5C1B (174340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19297673	19297673	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19297673delT								NT5C1B (526835 upstream) : OSR1 (253574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19786148	19786149	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19786148_19786149delAA								OSR1 (227776 upstream) : TTC32 (310369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19934739	19934742	+	IGR	DEL	GAAC	-	-	rs72577630	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19934739_19934742delGAAC								OSR1 (376367 upstream) : TTC32 (161776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19934791	19934794	+	IGR	DEL	GAAA	-	-	rs72315540	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19934791_19934794delGAAA								OSR1 (376419 upstream) : TTC32 (161724 downstream)																																			---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	21017180	21017180	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21017180delA	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744			hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	21986216	21986216	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21986216delA								APOB (719271 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23403693	23403694	+	IGR	INS	-	CA	CA	rs140307779	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23403693_23403694insCA								None (None upstream) : KLHL29 (351761 downstream)																																			---	---	---	---
LOC375190	375190	broad.mit.edu	37	2	24354531	24354532	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24354531_24354532insT	uc010ykl.1	+						LOC375190_uc002rew.2_Intron|LOC375190_uc002rfb.2_Intron	NM_001145710	NP_001139182			hypothetical protein LOC375190												0																		---	---	---	---
C2orf84	653140	broad.mit.edu	37	2	24410487	24410487	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24410487delT	uc002rfc.2	+						C2orf84_uc010eyc.2_Intron	NM_001040710	NP_001035800			hypothetical protein LOC653140												0																		---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25705489	25705489	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25705489delA	uc002rgh.2	-						DTNB_uc002rgg.2_Intron|DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26044264	26044266	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26044264_26044266delAAA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26118269	26118269	+	IGR	DEL	T	-	-	rs71399330		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26118269delT								ASXL2 (16957 upstream) : KIF3C (31186 downstream)																																			---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26166921	26166921	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26166921delT	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245			kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26911016	26911016	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26911016delC								CIB4 (46805 upstream) : KCNK3 (4565 downstream)																																			---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27913865	27913866	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27913865_27913866insT	uc002rlk.3	+							NM_018158	NP_060628			solute carrier family 4 (anion exchanger),							cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27983806	27983806	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27983806delA								SLC4A1AP (65960 upstream) : MRPL33 (10778 downstream)																																			---	---	---	---
RBKS	64080	broad.mit.edu	37	2	28038080	28038080	+	Intron	DEL	C	-	-	rs4464229	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28038080delC	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411			ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
RBKS	64080	broad.mit.edu	37	2	28065746	28065747	+	Intron	DEL	TT	-	-	rs78190424		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28065746_28065747delTT	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411			ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28301211	28301211	+	Intron	DEL	C	-	-	rs11363251		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28301211delC	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BRE	9577	broad.mit.edu	37	2	28493358	28493358	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28493358delG	uc002rlr.2	+						BRE_uc002rlp.1_Intron|BRE_uc002rlq.2_Intron|BRE_uc002rls.2_Intron|BRE_uc002rlt.2_Intron|BRE_uc002rlu.2_Intron|BRE_uc002rlv.2_Intron	NM_199194	NP_954664			brain and reproductive organ-expressed (TNFRSF1A						apoptosis|chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of anti-apoptosis|positive regulation of DNA repair|response to ionizing radiation|signal transduction	BRCA1-A complex|BRISC complex|cytoplasm|nuclear ubiquitin ligase complex	peroxisome targeting sequence binding|polyubiquitin binding|tumor necrosis factor receptor binding			lung(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ALK	238	broad.mit.edu	37	2	29569163	29569163	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29569163delA	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	30120379	30120379	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30120379delG	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				---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31208016	31208017	+	Intron	INS	-	TGAA	TGAA	rs138304703	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31208016_31208017insTGAA	uc002rnr.2	-						GALNT14_uc002rnq.2_Intron|GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848			N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	31700656	31700656	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31700656delT								XDH (63045 upstream) : SRD5A2 (49000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	31736484	31736484	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31736484delT								XDH (98873 upstream) : SRD5A2 (13172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	31739709	31739710	+	IGR	INS	-	TG	TG	rs146416653	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31739709_31739710insTG								XDH (102098 upstream) : SRD5A2 (9946 downstream)																																			---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32433748	32433750	+	Intron	DEL	TTG	-	-	rs67067770		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32433748_32433750delTTG	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	32493931	32493931	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32493931delT								NLRC4 (3130 upstream) : YIPF4 (9027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	32553536	32553536	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32553536delT								YIPF4 (21879 upstream) : BIRC6 (28560 downstream)																																			---	---	---	---
TTC27	55622	broad.mit.edu	37	2	32909059	32909059	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32909059delA	uc002rom.2	+						TTC27_uc010ymx.1_Intron	NM_017735	NP_060205			tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1																		---	---	---	---
LOC285045	285045	broad.mit.edu	37	2	33129211	33129212	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33129211_33129212insA	uc002roo.2	+						LOC285045_uc002rop.1_Intron|LOC285045_uc010ymy.1_Intron|LOC285045_uc002roq.1_Intron	NR_027098				Homo sapiens cDNA FLJ37863 fis, clone BRSSN2015907.												0																		---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33193795	33193797	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33193795_33193797delTTT	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	34049334	34049335	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34049334_34049335delCT								MYADML (96050 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34581481	34581482	+	IGR	INS	-	T	T	rs72542316	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34581481_34581482insT								MYADML (628197 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35042098	35042099	+	IGR	INS	-	AC	AC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35042098_35042099insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36347027	36347028	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36347027_36347028insC								None (None upstream) : CRIM1 (236369 downstream)																																			---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36681521	36681522	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36681521_36681522delAC	uc002rpd.2	+							NM_016441	NP_057525			cysteine-rich motor neuron 1 precursor						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)																---	---	---	---
STRN	6801	broad.mit.edu	37	2	37103521	37103521	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37103521delA	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	37680542	37680546	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37680542_37680546delTTTTT								QPCT (80078 upstream) : CDC42EP3 (190197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37979122	37979122	+	IGR	DEL	G	-	-	rs113440153		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37979122delG								CDC42EP3 (79796 upstream) : FAM82A1 (173340 downstream)																																			---	---	---	---
GALM	130589	broad.mit.edu	37	2	38938960	38938963	+	Intron	DEL	TCAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38938960_38938963delTCAC	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	39731331	39731331	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39731331delA	uc002rrq.2	+						uc002rrr.1_Intron					Homo sapiens cDNA FLJ33477 fis, clone BRAMY2002604.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	40143291	40143292	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40143291_40143292insT								THUMPD2 (136875 upstream) : SLC8A1 (195995 downstream)																																			---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40498320	40498321	+	Intron	INS	-	C	C	rs138396968	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40498320_40498321insC	uc002rrx.2	-						SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	41193306	41193307	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41193306_41193307delGA								SLC8A1 (453731 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41261928	41261929	+	IGR	INS	-	TT	TT	rs149741243	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41261928_41261929insTT								SLC8A1 (522353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41493619	41493620	+	IGR	INS	-	T	T	rs146035700	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41493619_41493620insT								SLC8A1 (754044 upstream) : PKDCC (781541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41575859	41575859	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41575859delA								SLC8A1 (836284 upstream) : PKDCC (699302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42186194	42186194	+	IGR	DEL	T	-	-	rs67149338		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42186194delT								None (None upstream) : PKDCC (88967 downstream)																																			---	---	---	---
EML4	27436	broad.mit.edu	37	2	42471246	42471247	+	Intron	INS	-	TG	TG	rs78324792		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42471246_42471247insTG	uc002rsi.2	+						EML4_uc002rsh.3_Intron|EML4_uc010fap.2_Intron	NM_019063	NP_061936			echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250								T	ALK	NSCLC								---	---	---	---
KCNG3	170850	broad.mit.edu	37	2	42679910	42679911	+	Intron	INS	-	GTGT	GTGT	rs141350357	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42679910_42679911insGTGT	uc002rsn.2	-						KCNG3_uc002rsm.2_Intron	NM_133329	NP_579875			potassium voltage-gated channel, subfamily G,							endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1																		---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42948471	42948471	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42948471delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43349669	43349669	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43349669delA								HAAO (329918 upstream) : ZFP36L2 (99873 downstream)																																			---	---	---	---
THADA	63892	broad.mit.edu	37	2	43628066	43628066	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43628066delT	uc002rsw.3	-						THADA_uc010far.2_Intron|THADA_uc002rsx.3_Intron|THADA_uc002rsy.3_Intron|THADA_uc010fas.1_Intron|THADA_uc002rsz.2_Intron|THADA_uc010fat.1_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	43837586	43837586	+	IGR	DEL	A	-	-	rs11358608		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43837586delA								THADA (14401 upstream) : PLEKHH2 (26853 downstream)																																			---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44225245	44225245	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44225245delA	uc002rtr.2	-						LRPPRC_uc010yob.1_5'Flank|LRPPRC_uc010faw.1_5'Flank	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	44293377	44293377	+	IGR	DEL	G	-	-	rs61062797		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44293377delG								LRPPRC (70233 upstream) : PPM1B (102623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	44359377	44359378	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44359377_44359378delAA								LRPPRC (136233 upstream) : PPM1B (36622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45178005	45178006	+	IGR	DEL	CG	-	-	rs148957308		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45178005_45178006delCG								SIX3 (5615 upstream) : SIX2 (54319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45339193	45339193	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45339193delG								SIX2 (102650 upstream) : SRBD1 (276627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45340811	45340812	+	IGR	INS	-	A	A	rs138045375	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45340811_45340812insA								SIX2 (104268 upstream) : SRBD1 (275008 downstream)																																			---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45617123	45617124	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45617123_45617124insT	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	46420581	46420582	+	IGR	INS	-	CA	CA	rs143983782	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46420581_46420582insCA								PRKCE (5453 upstream) : EPAS1 (103981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	47467493	47467494	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47467493_47467494delTT	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	2	47555027	47555029	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47555027_47555029delAAA	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47868454	47868455	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47868454_47868455delAA	uc002rvz.2	+							NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48935688	48935691	+	Intron	DEL	CACA	-	-	rs145444552		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48935688_48935691delCACA	uc002rwu.3	-						GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49286555	49286555	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49286555delA	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49352458	49352458	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49352458delA	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50504634	50504652	+	Intron	DEL	CTTTTTCCTTCCTTCCTTC	-	-	rs147518619		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50504634_50504652delCTTTTTCCTTCCTTCCTTC	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_Intron	NM_138735	NP_620072			neurexin 1 isoform beta 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	51491465	51491465	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51491465delT								NRXN1 (231791 upstream) : None (None downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53917760	53917761	+	Intron	INS	-	T	T	rs139249684	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53917760_53917761insT	uc002rxg.1	-						ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron|ASB3_uc002rxf.1_Intron	NM_016115	NP_057199			ankyrin repeat and SOCS box-containing protein 3						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54155657	54155658	+	Intron	INS	-	CA	CA	rs143410267	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54155657_54155658insCA	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	57001747	57001747	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57001747delT								CCDC85A (388439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57577699	57577700	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57577699_57577700insA								CCDC85A (964391 upstream) : VRK2 (557086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59228454	59228454	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59228454delT	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	60058388	60058388	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60058388delT								None (None upstream) : BCL11A (619915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60111490	60111491	+	IGR	DEL	CA	-	-	rs149127701		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60111490_60111491delCA								None (None upstream) : BCL11A (566812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60881178	60881178	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60881178delA								BCL11A (100545 upstream) : PAPOLG (102205 downstream)																																			---	---	---	---
USP34	9736	broad.mit.edu	37	2	61445299	61445300	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61445299_61445300insT	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)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61483709	61483709	+	Intron	DEL	A	-	-	rs34025877		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61483709delA	uc002sbe.2	-						USP34_uc002sbf.2_Intron	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)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61529271	61529271	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61529271delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62664710	62664712	+	IGR	DEL	ACA	-	-	rs72375598		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62664710_62664712delACA								B3GNT2 (212846 upstream) : TMEM17 (62644 downstream)																																			---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	62931711	62931711	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62931711delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_5'Flank|EHBP1_uc002sbx.2_5'Flank|EHBP1_uc002sbz.2_5'Flank|EHBP1_uc002scb.2_5'Flank|EHBP1_uc002sca.2_5'Flank	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	63753190	63753191	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63753190_63753191delTG	uc002sch.2	-						C2orf86_uc002sci.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																		---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63774687	63774688	+	Intron	INS	-	TA	TA	rs3077063		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63774687_63774688insTA	uc002sch.2	-						C2orf86_uc002sci.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																		---	---	---	---
PELI1	57162	broad.mit.edu	37	2	64353940	64353940	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64353940delA	uc002sct.3	-							NM_020651	NP_065702			pellino protein						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64414874	64414875	+	IGR	DEL	AA	-	-	rs11339144		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64414874_64414875delAA								PELI1 (43269 upstream) : HSPC159 (266452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64522067	64522068	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64522067_64522068delTC								PELI1 (150462 upstream) : HSPC159 (159259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64547046	64547047	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64547046_64547047delAA								PELI1 (175441 upstream) : HSPC159 (134280 downstream)																																			---	---	---	---
RAB1A	5861	broad.mit.edu	37	2	65316354	65316354	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65316354delT	uc002sdm.2	-						RAB1A_uc002sdn.2_Intron|RAB1A_uc010yqe.1_Intron|RAB1A_uc002sdo.2_Intron	NM_004161	NP_004152			RAB1A, member RAS oncogene family isoform 1						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65423840	65423841	+	IGR	INS	-	AC	AC	rs150265203	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65423840_65423841insAC								RAB1A (66405 upstream) : ACTR2 (30988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65446223	65446223	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65446223delT								RAB1A (88788 upstream) : ACTR2 (8606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66328184	66328184	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66328184delA								SPRED2 (668528 upstream) : MEIS1 (334348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66902720	66902720	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66902720delA								MEIS1 (102830 upstream) : ETAA1 (721722 downstream)																																			---	---	---	---
PLEK	5341	broad.mit.edu	37	2	68606649	68606650	+	Intron	DEL	AG	-	-	rs12713641	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68606649_68606650delAG	uc002sen.3	+						PLEK_uc010fde.2_Intron	NM_002664	NP_002655			pleckstrin						actin cytoskeleton reorganization|cortical actin cytoskeleton organization|hemopoietic progenitor cell differentiation|inhibition of phospholipase C activity involved in G-protein coupled receptor signaling pathway|integrin-mediated signaling pathway|negative regulation of calcium-mediated signaling|negative regulation of inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|platelet aggregation|positive regulation of actin filament bundle assembly|positive regulation of actin filament depolymerization|positive regulation of inositol-polyphosphate 5-phosphatase activity|positive regulation of integrin activation|positive regulation of platelet activation|protein kinase C signaling cascade|protein secretion by platelet|regulation of cell diameter|ruffle organization|thrombin receptor signaling pathway|vesicle docking involved in exocytosis	cytosol|extracellular region|membrane fraction|ruffle membrane|soluble fraction	phosphatidylinositol-3,4-bisphosphate binding|protein homodimerization activity|protein kinase C binding			ovary(1)	1		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)														---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69685840	69685841	+	3'UTR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69685840_69685841delCA	uc002sfp.2	-	22						NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
GMCL1	64395	broad.mit.edu	37	2	70100638	70100639	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70100638_70100639delTT	uc002sfu.2	+							NM_178439	NP_848526			germ cell-less						cell differentiation|multicellular organismal development|spermatogenesis	nuclear matrix				ovary(3)	3																		---	---	---	---
SNRNP27	11017	broad.mit.edu	37	2	70124316	70124316	+	Intron	DEL	T	-	-	rs3752781	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70124316delT	uc002sfw.2	+						SNRNP27_uc002sfv.2_Intron|SNRNP27_uc002sfx.2_Intron	NM_006857	NP_006848			small nuclear ribonucleoprotein 27kDa						mRNA processing|RNA splicing	nucleus	nucleic acid binding				0																		---	---	---	---
MXD1	4084	broad.mit.edu	37	2	70150713	70150714	+	Intron	INS	-	GTGT	GTGT	rs149960849	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70150713_70150714insGTGT	uc002sfy.2	+						MXD1_uc010yqp.1_Intron|MXD1_uc010yqq.1_Intron|MXD1_uc010yqr.1_Intron|MXD1_uc010yqs.1_Intron	NM_002357	NP_002348			MAX dimerization protein 1						cell proliferation|multicellular organismal development	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0																		---	---	---	---
MXD1	4084	broad.mit.edu	37	2	70153471	70153471	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70153471delT	uc002sfy.2	+						MXD1_uc010yqp.1_Intron|MXD1_uc010yqq.1_Intron|MXD1_uc010yqr.1_Intron|MXD1_uc010yqs.1_Intron	NM_002357	NP_002348			MAX dimerization protein 1						cell proliferation|multicellular organismal development	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0																		---	---	---	---
TGFA	7039	broad.mit.edu	37	2	70707197	70707200	+	Intron	DEL	TAGA	-	-	rs3836152		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70707197_70707200delTAGA	uc002sgs.3	-						TGFA_uc010fdq.2_Intron|TGFA_uc010fdr.2_Intron|TGFA_uc002sgt.3_Intron|TGFA_uc002sgu.2_Intron|TGFA_uc002sgv.2_Intron|TGFA_uc002sgw.2_Intron	NM_003236	NP_003227			transforming growth factor, alpha isoform 1						activation of MAPK activity|cell proliferation|positive regulation of cell division|positive regulation of epidermal growth factor receptor activity|positive regulation of epithelial cell proliferation|positive regulation of mitosis	cell surface|extracellular space|integral to membrane|plasma membrane	epidermal growth factor receptor binding|growth factor activity|MAP kinase kinase activity|signal transducer activity			prostate(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	71054469	71054469	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71054469delA								CLEC4F (6737 upstream) : CD207 (2879 downstream)																																			---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71517704	71517705	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71517704_71517705insT	uc010yqw.1	+						ZNF638_uc010fec.2_Intron	NM_014497	NP_055312			zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71679775	71679775	+	5'Flank	DEL	T	-	-	rs80339059		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71679775delT	uc002sie.2	+						DYSF_uc010feg.2_5'Flank|DYSF_uc010feh.2_5'Flank|DYSF_uc002sig.3_5'Flank|DYSF_uc010yqx.1_5'Flank|DYSF_uc010fee.2_5'Flank|DYSF_uc010fef.2_5'Flank|DYSF_uc010fei.2_5'Flank	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	72220213	72220217	+	IGR	DEL	TTTTT	-	-	rs68176538		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72220213_72220217delTTTTT								DYSF (306321 upstream) : CYP26B1 (136150 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72593410	72593410	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72593410delA	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	72613547	72613547	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72613547delA	uc010fep.2	-							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	73106652	73106653	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73106652_73106653delGA								EXOC6B (53475 upstream) : SPR (7859 downstream)																																			---	---	---	---
SFXN5	94097	broad.mit.edu	37	2	73250507	73250507	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73250507delG	uc002siq.2	-						SFXN5_uc002sio.2_Intron|SFXN5_uc010yrc.1_Intron|SFXN5_uc002sip.2_Intron|SFXN5_uc010fet.2_Intron	NM_144579	NP_653180			sideroflexin 5						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73548788	73548788	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73548788delT								EGR4 (27959 upstream) : ALMS1 (64098 downstream)																																			---	---	---	---
TPRKB	51002	broad.mit.edu	37	2	73961234	73961234	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73961234delT	uc002sjn.2	-						TPRKB_uc002sjm.2_Intron|TPRKB_uc002sjl.2_Intron|TPRKB_uc002sjo.2_Intron|TPRKB_uc010yrm.1_Intron	NM_016058	NP_057142			TP53RK binding protein						protein catabolic process	cytosol|nucleus	protein kinase binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74997487	74997487	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74997487delA								SEMA4F (88302 upstream) : HK2 (62295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	74999359	74999359	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74999359delA								SEMA4F (90174 upstream) : HK2 (60423 downstream)																																			---	---	---	---
TACR1	6869	broad.mit.edu	37	2	75351185	75351185	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75351185delT	uc002sng.2	-						TACR1_uc002snh.2_Intron	NM_001058	NP_001049			tachykinin receptor 1 isoform long						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	75822358	75822359	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75822358_75822359delAA								FAM176A (25510 upstream) : MRPL19 (51550 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77684722	77684723	+	Intron	DEL	AA	-	-	rs113451237		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77684722_77684723delAA	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	82080469	82080469	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82080469delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82735111	82735111	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82735111delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83448919	83448919	+	IGR	DEL	A	-	-	rs11284428		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83448919delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84128115	84128116	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84128115_84128116delCA								None (None upstream) : FUNDC2P2 (389690 downstream)																																			---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84904021	84904021	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84904021delA	uc010fgb.2	+						DNAH6_uc002sor.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																		---	---	---	---
ATOH8	84913	broad.mit.edu	37	2	85994161	85994161	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85994161delT	uc002sqn.2	+						ATOH8_uc002sqm.3_Intron	NM_032827	NP_116216			atonal homolog 8						cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86761675	86761675	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86761675delT	uc002srj.2	-						VPS24_uc002srk.2_Intron|VPS24_uc002srl.2_Intron|VPS24_uc010ytl.1_Intron	NM_016079	NP_057163			vacuolar protein sorting 24 isoform 1						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86924595	86924595	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86924595delA	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87123377	87123377	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87123377delT	uc002srs.3	+											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	87814833	87814833	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87814833delT	uc002srs.3	+						NCRNA00152_uc002ssk.3_Intron|NCRNA00152_uc010fgy.2_Intron|NCRNA00152_uc010fgz.2_Intron					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	88417968	88417968	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88417968delT								SMYD1 (5068 upstream) : FABP1 (4542 downstream)																																			---	---	---	---
FOXI3	344167	broad.mit.edu	37	2	88753743	88753744	+	5'Flank	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88753743_88753744delTT	uc010ytq.1	-							NM_001135649	NP_001129121			forkhead box I3						epidermal cell fate specification|otic placode formation|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88816619	88816622	+	IGR	DEL	CACA	-	-	rs148162833		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88816619_88816622delCACA								FOXI3 (64566 upstream) : C2orf51 (7547 downstream)																																			---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89075110	89075111	+	Intron	INS	-	TG	TG	rs146844333	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89075110_89075111insTG	uc002stf.2	+						FLJ40330_uc010fhf.2_Intron|FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
FLJ40330	645784	broad.mit.edu	37	2	89081969	89081970	+	Intron	INS	-	CGT	CGT	rs111987841		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89081969_89081970insCGT	uc010fhf.2	+						FLJ40330_uc010fhg.2_Intron|FLJ40330_uc010fhh.2_Intron					Homo sapiens mRNA; cDNA DKFZp434J1630 (from clone DKFZp434J1630).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	91696135	91696136	+	IGR	INS	-	GCTGGCTTGGCTGGATTG	GCTGGCTTGGCTGGATTG	rs141780744	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91696135_91696136insGCTGGCTTGGCTGGATTG								None (None upstream) : LOC654342 (109056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91890173	91890174	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91890173_91890174delTT								LOC654342 (42198 upstream) : GGT8P (73194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92036762	92036762	+	IGR	DEL	T	-	-	rs2318644		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92036762delT								GGT8P (66609 upstream) : FKSG73 (92397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92285841	92285841	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92285841delA								FKSG73 (155347 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92317890	92317890	+	IGR	DEL	T	-	-	rs7597972		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	96485670	96485670	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96485670delT	uc002suy.1	-											Homo sapiens cDNA FLJ33030 fis, clone THYMU2000171.																														---	---	---	---
KIAA1310	55683	broad.mit.edu	37	2	97292958	97292958	+	Intron	DEL	T	-	-	rs67661121		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97292958delT	uc002swn.3	-						KIAA1310_uc002swh.3_Intron|KIAA1310_uc002swi.3_Intron|KIAA1310_uc002swj.3_Intron|KIAA1310_uc002swk.3_Intron|KIAA1310_uc010fhz.2_Intron|KIAA1310_uc002swl.3_Intron|KIAA1310_uc002swm.3_Intron|KIAA1310_uc010yur.1_Intron|KIAA1310_uc002swp.1_Intron|KIAA1310_uc002swq.1_Intron|KIAA1310_uc010fhy.1_Intron	NM_001115016	NP_001108488			hypothetical protein LOC55683 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	97664087	97664087	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97664087delT								FAM178B (11786 upstream) : FAHD2B (85237 downstream)																																			---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99087131	99087131	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99087131delT	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696			inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	99355639	99355639	+	IGR	DEL	A	-	-	rs75235678		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99355639delA								MGAT4A (8050 upstream) : C2orf55 (54670 downstream)																																			---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99743001	99743001	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99743001delA	uc002szj.1	-	2					TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron|TSGA10_uc010yvn.1_Intron					Homo sapiens cDNA FLJ36889 fis, clone BNGH42009021.						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TXNDC9	10190	broad.mit.edu	37	2	99944726	99944729	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99944726_99944729delTTTT	uc002szz.2	-						TXNDC9_uc010yvp.1_Intron|TXNDC9_uc002taa.1_Intron	NM_005783	NP_005774			thioredoxin domain containing 9						cell redox homeostasis		protein binding				0																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100505176	100505177	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100505176_100505177delTT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	100775386	100775390	+	IGR	DEL	AACCC	-	-	rs10534767		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100775386_100775390delAACCC								AFF3 (16349 upstream) : LONRF2 (114364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101391880	101391881	+	IGR	INS	-	TT	TT	rs72546815	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101391880_101391881insTT								PDCL3 (198679 upstream) : NPAS2 (44732 downstream)																																			---	---	---	---
RFX8	731220	broad.mit.edu	37	2	102027051	102027053	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102027051_102027053delTTT	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136			regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
RFX8	731220	broad.mit.edu	37	2	102079670	102079670	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102079670delT	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136			regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	104987512	104987512	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104987512delA								None (None upstream) : LOC150568 (63293 downstream)																																			---	---	---	---
C2orf49	79074	broad.mit.edu	37	2	105954798	105954807	+	Intron	DEL	CCCCTTAGTA	-	-	rs11277813		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105954798_105954807delCCCCTTAGTA	uc002tcs.1	+						C2orf49_uc010fjd.1_Intron	NM_024093	NP_076998			ashwin							tRNA-splicing ligase complex					0																		---	---	---	---
FHL2	2274	broad.mit.edu	37	2	106051240	106051240	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106051240delT	uc002tdd.2	-						FHL2_uc002tdc.2_Intron	NM_201557	NP_963851			four and a half LIM domains 2						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent	actin cytoskeleton|focal adhesion|nucleus	androgen receptor binding|identical protein binding|transcription coactivator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107776824	107776824	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107776824delT								ST6GAL2 (273261 upstream) : LOC729121 (662696 downstream)																																			---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109222316	109222316	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109222316delA	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_5'Flank	NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						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																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	109954889	109954889	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109954889delT	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	110271471	110271471	+	IGR	DEL	G	-	-	rs77593632		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110271471delG								SH3RF3 (9264 upstream) : SEPT10 (28903 downstream)																																			---	---	---	---
MALL	7851	broad.mit.edu	37	2	110858953	110858954	+	Intron	INS	-	TT	TT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110858953_110858954insTT	uc002tfk.2	-						MALL_uc010fju.2_Intron	NM_005434	NP_005425			mal, T-cell differentiation protein-like						cholesterol homeostasis	clathrin-coated vesicle|Golgi membrane|integral to membrane|membrane raft|plasma membrane	protein binding			ovary(1)|skin(1)	2				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)														---	---	---	---
BCL2L11	10018	broad.mit.edu	37	2	111895346	111895346	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111895346delT	uc002tgv.1	+						BCL2L11_uc002tgu.1_Intron|BCL2L11_uc002tgw.1_Intron|BCL2L11_uc002tgx.1_Intron|BCL2L11_uc010fkd.1_Intron|BCL2L11_uc002tgy.1_Intron|BCL2L11_uc002tgz.1_Intron|BCL2L11_uc010fke.1_Intron|BCL2L11_uc002tha.1_Intron|BCL2L11_uc002thb.1_Intron|BCL2L11_uc002thc.1_Intron|BCL2L11_uc002thd.1_Intron	NM_138621	NP_619527			BCL2-like 11 isoform 1						activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria	cytosol|endomembrane system|mitochondrial outer membrane|plasma membrane	protein binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112451693	112451696	+	IGR	DEL	GAAG	-	-	rs147892766		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112451693_112451696delGAAG								LOC541471 (199001 upstream) : ANAPC1 (74945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	113364075	113364075	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113364075delT								CHCHD5 (17225 upstream) : SLC20A1 (39452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	113455278	113455280	+	IGR	DEL	TAA	-	-	rs113846292		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113455278_113455280delTAA								SLC20A1 (33880 upstream) : CKAP2L (40164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	113575950	113575950	+	IGR	DEL	A	-	-	rs150766573		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113575950delA								IL1A (32979 upstream) : IL1B (11387 downstream)																																			---	---	---	---
CBWD2	150472	broad.mit.edu	37	2	114217481	114217481	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114217481delA	uc002tju.2	+						CBWD2_uc010yxw.1_Intron|CBWD2_uc002tjv.2_Intron|CBWD2_uc010fkv.2_Intron	NM_172003	NP_742000			COBW domain-containing protein 2								ATP binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	114573163	114573163	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114573163delT								SLC35F5 (58763 upstream) : ACTR3 (74374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	114592414	114592414	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114592414delA								SLC35F5 (78014 upstream) : ACTR3 (55123 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115742797	115742797	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115742797delT	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	116407905	116407905	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116407905delT	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	116716048	116716048	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116716048delT								DPP10 (114112 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	116976913	116976913	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116976913delA								DPP10 (374977 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117344153	117344154	+	IGR	INS	-	GT	GT	rs149799208	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117344153_117344154insGT								DPP10 (742217 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118019333	118019333	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118019333delA								None (None upstream) : DDX18 (552922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118117609	118117609	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118117609delA								None (None upstream) : DDX18 (454646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118523014	118523015	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118523014_118523015delAA								None (None upstream) : DDX18 (49240 downstream)																																			---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121590066	121590067	+	Intron	INS	-	A	A	rs137994071	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121590066_121590067insA	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261			GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	121870339	121870339	+	IGR	DEL	T	-	-	rs58382175		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121870339delT								GLI2 (120111 upstream) : TFCP2L1 (103827 downstream)																																			---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122138881	122138882	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122138881_122138882delTT	uc002tnc.2	-						CLASP1_uc010yyv.1_Intron|CLASP1_uc002tmz.2_Intron|CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tmy.2_5'Flank|CLASP1_uc002tnf.2_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	122565296	122565296	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122565296delT								TSN (39870 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122691783	122691783	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122691783delA								TSN (166357 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124217548	124217548	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124217548delT								None (None upstream) : CNTNAP5 (565316 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125249333	125249333	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125249333delT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125596997	125596998	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125596997_125596998delAC	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	125745548	125745549	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125745548_125745549insA								CNTNAP5 (72687 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127324443	127324443	+	IGR	DEL	G	-	-	rs112787850		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127324443delG								None (None upstream) : GYPC (89241 downstream)																																			---	---	---	---
GYPC	2995	broad.mit.edu	37	2	127432039	127432040	+	Intron	DEL	GA	-	-	rs11313735		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127432039_127432040delGA	uc002tnq.2	+						GYPC_uc002tnr.2_Intron|GYPC_uc010flv.2_Intron	NM_002101	NP_002092			glycophorin C isoform 1							cortical cytoskeleton|integral to plasma membrane	protein binding			central_nervous_system(1)	1	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)														---	---	---	---
IWS1	55677	broad.mit.edu	37	2	128266830	128266831	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128266830_128266831insA	uc002ton.2	-						IWS1_uc010yzl.1_Intron|IWS1_uc010fma.2_Intron	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	129554690	129554691	+	IGR	INS	-	AGAC	AGAC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129554690_129554691insAGAC								HS6ST1 (478519 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129933436	129933436	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129933436delT								HS6ST1 (857265 upstream) : LOC389033 (746999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130755251	130755251	+	IGR	DEL	A	-	-	rs35322281		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130755251delA								RAB6C (14940 upstream) : LOC440905 (28321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131361297	131361297	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131361297delA								LOC150527 (53826 upstream) : C2orf14 (76326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131628241	131628242	+	Intron	INS	-	GGGAA	GGGAA	rs141646984	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131628241_131628242insGGGAA	uc002try.1	+											Homo sapiens cDNA FLJ45181 fis, clone BRAWH3047644, highly  similar to Homo sapiens Rho guanine nucleotide exchange factor (GEF) 4 (ARHGEF4).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	132177539	132177539	+	IGR	DEL	T	-	-	rs77851707		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132177539delT								LOC150786 (55808 upstream) : LOC401010 (22195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132788556	132788557	+	IGR	INS	-	AAAC	AAAC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132788556_132788557insAAAC								C2orf27B (229322 upstream) : NCRNA00164 (116607 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133008110	133008111	+	Intron	INS	-	G	G	rs143444031	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133008110_133008111insG	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133016676	133016677	+	5'Flank	INS	-	TGTC	TGTC	rs67307110		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	133024493	133024494	+	IGR	DEL	GG	-	-	rs138081439		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133024493_133024494delGG								NCRNA00164 (8951 upstream) : GPR39 (149653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133047403	133047404	+	IGR	INS	-	T	T	rs144234232	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133047403_133047404insT								NCRNA00164 (31861 upstream) : GPR39 (126743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133053343	133053344	+	IGR	INS	-	A	A	rs140692458	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133053343_133053344insA								NCRNA00164 (37801 upstream) : GPR39 (120803 downstream)																																			---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133756540	133756540	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133756540delT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135346416	135346416	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135346416delG	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135765151	135765152	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135765151_135765152insT	uc002tue.1	-						YSK4_uc010fne.1_Intron|YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Intron|YSK4_uc010zbg.1_Intron|YSK4_uc002tui.3_Intron	NM_025052	NP_079328			Yeast Sps1/Ste20-related kinase 4 isoform 1								ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135834839	135834841	+	Intron	DEL	CAA	-	-	rs111433011		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135834839_135834841delCAA	uc002tuj.2	+						RAB3GAP1_uc010fnf.2_Intron|RAB3GAP1_uc010fng.2_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)														---	---	---	---
RAB3GAP1	22930	broad.mit.edu	37	2	135875036	135875038	+	Intron	DEL	CTG	-	-	rs68149706	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135875036_135875038delCTG	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)														---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	136139060	136139061	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136139060_136139061delAG	uc002tum.2	-						ZRANB3_uc002tuk.2_Intron|ZRANB3_uc002tul.2_Intron|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519			zinc finger, RAN-binding domain containing 3							intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	137313644	137313644	+	IGR	DEL	A	-	-	rs695123		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137313644delA								CXCR4 (437919 upstream) : THSD7B (209471 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137587695	137587696	+	Intron	DEL	CA	-	-	rs112704885		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137587695_137587696delCA	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)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138206371	138206373	+	Intron	DEL	AAC	-	-	rs111706284		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138206371_138206373delAAC	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138263623	138263623	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138263623delA	uc002tva.1	+						THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	138530227	138530227	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138530227delA								THSD7B (94940 upstream) : HNMT (191363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139579157	139579157	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139579157delT								NXPH2 (41346 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139985390	139985390	+	IGR	DEL	T	-	-	rs75003221		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139985390delT								NXPH2 (447579 upstream) : None (None downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141625542	141625542	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141625542delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	143020664	143020664	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143020664delC								LRP1B (131394 upstream) : KYNU (614531 downstream)																																			---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144237329	144237329	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144237329delA	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
ARHGAP15	55843	broad.mit.edu	37	2	144407021	144407021	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144407021delT	uc002tvm.3	+						ARHGAP15_uc002tvn.2_Intron	NM_018460	NP_060930			ARHGAP15						regulation of cell shape|small GTPase mediated signal transduction	cytosol|membrane	protein binding|Rac GTPase activator activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(221;0.151)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144949677	144949677	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144949677delT	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	145325522	145325522	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145325522delT								ZEB2 (47591 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	145563398	145563398	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145563398delT	uc002twc.2	+											Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145779951	145779952	+	Intron	DEL	AA	-	-	rs111685576		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145779951_145779952delAA	uc002twc.2	+						uc002twd.2_5'Flank|uc002twe.2_5'Flank					Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	146666657	146666658	+	IGR	INS	-	CA	CA	rs143177023	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146666657_146666658insCA								None (None upstream) : PABPC1P2 (677967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147232501	147232501	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147232501delA								None (None upstream) : PABPC1P2 (112124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147997258	147997258	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147997258delT								PABPC1P2 (648701 upstream) : ACVR2A (604828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148551121	148551122	+	IGR	INS	-	AC	AC	rs148320783	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148551121_148551122insAC								None (None upstream) : ACVR2A (50964 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148605869	148605869	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148605869delT	uc002twg.2	+						ACVR2A_uc010zbn.1_Intron|ACVR2A_uc002twh.2_Intron	NM_001616	NP_001607			activin A receptor, type IIA precursor						activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	149337493	149337493	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149337493delC								MBD5 (66451 upstream) : EPC2 (65067 downstream)																																			---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149653442	149653445	+	Intron	DEL	CACC	-	-	rs35534052	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149653442_149653445delCACC	uc010zbu.1	+							NM_004522	NP_004513			kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)														---	---	---	---
LYPD6	130574	broad.mit.edu	37	2	150270297	150270297	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150270297delG	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	151774998	151775001	+	IGR	DEL	AGGG	-	-	rs6722158		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151774998_151775001delAGGG								RND3 (430818 upstream) : RBM43 (329728 downstream)																																			---	---	---	---
TNFAIP6	7130	broad.mit.edu	37	2	152214427	152214429	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152214427_152214429delTTT	uc002txk.2	+							NM_007115	NP_009046			tumor necrosis factor, alpha-induced protein 6						cell adhesion|cell-cell signaling|inflammatory response|signal transduction		hyaluronic acid binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152302071	152302071	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152331352	152331352	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152331352delT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc002txp.2_Intron|uc010fnw.1_5'Flank	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)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152725791	152725792	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152725791_152725792delAG	uc002tya.2	-						CACNB4_uc002txy.2_Intron|CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron|CACNB4_uc002tyb.2_3'UTR	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)													---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153294087	153294087	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153294087delT	uc002tye.2	+							NM_052905	NP_443137			formin-like 2						actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	154729456	154729457	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154729456_154729457insT	uc002tyr.3	+							NM_052917	NP_443149			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155552462	155552462	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155552462delA	uc002tyv.1	+						KCNJ3_uc010zce.1_5'Flank	NM_002239	NP_002230			potassium inwardly-rectifying channel J3						synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	155972682	155972683	+	IGR	INS	-	A	A	rs139690516	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155972682_155972683insA								KCNJ3 (259668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156791609	156791609	+	IGR	DEL	T	-	-	rs16839799	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156791609delT								None (None upstream) : NR4A2 (389337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157252705	157252705	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157252705delG								NR4A2 (63418 upstream) : GPD2 (39260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157925385	157925385	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157925385delT								GPD2 (455138 upstream) : GALNT5 (188955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	159673074	159673085	+	IGR	DEL	CACACACACACA	-	-	rs143475670		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159673074_159673085delCACACACACACA								DAPL1 (580 upstream) : TANC1 (152061 downstream)																																			---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159954483	159954483	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159954483delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	160167737	160167738	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160167737_160167738delAT								WDSUB1 (24501 upstream) : BAZ2B (7754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	160953715	160953716	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160953715_160953716insA								PLA2R1 (34594 upstream) : ITGB6 (2468 downstream)																																			---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161071129	161071129	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161071129delT	uc010fow.1	-											Synthetic construct DNA, clone: pF1KB8424, Homo sapiens ITGB6 gene for integrin, beta 6, without stop codon, in Flexi system.						cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161654149	161654149	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161654149delT								RBMS1 (303831 upstream) : TANK (339317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	162133771	162133771	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162133771delT								TANK (41089 upstream) : PSMD14 (31015 downstream)																																			---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162769160	162769160	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162769160delA	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																		---	---	---	---
IFIH1	64135	broad.mit.edu	37	2	163156837	163156837	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163156837delA	uc002uce.2	-							NM_022168	NP_071451			interferon induced with helicase C domain 1						detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165875867	165875869	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165875867_165875869delTTT								SLC38A11 (63832 upstream) : SCN3A (68163 downstream)																																			---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165996271	165996271	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165996271delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	166081956	166081956	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166081956delA								SCN3A (21379 upstream) : SCN2A (13956 downstream)																																			---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166097169	166097170	+	Intron	INS	-	TGTGTGTG	TGTGTGTG	rs149309256	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166097169_166097170insTGTGTGTG	uc002udc.2	+							NM_001040142	NP_001035232			sodium channel, voltage-gated, type II, alpha						myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	166253735	166253735	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166253735delT								SCN2A (4917 upstream) : CSRNP3 (72422 downstream)																																			---	---	---	---
GALNT3	2591	broad.mit.edu	37	2	166611928	166611928	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166611928delA	uc010fph.1	-						GALNT3_uc010fpi.1_Intron	NM_004482	NP_004473			polypeptide N-acetylgalactosaminyltransferase 3						protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166748085	166748088	+	Intron	DEL	ATTC	-	-	rs148569616		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166748085_166748088delATTC	uc002udk.2	-						TTC21B_uc002udj.1_5'Flank	NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	167986380	167986382	+	Intron	DEL	AAA	-	-	rs72217262		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167986380_167986382delAAA	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	169641174	169641174	+	Intron	DEL	T	-	-	rs77463321		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169641174delT	uc002ued.2	-						NOSTRIN_uc002uef.2_5'Flank					Homo sapiens LAG1 longevity assurance homolog 6 (S. cerevisiae), mRNA (cDNA clone IMAGE:4827066).																														---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170709969	170709969	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170709969delT	uc010zdi.1	+							NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170730684	170730684	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170730684delT	uc010zdi.1	+							NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171360163	171360163	+	Intron	DEL	T	-	-	rs67426088		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171360163delT	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	172033351	172033351	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172033351delT	uc002ugp.2	-							NM_001136554	NP_001130026			tousled-like kinase 1 isoform 2						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172347462	172347462	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172347462delA								DCAF17 (5902 upstream) : CYBRD1 (31404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	172361751	172361751	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172361751delA								DCAF17 (20191 upstream) : CYBRD1 (17115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	173114725	173114726	+	IGR	INS	-	CAA	CAA	rs142732981	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173114725_173114726insCAA								DLX2 (147247 upstream) : ITGA6 (177356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174435388	174435389	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174435388_174435389delTG								CDCA7 (201670 upstream) : SP3 (337870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176196635	176196635	+	IGR	DEL	C	-	-	rs56886464		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176196635delC								ATP5G3 (150145 upstream) : KIAA1715 (593775 downstream)																																			---	---	---	---
HOXD12	3238	broad.mit.edu	37	2	176963122	176963122	+	5'Flank	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176963122delC	uc010zev.1	+						HOXD12_uc010zew.1_5'Flank	NM_021193	NP_067016			homeobox D12							nuclear chromosome	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)														---	---	---	---
HOXD9	3235	broad.mit.edu	37	2	176987334	176987334	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176987334delT	uc010zex.1	+							NM_014213	NP_055028			homeobox D9							nucleus	sequence-specific DNA binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	177602369	177602369	+	IGR	DEL	A	-	-	rs145464348	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177602369delA								MIR1246 (136589 upstream) : HNRNPA3 (475053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177819063	177819064	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177819063_177819064delGA								MIR1246 (353283 upstream) : HNRNPA3 (258358 downstream)																																			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178097779	178097779	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178097779delT	uc002ulh.3	-						NFE2L2_uc002ulg.3_Intron|NFE2L2_uc010zfa.1_Intron|NFE2L2_uc002uli.3_Intron|NFE2L2_uc010fra.2_3'UTR	NM_006164	NP_006155			nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178215524	178215525	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178215524_178215525delTG	uc002uli.3	-						LOC100130691_uc002ulk.1_Intron	NM_001145412	NP_001138884			nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178357853	178357853	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178357853delT	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650			alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)															---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178912190	178912191	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178912190_178912191delAA	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	180879062	180879063	+	IGR	DEL	AA	-	-	rs68061208		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180879062_180879063delAA								CWC22 (7222 upstream) : UBE2E3 (966049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	182224455	182224455	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182224455delA	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																														---	---	---	---
PPP1R1C	151242	broad.mit.edu	37	2	182834863	182834863	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182834863delT	uc002uon.2	+											Homo sapiens protein phosphatase 1 regulatory subunit 1A mRNA, complete cds.						signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183249068	183249068	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183249068delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	184489839	184489839	+	IGR	DEL	G	-	-	rs112456840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184489839delG								NUP35 (463432 upstream) : ZNF804A (973254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	184569884	184569886	+	IGR	DEL	CAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184569884_184569886delCAC								NUP35 (543477 upstream) : ZNF804A (893207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185881249	185881250	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185881249_185881250insA								ZNF804A (77037 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186245766	186245766	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186245766delA								ZNF804A (441554 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186609706	186609707	+	5'Flank	DEL	GT	-	-	rs71411141		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186609706_186609707delGT	uc002upl.2	+						uc002upj.1_5'Flank|uc010frr.1_5'Flank					Homo sapiens cDNA FLJ34780 fis, clone NT2NE2003705, weakly similar to U2 SMALL NUCLEAR RIBONUCLEOPROTEIN AUXILIARY FACTOR 35 KDA SUBUNIT RELATED-PROTEIN 2.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	186681775	186681775	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186681775delA	uc002upm.2	+						uc010zfu.1_Intron					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	186821298	186821298	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186821298delT								None (None upstream) : ZC3H15 (529587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187312273	187312273	+	IGR	DEL	A	-	-	rs79761547		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187312273delA								None (None upstream) : ZC3H15 (38612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187399877	187399877	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187399877delT								ZC3H15 (25792 upstream) : ITGAV (54913 downstream)																																			---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187588840	187588840	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187588840delA	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	189029060	189029060	+	IGR	DEL	T	-	-	rs77408533		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189029060delT								TFPI (609841 upstream) : GULP1 (127544 downstream)																																			---	---	---	---
DIRC1	116093	broad.mit.edu	37	2	189607618	189607619	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189607618_189607619delAC	uc002uqi.1	-							NM_052952	NP_443184			disrupted in renal carcinoma 1												0			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	189827051	189827052	+	IGR	INS	-	GGAA	GGAA	rs149055113	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189827051_189827052insGGAA								DIRC1 (172220 upstream) : COL3A1 (12047 downstream)																																			---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189861394	189861395	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189861394_189861395delTG	uc002uqj.1	+							NM_000090	NP_000081			collagen type III alpha 1 preproprotein						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	190366158	190366158	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190366158delT								WDR75 (25894 upstream) : SLC40A1 (59160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192363117	192363117	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192363117delA								MYO1B (73002 upstream) : OBFC2A (179681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192424427	192424427	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192424427delC								MYO1B (134312 upstream) : OBFC2A (118371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193348137	193348137	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193348137delT								TMEFF2 (288493 upstream) : PCGEM1 (266434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193648189	193648189	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193648189delA								PCGEM1 (6568 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193820670	193820670	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193820670delT								PCGEM1 (179049 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194719097	194719097	+	IGR	DEL	A	-	-	rs28546483		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194719097delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196062480	196062481	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196062480_196062481delGT								None (None upstream) : SLC39A10 (459051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196352546	196352546	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196352546delA								None (None upstream) : SLC39A10 (168986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196404008	196404008	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196404008delA								None (None upstream) : SLC39A10 (117524 downstream)																																			---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198359954	198359954	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198359954delA	uc002uui.2	-						HSPD1_uc002uuj.2_Intron|HSPD1_uc010zgx.1_Intron|HSPD1_uc010fsm.2_5'UTR|HSPD1_uc002uuk.2_Intron	NM_002156	NP_002147			chaperonin						'de novo' protein folding|activation of caspase activity|B cell cytokine production|B cell proliferation|chaperone-mediated protein complex assembly|interspecies interaction between organisms|isotype switching to IgG isotypes|MyD88-dependent toll-like receptor signaling pathway|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of interferon-alpha production|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of macrophage activation|positive regulation of T cell activation|positive regulation of T cell mediated immune response to tumor cell|protein maturation|protein refolding|protein stabilization|response to unfolded protein|T cell activation	cell surface|coated pit|coated vesicle|cytosol|early endosome|extracellular space|lipopolysaccharide receptor complex|mitochondrial inner membrane|mitochondrial matrix|stored secretory granule	ATP binding|ATPase activity|cell surface binding|chaperone binding|DNA replication origin binding|lipopolysaccharide binding|p53 binding|single-stranded DNA binding				0			Epithelial(96;0.225)															---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198752814	198752814	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198752814delA	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)													---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200329814	200329815	+	5'UTR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200329814_200329815delTC	uc002uva.1	-	1						NM_015265	NP_056080			SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	200609154	200609155	+	IGR	INS	-	AC	AC	rs144649594	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200609154_200609155insAC								FLJ32063 (267496 upstream) : C2orf69 (166824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	201117443	201117446	+	IGR	DEL	ACAC	-	-	rs113593485		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201117443_201117446delACAC								C2orf47 (288598 upstream) : SPATS2L (53158 downstream)																																			---	---	---	---
SGOL2	151246	broad.mit.edu	37	2	201398239	201398240	+	Intron	DEL	TA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201398239_201398240delTA	uc002uvw.2	+						SGOL2_uc002uvv.3_Intron|SGOL2_uc010zhd.1_Intron|SGOL2_uc010zhe.1_Intron	NM_152524	NP_689737			shugoshin-like 2 isoform 1						cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	201563734	201563734	+	IGR	DEL	T	-	-	rs56213910		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201563734delT								AOX1 (27519 upstream) : AOX2P (71661 downstream)																																			---	---	---	---
ALS2CR11	151254	broad.mit.edu	37	2	202358877	202358877	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202358877delT	uc002uye.2	-						ALS2CR11_uc002uyf.2_Frame_Shift_Del_p.K729fs|ALS2CR11_uc010fti.2_Intron	NM_152525	NP_689738			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203060913	203060914	+	Intron	INS	-	C	C	rs35993818		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203060913_203060914insC	uc002uyy.1	+											RecName: Full=Uncharacterized protein KIAA2012;																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	203442132	203442132	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203442132delT								BMPR2 (9659 upstream) : FAM117B (57769 downstream)																																			---	---	---	---
ICA1L	130026	broad.mit.edu	37	2	203706749	203706749	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203706749delT	uc002uzh.1	-						ICA1L_uc002uzi.1_Intron|ICA1L_uc002uzk.1_Intron	NM_138468	NP_612477			islet cell autoantigen 1,69kDa-like isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204180632	204180632	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204180632delT								CYP20A1 (10070 upstream) : ABI2 (12371 downstream)																																			---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204210755	204210756	+	Intron	INS	-	CA	CA	rs147596774	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204210755_204210756insCA	uc002vaa.2	+						ABI2_uc010zig.1_Intron|ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204638924	204638924	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204638924delG								CD28 (36368 upstream) : CTLA4 (93585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204664912	204664912	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204664912delA								CD28 (62356 upstream) : CTLA4 (67597 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205691747	205691747	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205691747delA	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)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205763980	205763983	+	Intron	DEL	CCTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205763980_205763983delCCTT	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)														---	---	---	---
KLF7	8609	broad.mit.edu	37	2	207966850	207966851	+	Intron	DEL	TC	-	-	rs56843018		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207966850_207966851delTC	uc002vbz.1	-						KLF7_uc002vca.1_Intron|KLF7_uc010zix.1_Intron	NM_003709	NP_003700			Kruppel-like factor 7 (ubiquitous)						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			central_nervous_system(1)|skin(1)	2				LUSC - Lung squamous cell carcinoma(261;0.0856)|Lung(261;0.166)|Epithelial(149;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	208670220	208670220	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208670220delT								FZD5 (36077 upstream) : PLEKHM3 (15792 downstream)																																			---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208772238	208772238	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208772238delA	uc002vcl.2	-						PLEKHM3_uc002vcm.2_Intron	NM_001080475	NP_001073944			pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	210062064	210062065	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210062064_210062065insA								PTH2R (357246 upstream) : MAP2 (226706 downstream)																																			---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210422535	210422535	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210422535delG	uc002vdc.1	+						MAP2_uc002vdd.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
UNC80	285175	broad.mit.edu	37	2	210656096	210656096	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210656096delT	uc010zjc.1	+						UNC80_uc002vdj.1_Intron	NM_032504	NP_115893			chromosome 2 open reading frame 21 isoform 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	211717583	211717583	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211717583delA								CPS1 (173754 upstream) : ERBB4 (522859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	212150761	212150761	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212150761delT								CPS1 (606932 upstream) : ERBB4 (89681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	213600858	213600859	+	IGR	INS	-	TCTC	TCTC	rs146721850	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213600858_213600859insTCTC								ERBB4 (197506 upstream) : IKZF2 (263554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	214123277	214123277	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214123277delT								IKZF2 (106944 upstream) : SPAG16 (25839 downstream)																																			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214230186	214230186	+	Intron	DEL	T	-	-	rs34943979		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214230186delT	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron|SPAG16_uc002vep.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)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214701672	214701673	+	Intron	INS	-	TCTC	TCTC	rs143142554	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214701672_214701673insTCTC	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	215417106	215417106	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215417106delT	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	215457782	215457782	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215457782delT								VWC2L (17129 upstream) : BARD1 (135493 downstream)																																			---	---	---	---
BARD1	580	broad.mit.edu	37	2	215657782	215657782	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215657782delC	uc002veu.2	-						BARD1_uc010zjm.1_Intron	NM_000465	NP_000456			BRCA1 associated RING domain 1						cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)										Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	217081399	217081399	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217081399delA								XRCC5 (10385 upstream) : MARCH4 (41187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217095447	217095447	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217095447delT								XRCC5 (24433 upstream) : MARCH4 (27139 downstream)																																			---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217163835	217163835	+	Intron	DEL	T	-	-	rs112707796		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217163835delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	217385594	217385595	+	IGR	INS	-	G	G	rs149347699	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217385594_217385595insG								RPL37A (19408 upstream) : IGFBP2 (112532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217390117	217390117	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217390117delA								RPL37A (23931 upstream) : IGFBP2 (108010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217412220	217412223	+	IGR	DEL	CATT	-	-	rs34713238		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217412220_217412223delCATT								RPL37A (46034 upstream) : IGFBP2 (85904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217464212	217464214	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217464212_217464214delTTT								RPL37A (98026 upstream) : IGFBP2 (33913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217532449	217532450	+	IGR	DEL	AA	-	-	rs71984536		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217532449_217532450delAA								IGFBP2 (3293 upstream) : IGFBP5 (4379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217616621	217616623	+	IGR	DEL	ACA	-	-	rs149754739		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217616621_217616623delACA								IGFBP5 (56349 upstream) : TNP1 (107561 downstream)																																			---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218726999	218727000	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218726999_218727000delAA	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc010zjv.1_Intron|TNS1_uc010fvj.1_Intron|TNS1_uc010fvk.1_Intron|TNS1_uc002vgu.3_Intron|TNS1_uc010fvi.1_Intron	NM_022648	NP_072174			tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)														---	---	---	---
USP37	57695	broad.mit.edu	37	2	219388534	219388534	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219388534delT	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986			ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219717804	219717805	+	IGR	DEL	GT	-	-	rs112289133		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219717804_219717805delGT								PRKAG3 (21292 upstream) : WNT6 (6741 downstream)																																	OREG0015206	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC23A3	151295	broad.mit.edu	37	2	220028426	220028426	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220028426delT	uc010zks.1	-						NHEJ1_uc002vjp.3_5'Flank|NHEJ1_uc002vjq.3_Intron|SLC23A3_uc010zkr.1_Intron|SLC23A3_uc010fwb.2_Intron	NM_001144889	NP_001138361			solute carrier family 23 (nucleobase						transmembrane transport	integral to membrane	protein binding|transporter activity				0		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	221202854	221202857	+	IGR	DEL	ACTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221202854_221202857delACTC								SLC4A3 (696153 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222970987	222970987	+	IGR	DEL	T	-	-	rs5838926		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222970987delT								EPHA4 (532065 upstream) : PAX3 (93620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	224090228	224090228	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224090228delA								KCNE4 (169875 upstream) : SCG2 (371432 downstream)																																			---	---	---	---
SCG2	7857	broad.mit.edu	37	2	224468282	224468282	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224468282delT	uc002vnm.2	-							NM_003469	NP_003460			secretogranin II precursor						angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space|stored secretory granule	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	224472579	224472580	+	IGR	DEL	TT	-	-	rs11322817		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224472579_224472580delTT								SCG2 (5458 upstream) : AP1S3 (147468 downstream)																																			---	---	---	---
SERPINE2	5270	broad.mit.edu	37	2	224866695	224866697	+	Intron	DEL	TTT	-	-	rs10706128		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224866695_224866697delTTT	uc002vnu.2	-						SERPINE2_uc002vnt.2_Intron|SERPINE2_uc010zlr.1_Intron|SERPINE2_uc002vnv.2_Intron	NM_006216	NP_006207			plasminogen activator inhibitor type 1, member 2						negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	224960178	224960179	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224960178_224960179delAA								SERPINE2 (56142 upstream) : FAM124B (283237 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225719572	225719579	+	Intron	DEL	CCAACCAA	-	-	rs72305904		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225719572_225719579delCCAACCAA	uc010fwz.1	-						DOCK10_uc002vob.2_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								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)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225832449	225832449	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225832449delA	uc010fwz.1	-						DOCK10_uc002vod.1_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								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	226825285	226825285	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226825285delA								KIAA1486 (229814 upstream) : IRS1 (770749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	227029689	227029692	+	Intron	DEL	ATAG	-	-	rs13394767	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227029689_227029692delATAG	uc002vog.1	+											Homo sapiens similar to Alu subfamily SX sequence contamination warning entry, mRNA (cDNA clone IMAGE:4246459), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	227096109	227096109	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227096109delT								KIAA1486 (500638 upstream) : IRS1 (499925 downstream)																																			---	---	---	---
RHBDD1	84236	broad.mit.edu	37	2	227783080	227783080	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227783080delA	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652			rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)														---	---	---	---
RHBDD1	84236	broad.mit.edu	37	2	227796589	227796589	+	Intron	DEL	A	-	-	rs75740261		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227796589delA	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652			rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228665714	228665715	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228665714_228665715delTC								SLC19A3 (82969 upstream) : CCL20 (12843 downstream)																																			---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228940137	228940138	+	Intron	INS	-	T	T	rs148477834	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228940137_228940138insT	uc002vpq.2	-						SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron	NM_001142644	NP_001136116			sphingosine kinase type 1-interacting protein							cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	229424915	229424915	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229424915delT								SPHKAP (378554 upstream) : PID1 (463775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229530683	229530683	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229530683delA								SPHKAP (484322 upstream) : PID1 (358007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232566033	232566033	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232566033delA								C2orf57 (107041 upstream) : PTMA (7202 downstream)																																			---	---	---	---
PDE6D	5147	broad.mit.edu	37	2	232632036	232632037	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232632036_232632037delTT	uc002vse.1	-						PDE6D_uc002vsf.1_Intron	NM_002601	NP_002592			phosphodiesterase 6D						regulation of GTP catabolic process|response to stimulus|visual perception		3',5'-cyclic-nucleotide phosphodiesterase activity|GTPase inhibitor activity|protein binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.142)		Epithelial(121;2.19e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00145)|LUSC - Lung squamous cell carcinoma(224;0.0125)|Lung(119;0.0154)														---	---	---	---
EFHD1	80303	broad.mit.edu	37	2	233494658	233494659	+	Intron	INS	-	TTTG	TTTG	rs146596863	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233494658_233494659insTTTG	uc010fyf.2	+							NM_025202	NP_079478			EF-hand domain family, member D1								calcium ion binding|protein binding				0		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	234120304	234120305	+	IGR	INS	-	A	A	rs147043577	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234120304_234120305insA								INPP5D (3756 upstream) : ATG16L1 (39912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	234699094	234699094	+	IGR	DEL	C	-	-	rs67025076		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234699094delC								UGT1A10 (17145 upstream) : HJURP (46393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235691798	235691799	+	IGR	DEL	CA	-	-	rs112748604		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235691798_235691799delCA								ARL4C (286105 upstream) : SH3BP4 (168829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235855472	235855472	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235855472delT								ARL4C (449779 upstream) : SH3BP4 (5156 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236692608	236692615	+	Intron	DEL	GGACGGAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236692608_236692615delGGACGGAC	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236728527	236728527	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236728527delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236803999	236804000	+	Intron	INS	-	A	A	rs150150916	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236803999_236804000insA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ASB18	401036	broad.mit.edu	37	2	237135090	237135090	+	Intron	DEL	A	-	-	rs35773937		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237135090delA	uc010znh.1	-							NM_212556	NP_997721			ankyrin repeat and SOCS box-containing 18						intracellular signal transduction					ovary(1)	1		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	237924695	237924695	+	IGR	DEL	A	-	-	rs79503574		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237924695delA								CXCR7 (433703 upstream) : COPS8 (69389 downstream)																																			---	---	---	---
KLHL30	377007	broad.mit.edu	37	2	239053066	239053093	+	Intron	DEL	AGGAAGGAAGGCAGGCAGGCAGGCAGGC	-	-	rs72337425	by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239053066_239053093delAGGAAGGAAGGCAGGCAGGCAGGCAGGC	uc002vxr.1	+							NM_198582	NP_940984			kelch-like 30												0		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239182140	239182143	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239182140_239182143delTTTT	uc002vyc.2	-						PER2_uc010znv.1_Intron|PER2_uc010znw.1_Intron|PER2_uc010fyx.1_Intron	NM_022817	NP_073728			period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239322351	239322356	+	IGR	DEL	AGTTGC	-	-	rs146004922		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239322351_239322356delAGTTGC								TRAF3IP1 (12812 upstream) : ASB1 (13270 downstream)																																			---	---	---	---
NDUFA10	4705	broad.mit.edu	37	2	240938281	240938281	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240938281delT	uc002vyn.2	-						NDUFA10_uc010fzc.1_Intron	NM_004544	NP_004535			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)													---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241724244	241724244	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241724244delA	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)														---	---	---	---
C2orf54	79919	broad.mit.edu	37	2	241834401	241834402	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241834401_241834402delCA	uc002wae.3	-						C2orf54_uc002wac.2_5'Flank|C2orf54_uc002wad.2_5'Flank	NM_001085437	NP_001078906			hypothetical protein LOC79919 isoform 1												0		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	242165845	242165846	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242165845_242165846delTT								ANO7 (1054 upstream) : HDLBP (833 downstream)																																			---	---	---	---
ATG4B	23192	broad.mit.edu	37	2	242608183	242608184	+	Intron	INS	-	T	T	rs138661495		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242608183_242608184insT	uc002wbv.2	+						ATG4B_uc002wbu.2_Intron|ATG4B_uc002wbw.2_Intron|ATG4B_uc010zox.1_Intron|ATG4B_uc010zoy.1_Intron|ATG4B_uc010fzp.2_Intron|ATG4B_uc010zoz.1_Intron|ATG4B_uc002wby.2_Intron	NM_013325	NP_037457			APG4 autophagy 4 homolog B isoform a						autophagic vacuole assembly|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	103891	103891	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103891delA								None (None upstream) : CHL1 (134759 downstream)																																			---	---	---	---
CHL1	10752	broad.mit.edu	37	3	322597	322598	+	Intron	DEL	CA	-	-	rs72153691		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:322597_322598delCA	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.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	1558682	1558687	+	IGR	DEL	TCTCTC	-	-	rs113826794		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1558682_1558687delTCTCTC								CNTN6 (113405 upstream) : CNTN4 (581863 downstream)																																			---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2232189	2232189	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2232189delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2233266	2233266	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2233266delT	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2515699	2515699	+	Intron	DEL	A	-	-	rs72283945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2515699delA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	3941733	3941734	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3941733_3941734delCA	uc003bps.1	-							NM_182760				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)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	3947387	3947390	+	Intron	DEL	CACA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3947387_3947390delCACA	uc003bps.1	-							NM_182760				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)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4215498	4215498	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4215498delG	uc003bps.1	-							NM_182760				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)														---	---	---	---
SETMAR	6419	broad.mit.edu	37	3	4349711	4349711	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4349711delA	uc011asp.1	+						SUMF1_uc003bps.1_Intron|SETMAR_uc003bpw.3_Intron|SETMAR_uc003bpy.3_Intron|SETMAR_uc011asq.1_Intron|SETMAR_uc011asr.1_Intron|SETMAR_uc010hbx.2_Intron	NM_006515	NP_006506			SET domain and mariner transposase fusion						DNA integration|DNA repair|transposition, DNA-mediated	chromosome|nucleus	DNA binding|endonuclease activity|histone-lysine N-methyltransferase activity|transposase activity|zinc ion binding			ovary(1)	1		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)									Chromatin_Structure|Direct_reversal_of_damage					---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5211251	5211252	+	Intron	DEL	TC	-	-	rs144394825	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5211251_5211252delTC	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)														---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5212424	5212424	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5212424delT	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	5383594	5383595	+	IGR	DEL	GC	-	-	rs72420132		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5383594_5383595delGC								EDEM1 (121945 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5925091	5925091	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5925091delA								EDEM1 (663442 upstream) : GRM7 (977711 downstream)																																			---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8721339	8721339	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8721339delC	uc003bqz.2	-						C3orf32_uc003bqx.2_5'Flank|C3orf32_uc003bqy.2_Intron	NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
THUMPD3	25917	broad.mit.edu	37	3	9409071	9409072	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9409071_9409072insT	uc003bro.3	+						LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Intron	NM_001114092	NP_001107564			THUMP domain containing 3								methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)														---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10081677	10081677	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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				---	---	---	---
VHL	7428	broad.mit.edu	37	3	10181333	10181334	+	5'Flank	INS	-	T	T	rs112758503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10181333_10181334insT	uc003bvc.2	+						VHL_uc003bvd.2_5'Flank	NM_000551	NP_000542			von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding			kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)			1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	3	10795557	10795557	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10795557delA								ATP2B2 (45841 upstream) : LOC285370 (5612 downstream)																																			---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11641845	11641847	+	Intron	DEL	AAA	-	-	rs72379290		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11641845_11641847delAAA	uc003bwf.2	-						VGLL4_uc010hdx.1_Intron|VGLL4_uc003bwg.2_Intron|VGLL4_uc011aun.1_Intron	NM_014667	NP_055482			vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	12036772	12036774	+	IGR	DEL	CAT	-	-	rs139476028		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12036772_12036774delCAT								C3orf31 (148420 upstream) : SYN2 (9088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	12304140	12304140	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12304140delA								SYN2 (70610 upstream) : PPARG (25209 downstream)																																			---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12388096	12388096	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12388096delT	uc003bwr.2	+						PPARG_uc003bws.2_Intron|PPARG_uc003bwu.2_Intron|PPARG_uc003bwv.2_Intron|PPARG_uc003bwq.1_Intron|PPARG_uc010hdz.1_Intron|PPARG_uc003bwt.1_Intron	NM_138712	NP_619726			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
Unknown	0	broad.mit.edu	37	3	12476934	12476934	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12476934delA								PPARG (1080 upstream) : TSEN2 (48997 downstream)																																			---	---	---	---
MKRN2	23609	broad.mit.edu	37	3	12622504	12622504	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12622504delT	uc003bxd.2	+						MKRN2_uc003bxe.2_Intron|MKRN2_uc011aus.1_Intron	NM_014160	NP_054879			makorin ring finger protein 2							intracellular	ligase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12684387	12684388	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12684387_12684388insA	uc003bxf.3	-						RAF1_uc011auu.1_Intron	NM_002880	NP_002871			v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	3	12771146	12771147	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12771146_12771147delTT								RAF1 (65446 upstream) : TMEM40 (4245 downstream)																																			---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	12944144	12944144	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12944144delA	uc003bxt.2	-						IQSEC1_uc003bxu.3_Intron|IQSEC1_uc011auw.1_Intron	NM_014869	NP_055684			IQ motif and Sec7 domain 1 isoform b						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	13065872	13065879	+	Intron	DEL	TCCATCCA	-	-	rs141992079		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13065872_13065879delTCCATCCA	uc011auw.1	-							NM_001134382	NP_001127854			IQ motif and Sec7 domain 1 isoform a						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
TPRXL	348825	broad.mit.edu	37	3	13994516	13994517	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13994516_13994517insA	uc011avd.1	+							NR_002223				RecName: Full=Putative protein TPRXL;												0																		---	---	---	---
NR2C2	7182	broad.mit.edu	37	3	15078717	15078718	+	Intron	DEL	TG	-	-	rs60075101		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15078717_15078718delTG	uc003bzj.3	+						NR2C2_uc003bzi.2_Intron	NM_003298	NP_003289			nuclear receptor subfamily 2, group C, member 2						cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16374345	16374346	+	Intron	INS	-	CTAC	CTAC	rs147565584	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16374345_16374346insCTAC	uc003cay.2	-						RFTN1_uc010hes.2_Intron|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16406691	16406692	+	Intron	INS	-	A	A	rs143773309	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16406691_16406692insA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	16605510	16605510	+	IGR	DEL	A	-	-	rs144954444		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16605510delA								RFTN1 (50288 upstream) : DAZL (22793 downstream)																																			---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17260972	17260972	+	Intron	DEL	T	-	-	rs112259360		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17260972delT	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																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17747476	17747478	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17747476_17747478delTTT	uc003cbf.2	-						TBC1D5_uc003cbe.2_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	18598307	18598308	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18598307_18598308delTG								SATB1 (118055 upstream) : KCNH8 (591709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18706790	18706791	+	IGR	INS	-	T	T	rs144126053	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18706790_18706791insT								SATB1 (226538 upstream) : KCNH8 (483226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18945967	18945967	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18945967delT								SATB1 (465715 upstream) : KCNH8 (244050 downstream)																																			---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19209504	19209506	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19209504_19209506delTTT	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19245915	19245918	+	Intron	DEL	AGAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19245915_19245918delAGAG	uc003cbk.1	+						KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	19655673	19655673	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19655673delT								KCNH8 (78538 upstream) : EFHB (265295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19790648	19790648	+	IGR	DEL	C	-	-	rs143490995		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19790648delC								KCNH8 (213513 upstream) : EFHB (130320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20828971	20828971	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20828971delT								SGOL1 (601288 upstream) : VENTXP7 (618247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21233529	21233530	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21233529_21233530insG								None (None upstream) : VENTXP7 (213688 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22086605	22086605	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22086605delA	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
UBE2E1	7324	broad.mit.edu	37	3	23908559	23908560	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23908559_23908560insT	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332			ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|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 K48-linked ubiquitination	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
THRB	7068	broad.mit.edu	37	3	24310879	24310882	+	Intron	DEL	CGCG	-	-	rs10575859		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24310879_24310882delCGCG	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
THRB	7068	broad.mit.edu	37	3	24459821	24459822	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24459821_24459822delTT	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	24807574	24807574	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24807574delA								THRB (271121 upstream) : RARB (408249 downstream)																																			---	---	---	---
RARB	5915	broad.mit.edu	37	3	25251223	25251223	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25251223delA	uc011awl.1	+							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)													---	---	---	---
RARB	5915	broad.mit.edu	37	3	25593449	25593449	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25593449delT	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)													---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25663482	25663482	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25663482delA	uc011awn.1	-						TOP2B_uc003cdj.2_Intron|TOP2B_uc011awm.1_5'Flank|TOP2B_uc010hff.1_5'Flank	NM_001068	NP_001059			DNA topoisomerase II, beta isozyme						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																		---	---	---	---
NEK10	152110	broad.mit.edu	37	3	27204850	27204851	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27204850_27204851insT	uc010hfk.2	-						NEK10_uc003cds.1_Intron|NEK10_uc010hfj.2_Intron					RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;								ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13																		---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29401517	29401517	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29401517delT	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29421704	29421705	+	Intron	DEL	CA	-	-	rs72253209		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29421704_29421705delCA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29842496	29842497	+	Intron	INS	-	CA	CA	rs145346426	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29842496_29842497insCA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	30346513	30346513	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30346513delA								RBMS3 (299894 upstream) : TGFBR2 (301481 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30854870	30854871	+	Intron	INS	-	CAGA	CAGA	rs138611872	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30854870_30854871insCAGA	uc003cep.2	-						GADL1_uc003ceq.1_Intron	NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	31164238	31164238	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31164238delT								GADL1 (228085 upstream) : STT3B (410253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31210876	31210876	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31210876delT								GADL1 (274723 upstream) : STT3B (363615 downstream)																																			---	---	---	---
STT3B	201595	broad.mit.edu	37	3	31600639	31600646	+	Intron	DEL	GTGTGTGT	-	-	rs9873815		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31600639_31600646delGTGTGTGT	uc011axe.1	+						STT3B_uc010hft.1_Intron|STT3B_uc003cer.1_Intron	NM_178862	NP_849193			source of immunodominant MHC-associated						protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32051633	32051635	+	IGR	DEL	TTT	-	-	rs11303839		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32051633_32051635delTTT								ZNF860 (18513 upstream) : GPD1L (96509 downstream)																																			---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32804818	32804818	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32804818delA	uc003cfc.1	+						CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257			CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
UBP1	7342	broad.mit.edu	37	3	33433845	33433845	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33433845delT	uc003cfq.3	-						FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|UBP1_uc003cfr.3_Intron|UBP1_uc010hga.2_Intron	NM_014517	NP_055332			upstream binding protein 1 (LBP-1a) isoform a						negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			kidney(2)	2																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33546759	33546761	+	Intron	DEL	AAA	-	-	rs60740364		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33546759_33546761delAAA	uc003cfu.2	-						CLASP2_uc003cfs.2_Intron|CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33650237	33650247	+	Intron	DEL	TTTTTTTTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33650237_33650247delTTTTTTTTTTT	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc003cfv.2_Intron|CLASP2_uc011axu.1_Intron|CLASP2_uc003cfw.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33896940	33896942	+	Intron	DEL	AAG	-	-	rs80352187		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33896940_33896942delAAG	uc003cfx.2	+						PDCD6IP_uc003cfy.2_Intron|PDCD6IP_uc011axw.1_Intron	NM_013374	NP_037506			programmed cell death 6 interacting protein						apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	33960604	33960604	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33960604delA								PDCD6IP (49410 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34513872	34513872	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34513872delT								PDCD6IP (602678 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34724462	34724462	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34724462delT								PDCD6IP (813268 upstream) : ARPP21 (956619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34817586	34817586	+	IGR	DEL	T	-	-	rs34300275		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34817586delT								PDCD6IP (906392 upstream) : ARPP21 (863495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36610725	36610725	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36610725delA								STAC (21229 upstream) : DCLK3 (143188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36696552	36696552	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36696552delA								STAC (107056 upstream) : DCLK3 (57361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36723982	36723982	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36723982delA								STAC (134486 upstream) : DCLK3 (29931 downstream)																																			---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37333375	37333375	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37333375delT	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069			golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37564761	37564761	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37564761delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	38300212	38300213	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38300212_38300213insT								OXSR1 (3234 upstream) : SLC22A13 (7085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39037310	39037311	+	IGR	INS	-	TCTATCTA	TCTATCTA	rs57106365		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39037310_39037311insTCTATCTA								SCN11A (45258 upstream) : WDR48 (56196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39295470	39295471	+	IGR	INS	-	A	A	rs138954715	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39295470_39295471insA								XIRP1 (61393 upstream) : CX3CR1 (9515 downstream)																																			---	---	---	---
SLC25A38	54977	broad.mit.edu	37	3	39436230	39436230	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39436230delT	uc003cjo.2	+							NM_017875	NP_060345			solute carrier family 25, member 38						erythrocyte differentiation|heme biosynthetic process|transport	integral to membrane|mitochondrial inner membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40396124	40396124	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40396124delT								EIF1B (42211 upstream) : ENTPD3 (32549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40648122	40648122	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40648122delA								ZNF621 (67079 upstream) : CTNNB1 (588279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40947273	40947273	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40947273delG								ZNF621 (366230 upstream) : CTNNB1 (289128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	41098676	41098677	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41098676_41098677insA								ZNF621 (517633 upstream) : CTNNB1 (137724 downstream)																																			---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41407348	41407348	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41407348delA	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	41512550	41512551	+	Intron	INS	-	A	A	rs147919205	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41512550_41512551insA	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	41796778	41796778	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41796778delT	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	41910160	41910160	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41910160delT	uc003ckv.3	-						ULK4_uc003ckw.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	42027417	42027418	+	IGR	DEL	AA	-	-	rs34176779		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42027417_42027418delAA								ULK4 (23757 upstream) : TRAK1 (105328 downstream)																																			---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42202060	42202061	+	Intron	DEL	TG	-	-	rs59260540		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44810511	44810511	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44810511delT	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)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45561625	45561625	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45561625delT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	46157451	46157451	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46157451delT								XCR1 (88472 upstream) : CCR3 (47645 downstream)																																			---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47020473	47020473	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47020473delA	uc003cqp.2	+						CCDC12_uc003cqo.2_5'Flank|CCDC12_uc011baq.1_5'Flank|CCDC12_uc011bar.1_5'Flank	NM_015175	NP_055990			neurobeachin-like 2								binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)														---	---	---	---
SETD2	29072	broad.mit.edu	37	3	47127923	47127923	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47127923delA	uc003cqs.2	-						SETD2_uc003cqv.2_Intron|SETD2_uc003cqt.1_5'Flank	NM_014159	NP_054878			SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)				N|F|S|Mis		clear cell renal carcinoma								---	---	---	---
SCAP	22937	broad.mit.edu	37	3	47492506	47492507	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47492506_47492507delAA	uc003crh.1	-						SCAP_uc011baz.1_Intron|SCAP_uc003crg.2_Intron	NM_012235	NP_036367			SREBF chaperone protein						cholesterol metabolic process|negative regulation of cholesterol biosynthetic process|positive regulation of low-density lipoprotein particle receptor biosynthetic process|positive regulation of transcription via sterol regulatory element binding involved in ER-nuclear sterol response pathway	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane	unfolded protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48136913	48136913	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48136913delT								MAP4 (6144 upstream) : CDC25A (61755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	48159239	48159239	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48159239delA								MAP4 (28470 upstream) : CDC25A (39429 downstream)																																			---	---	---	---
CDC25A	993	broad.mit.edu	37	3	48201902	48201905	+	Intron	DEL	TTTT	-	-	rs35304690		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48201902_48201905delTTTT	uc003csh.1	-						CDC25A_uc003csi.1_Intron	NM_001789	NP_001780			cell division cycle 25A isoform a						cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|kidney(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)														---	---	---	---
PFKFB4	5210	broad.mit.edu	37	3	48583738	48583739	+	Intron	INS	-	TG	TG	rs144720503	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48583738_48583739insTG	uc003ctv.2	-						PFKFB4_uc003ctw.2_Intron|PFKFB4_uc010hkc.2_Intron|PFKFB4_uc003ctx.2_Intron|PFKFB4_uc010hkb.2_Intron|PFKFB4_uc011bbm.1_Intron|PFKFB4_uc011bbn.1_Intron	NM_004567	NP_004558			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			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)														---	---	---	---
RHOA	387	broad.mit.edu	37	3	49397901	49397901	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49397901delT	uc003cwu.2	-						RHOA_uc010hku.2_Intron|GPX1_uc011bcl.1_5'Flank|GPX1_uc011bcm.1_5'Flank	NM_001664	NP_001655			ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)													---	---	---	---
RNF123	63891	broad.mit.edu	37	3	49747441	49747441	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49747441delT	uc003cxh.2	+						RNF123_uc010hky.1_Intron|RNF123_uc003cxi.2_Intron	NM_022064	NP_071347			ring finger protein 123							cytoplasm	ligase activity|protein binding|zinc ion binding			kidney(3)|ovary(1)|lung(1)|breast(1)|skin(1)	7				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)														---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49766389	49766390	+	Intron	INS	-	T	T	rs76252499		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49766389_49766390insT	uc003cxm.1	-						IP6K1_uc003cxn.1_Intron|IP6K1_uc011bcv.1_Intron|IP6K1_uc003cxo.2_Intron	NM_153273	NP_695005			inositol hexakisphosphate kinase 1 isoform 1						phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49826456	49826457	+	5'Flank	DEL	AA	-	-	rs76001741		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49826456_49826457delAA	uc003cxm.1	-						IP6K1_uc003cxn.1_5'Flank|IP6K1_uc011bcv.1_5'Flank|IP6K1_uc003cxo.2_5'Flank	NM_153273	NP_695005			inositol hexakisphosphate kinase 1 isoform 1						phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
MAPKAPK3	7867	broad.mit.edu	37	3	50650737	50650737	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50650737delA	uc003day.1	+						CISH_uc010hlq.2_5'Flank|CISH_uc003dax.2_5'Flank	NM_004635	NP_004626			mitogen-activated protein kinase-activated						activation 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|Ras protein signal transduction|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|MAP kinase kinase activity|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51603404	51603404	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51603404delT	uc011bdt.1	+						RAD54L2_uc003dbh.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)														---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51738902	51738903	+	5'Flank	INS	-	GT	GT	rs138178730	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51738902_51738903insGT	uc010hlv.2	+						GRM2_uc003dbo.3_5'Flank|GRM2_uc010hlu.2_5'Flank	NM_000839	NP_000830			glutamate receptor, metabotropic 2 isoform a						synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51746310	51746310	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746310delA	uc010hlv.2	+						GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_Intron	NM_000839	NP_000830			glutamate receptor, metabotropic 2 isoform a						synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
GPR62	118442	broad.mit.edu	37	3	51988751	51988752	+	5'Flank	DEL	AA	-	-	rs76122118		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51988751_51988752delAA	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)														---	---	---	---
PPM1M	132160	broad.mit.edu	37	3	52277437	52277437	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52277437delA	uc003ddf.3	+						PPM1M_uc011bed.1_5'Flank|PPM1M_uc010hmd.2_5'Flank|PPM1M_uc003ddg.3_5'Flank					RecName: Full=Protein phosphatase 1M;          EC=3.1.3.16; AltName: Full=Protein phosphatase 2C isoform eta;          Short=PP2C-eta;          Short=PP2CE;						protein dephosphorylation	nucleus	CTD phosphatase activity|manganese ion binding				0				BRCA - Breast invasive adenocarcinoma(193;2.4e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)														---	---	---	---
NT5DC2	64943	broad.mit.edu	37	3	52559178	52559181	+	Intron	DEL	GGGT	-	-	rs61419666		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52559178_52559181delGGGT	uc003deo.2	-						NT5DC2_uc003dem.2_Intron|NT5DC2_uc003den.2_Intron|NT5DC2_uc010hmi.2_Intron|NT5DC2_uc010hmj.2_Intron	NM_022908	NP_075059			5'-nucleotidase domain containing 2 isoform 2								hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	53460969	53460970	+	IGR	DEL	TT	-	-	rs112496130		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53460969_53460970delTT								DCP1A (79332 upstream) : CACNA1D (68061 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54191863	54191871	+	Intron	DEL	AAAAAAAAA	-	-	rs5849032		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54191863_54191871delAAAAAAAAA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.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	54367161	54367161	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54367161delT	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	54785334	54785334	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54785334delT	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	54800168	54800168	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54800168delA	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	54952349	54952349	+	Intron	DEL	T	-	-	rs72173538		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54952349delT	uc003dhf.2	+						CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	55352868	55352869	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55352868_55352869delCT								CACNA2D3 (244286 upstream) : WNT5A (146875 downstream)																																			---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56087824	56087824	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56087824delT	uc003dhr.1	-						ERC2_uc003dht.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)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	57038042	57038042	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57038042delC	uc003dih.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	57718506	57718506	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57718506delA								FAM116A (39690 upstream) : SLMAP (24668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59662301	59662302	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59662301_59662302delAA								C3orf67 (626543 upstream) : FHIT (72736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59706097	59706100	+	IGR	DEL	TTTC	-	-	rs5849292		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59706097_59706100delTTTC								C3orf67 (670339 upstream) : FHIT (28938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	61519060	61519060	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61519060delA								FHIT (281927 upstream) : PTPRG (28183 downstream)																																			---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62549686	62549686	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62549686delT	uc003dll.2	-						CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
LOC285401	285401	broad.mit.edu	37	3	63077665	63077665	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63077665delA	uc003dlo.2	+						LOC285401_uc010hnr.1_Intron					Homo sapiens, clone IMAGE:5557531, mRNA.												0																		---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63948767	63948767	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63948767delT	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64203868	64203868	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64203868delC	uc003dmf.2	-							NM_198859	NP_942559			prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64441502	64441502	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64441502delA								PRICKLE2 (230371 upstream) : ADAMTS9 (59831 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64560396	64560397	+	Intron	INS	-	AC	AC	rs149655140	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64560396_64560397insAC	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron|uc003dmi.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65640300	65640300	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65640300delT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65872119	65872120	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65872119_65872120insA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	66001491	66001494	+	Intron	DEL	TCTT	-	-	rs139515607		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66001491_66001494delTCTT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66501734	66501736	+	Intron	DEL	AAA	-	-	rs35826327		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66501734_66501736delAAA	uc003dmx.2	-						LRIG1_uc010hnz.2_Intron|LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356			leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66652915	66652915	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66652915delA								LRIG1 (102070 upstream) : KBTBD8 (395812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67866924	67866924	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67866924delT	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
FAM19A4	151647	broad.mit.edu	37	3	68929208	68929209	+	Intron	DEL	AC	-	-	rs72123292		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68929208_68929209delAC	uc003dnh.1	-						FAM19A4_uc003dni.1_Intron	NM_182522	NP_872328			family with sequence similarity 19 (chemokine							extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	69066347	69066348	+	IGR	DEL	TT	-	-	rs147553786		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69066347_69066348delTT								C3orf64 (3573 upstream) : TMF1 (2632 downstream)																																			---	---	---	---
UBA3	9039	broad.mit.edu	37	3	69124882	69124882	+	Intron	DEL	T	-	-	rs67282982		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69124882delT	uc003dno.2	-						UBA3_uc003dnq.2_Intron|UBA3_uc011bfy.1_Intron|UBA3_uc011bfz.1_Intron	NM_003968	NP_003959			ubiquitin-activating enzyme 3 isoform 1						protein neddylation|proteolysis	nucleus	acid-amino acid ligase activity|ATP binding|protein heterodimerization activity			ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.98e-05)|Epithelial(33;0.000363)|LUSC - Lung squamous cell carcinoma(21;0.012)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.206)|Kidney(39;0.241)														---	---	---	---
ARL6IP5	10550	broad.mit.edu	37	3	69141748	69141748	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69141748delG	uc003dnr.2	+							NM_006407	NP_006398			ADP-ribosylation-like factor 6 interacting						L-glutamate transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	70170619	70170619	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70170619delA								MITF (153133 upstream) : FOXP1 (834118 downstream)																																			---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71288864	71288864	+	Intron	DEL	G	-	-	rs2568844	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71288864delG	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003dos.2_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								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71505404	71505405	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71505404_71505405delAG	uc003dop.2	-						FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dos.2_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								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71580657	71580657	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71580657delA	uc003dop.2	-						FOXP1_uc003doo.2_Intron|FOXP1_uc003dos.2_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	71991163	71991163	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71991163delT								PROK2 (156806 upstream) : RYBP (432588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72060933	72060933	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72060933delT								PROK2 (226576 upstream) : RYBP (362818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72276087	72276089	+	IGR	DEL	AAA	-	-	rs144139739		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72276087_72276089delAAA								PROK2 (441730 upstream) : RYBP (147662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73355839	73355840	+	IGR	INS	-	T	T	rs35282666		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73355839_73355840insT								PPP4R2 (240828 upstream) : PDZRN3 (75812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73357917	73357917	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73357917delA								PPP4R2 (242906 upstream) : PDZRN3 (73735 downstream)																																			---	---	---	---
ZNF717	100131827	broad.mit.edu	37	3	75761328	75761328	+	Intron	DEL	A	-	-	rs146502045		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75761328delA	uc003dpw.3	-											Homo sapiens cDNA FLJ41782 fis, clone IMR322018192, weakly  similar to ZINC FINGER PROTEIN 90.						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	75988307	75988308	+	IGR	INS	-	AC	AC	rs147036991		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75988307_75988308insAC								ZNF717 (153637 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76931238	76931239	+	IGR	DEL	TG	-	-	rs71629622		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76931238_76931239delTG								None (None upstream) : ROBO2 (158055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	77756580	77756580	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77756580delA								ROBO2 (59919 upstream) : ROBO1 (889808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	77846616	77846616	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77846616delA								ROBO2 (149955 upstream) : ROBO1 (799772 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79501066	79501067	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79501066_79501067delAA	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	80586736	80586737	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80586736_80586737delAA								ROBO1 (769677 upstream) : GBE1 (952113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81512317	81512318	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81512317_81512318insG								None (None upstream) : GBE1 (26532 downstream)																																			---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81541861	81541868	+	Intron	DEL	TTCCTTCC	-	-	rs67220037		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81541861_81541868delTTCCTTCC	uc003dqg.2	-							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	81993696	81993697	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81993696_81993697delTT								GBE1 (182746 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82574069	82574069	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82574069delT								GBE1 (763119 upstream) : None (None downstream)																																			---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85060873	85060874	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85060873_85060874delTT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85065942	85065943	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85065942_85065943insA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85322247	85322247	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85322247delA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86727193	86727195	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86727193_86727195delTTT								CADM2 (609245 upstream) : VGLL3 (259930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87198402	87198403	+	IGR	DEL	GA	-	-	rs113293539		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87198402_87198403delGA								VGLL3 (158145 upstream) : CHMP2B (78010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87956347	87956348	+	IGR	INS	-	T	T	rs34920865		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87956347_87956348insT								POU1F1 (630610 upstream) : HTR1F (75378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88479927	88479927	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88479927delA								C3orf38 (272814 upstream) : EPHA3 (676747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88993463	88993466	+	IGR	DEL	ACAC	-	-	rs72255928		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88993463_88993466delACAC								C3orf38 (786350 upstream) : EPHA3 (163208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90486773	90486773	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90486773delA								EPHA3 (955491 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	94111441	94111441	+	IGR	DEL	A	-	-	rs34374407		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94111441delA								NSUN3 (265811 upstream) : LOC255025 (545666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95254516	95254517	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95254516_95254517delAA								LOC255025 (359437 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95397836	95397839	+	Intron	DEL	CAAG	-	-	rs71792680		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95397836_95397839delCAAG	uc003dro.1	-											Homo sapiens cDNA FLJ34909 fis, clone NT2RI2009301, moderately similar to BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL PRECURSOR.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	95759024	95759024	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95759024delT								LOC255025 (863945 upstream) : EPHA6 (774401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95793471	95793471	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95793471delT								LOC255025 (898392 upstream) : EPHA6 (739954 downstream)																																			---	---	---	---
CRYBG3	131544	broad.mit.edu	37	3	97615825	97615825	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97615825delT	uc003drx.2	+							NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	99032503	99032504	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99032503_99032504insT								DCBLD2 (411970 upstream) : COL8A1 (324950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99326388	99326388	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99326388delG								DCBLD2 (705855 upstream) : COL8A1 (31066 downstream)																																			---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100330087	100330088	+	Intron	INS	-	TTTCCTTC	TTTCCTTC	rs71981038		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100330087_100330088insTTTCCTTC	uc003duc.2	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	100904183	100904206	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAGGAAA	-	-	rs74986375	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100904183_100904206delGAAGGAAGGAAGGAAGGAAGGAAA								ABI3BP (191849 upstream) : IMPG2 (41082 downstream)																																			---	---	---	---
FAM55C	91775	broad.mit.edu	37	3	101506911	101506912	+	Intron	INS	-	TT	TT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101506911_101506912insTT	uc003dvn.2	+						FAM55C_uc010hpn.2_Intron	NM_145037	NP_659474			hypothetical protein LOC91775 precursor							extracellular region				ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	101580674	101580675	+	IGR	INS	-	GT	GT	rs145451355	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101580674_101580675insGT								NFKBIZ (809 upstream) : LOC152225 (79028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102363987	102363988	+	IGR	INS	-	AC	AC	rs28587413	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102363987_102363988insAC								ZPLD1 (165302 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102961630	102961630	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102961630delG								ZPLD1 (762945 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103903226	103903233	+	IGR	DEL	GCACTCCA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103903226_103903233delGCACTCCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104111183	104111184	+	IGR	INS	-	C	C	rs142999184	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104111183_104111184insC								None (None upstream) : ALCAM (974529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104869134	104869136	+	IGR	DEL	ATG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104869134_104869136delATG								None (None upstream) : ALCAM (216577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104986774	104986775	+	IGR	INS	-	T	T	rs140537819	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104986774_104986775insT								None (None upstream) : ALCAM (98938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106143693	106143694	+	IGR	INS	-	TCTC	TCTC	rs148361212	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106143693_106143694insTCTC								CBLB (555427 upstream) : LOC100302640 (411966 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106821890	106821890	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106821890delT	uc003dwf.3	-											Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106852418	106852419	+	Intron	DEL	AA	-	-	rs151154477		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106852418_106852419delAA	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106882567	106882567	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106882567delA	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	107217867	107217868	+	IGR	DEL	TT	-	-	rs149567464		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107217867_107217868delTT								CCDC54 (120386 upstream) : BBX (23915 downstream)																																			---	---	---	---
BBX	56987	broad.mit.edu	37	3	107348430	107348430	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107348430delT	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.3_Intron	NM_001142568	NP_001136040			HMG-BOX transcription factor BBX isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	107672250	107672251	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107672250_107672251delAA								LOC285205 (24499 upstream) : CD47 (89690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	108841235	108841236	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108841235_108841236delAC								MORC1 (4242 upstream) : C3orf66 (55776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109326684	109326684	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109326684delT								FLJ25363 (112670 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109662296	109662297	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109662296_109662297delTG								FLJ25363 (448282 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	111073694	111073694	+	IGR	DEL	T	-	-	rs79497800		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111073694delT								PVRL3 (161321 upstream) : CD96 (187232 downstream)																																			---	---	---	---
C3orf52	79669	broad.mit.edu	37	3	111839225	111839225	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111839225delA	uc011bht.1	+						C3orf52_uc003dyr.1_Intron	NM_024616	NP_078892			TPA-induced transmembrane protein							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
BTLA	151888	broad.mit.edu	37	3	112209452	112209455	+	Intron	DEL	ACAC	-	-	rs72194431		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112209452_112209455delACAC	uc003dza.3	-						BTLA_uc003dzb.3_Intron	NM_181780	NP_861445			B and T lymphocyte associated isoform 1						T cell costimulation		receptor activity				0		Acute lymphoblastic leukemia(4;1.34e-07)|all_hematologic(4;0.000361)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	112887185	112887185	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112887185delT								C3orf17 (148630 upstream) : BOC (43227 downstream)																																			---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113252385	113252385	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113252385delC	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169			SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113287469	113287474	+	Intron	DEL	AAAAGA	-	-	rs59222879		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113287469_113287474delAAAAGA	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron	NM_017699	NP_060169			SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115593757	115593757	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115593757delA	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	117852201	117852205	+	IGR	DEL	AGGAA	-	-	rs66945036		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117852201_117852205delAGGAA								None (None upstream) : IGSF11 (767276 downstream)																																			---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119805649	119805649	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119805649delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628			glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)													---	---	---	---
GPR156	165829	broad.mit.edu	37	3	119920021	119920022	+	Intron	INS	-	TTGTTTT	TTGTTTT	rs142201268	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119920021_119920022insTTGTTTT	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547			G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	119979089	119979089	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119979089delA								GPR156 (15764 upstream) : LRRC58 (64487 downstream)																																			---	---	---	---
FSTL1	11167	broad.mit.edu	37	3	120161242	120161243	+	Intron	INS	-	G	G	rs144307534	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120161242_120161243insG	uc003eds.2	-						FSTL1_uc011bjh.1_Intron|FSTL1_uc010hrb.2_Intron	NM_007085	NP_009016			follistatin-like 1 precursor						BMP signaling pathway	extracellular space	calcium ion binding|heparin binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(114;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	120261205	120261205	+	IGR	DEL	T	-	-	rs141069063		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120261205delT								FSTL1 (91287 upstream) : NDUFB4 (53923 downstream)																																			---	---	---	---
GTF2E1	2960	broad.mit.edu	37	3	120463775	120463776	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120463775_120463776delTT	uc003edz.3	+						RABL3_uc003edx.2_5'Flank|GTF2E1_uc003edy.2_Intron	NM_005513	NP_005504			general transcription factor IIE, polypeptide 1,						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)														---	---	---	---
IQCB1	9657	broad.mit.edu	37	3	121522838	121522838	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121522838delT	uc010hre.1	-						IQCB1_uc003eek.2_Intron|IQCB1_uc010hrf.1_Intron	NM_001023570	NP_001018864			IQ motif containing B1 isoform a						cilium assembly|maintenance of organ identity|photoreceptor cell maintenance	centrosome|photoreceptor connecting cilium	calmodulin binding				0				GBM - Glioblastoma multiforme(114;0.0983)														---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122414253	122414253	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122414253delT	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)														---	---	---	---
HSPBAP1	79663	broad.mit.edu	37	3	122502209	122502209	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122502209delT	uc003efu.1	-						HSPBAP1_uc003efv.1_Intron	NM_024610	NP_078886			Hspb associated protein 1							cytoplasm				ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124127564	124127564	+	Intron	DEL	A	-	-	rs148423023		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124127564delA	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																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124394425	124394425	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124394425delT	uc003ehg.2	+						KALRN_uc003ehk.2_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																		---	---	---	---
ITGB5	3693	broad.mit.edu	37	3	124513644	124513645	+	Intron	INS	-	AAGA	AAGA	rs146073504	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124513644_124513645insAAGA	uc003eho.2	-						ITGB5_uc010hrx.2_Intron	NM_002213	NP_002204			integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)														---	---	---	---
OSBPL11	114885	broad.mit.edu	37	3	125300654	125300654	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125300654delA	uc003eic.2	-							NM_022776	NP_073613			oxysterol binding protein-like 11						lipid transport		lipid binding			ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125322722	125322723	+	IGR	DEL	TT	-	-	rs139499855		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125322722_125322723delTT								OSBPL11 (8341 upstream) : MIR548I1 (186524 downstream)																																			---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126221879	126221880	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126221879_126221880delTG	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	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)														---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126720404	126720404	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126720404delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	127086465	127086465	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127086465delA	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	127209437	127209437	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127209437delG	uc003ejk.2	-											Homo sapiens cDNA FLJ25806 fis, clone TST07194.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	128325980	128325980	+	IGR	DEL	A	-	-	rs66866549		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128325980delA								C3orf27 (31051 upstream) : RPN1 (12833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	128577308	128577309	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128577308_128577309delGT								RAB7A (43667 upstream) : ACAD9 (21024 downstream)																																			---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128602506	128602506	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128602506delT	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	128916526	128916527	+	IGR	DEL	TG	-	-	rs71620048		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128916526_128916527delTG								CNBP (13716 upstream) : COPG (51926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	129089595	129089596	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129089595_129089596delGT								C3orf47 (46183 upstream) : RPL32P3 (12082 downstream)																																			---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130063610	130063610	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130063610delT	uc010htj.1	+						COL29A1_uc010hti.1_5'Flank	NM_153264	NP_694996			collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0																		---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131842267	131842270	+	Intron	DEL	ACAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131842267_131842270delACAA	uc003eom.2	-							NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132690308	132690308	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132690308delA								NCRNA00119 (97258 upstream) : TMEM108 (66863 downstream)																																			---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133191795	133191796	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133191795_133191796insT	uc003epn.1	+							NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	133252523	133252524	+	IGR	INS	-	TTGTTG	TTGTTG	rs146380007	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133252523_133252524insTTGTTG								BFSP2 (58467 upstream) : CDV3 (39910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	133881079	133881080	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133881079_133881080delTT								RYK (-88507 upstream) : RYK (-5102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	133905228	133905228	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133905228delA								RYK (-64358 upstream) : RYK (-29250 downstream)																																			---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134793746	134793746	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134793746delC	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron|EPHB1_uc003equ.2_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	135186007	135186008	+	IGR	DEL	AC	-	-	rs10541746		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135186007_135186008delAC								EPHB1 (206702 upstream) : PPP2R3A (498559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135358671	135358671	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135358671delT								EPHB1 (379366 upstream) : PPP2R3A (325896 downstream)																																			---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135827542	135827542	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135827542delT	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron|PPP2R3A_uc003eqw.1_Intron	NM_002718	NP_002709			protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135923274	135923274	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135923274delA								MSL2 (8586 upstream) : PCCB (45893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136529476	136529476	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136529476delA								STAG1 (58231 upstream) : TMEM22 (8385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137428694	137428695	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137428694_137428695delTT								IL20RB (698774 upstream) : SOX14 (54884 downstream)																																			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139944329	139944332	+	Intron	DEL	TTTG	-	-	rs67258038		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139944329_139944332delTTTG	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	140501088	140501089	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140501088_140501089delCA								TRIM42 (81097 upstream) : SLC25A36 (159573 downstream)																																			---	---	---	---
SPSB4	92369	broad.mit.edu	37	3	140790323	140790323	+	Intron	DEL	T	-	-	rs112063222		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140790323delT	uc003ett.2	+						SPSB4_uc010hum.2_Intron	NM_080862	NP_543138			splA/ryanodine receptor domain and SOCS box						intracellular signal transduction	cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	141419983	141419983	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141419983delT								RASA2 (88786 upstream) : RNF7 (37068 downstream)																																			---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141497917	141497917	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141497917delC	uc011bnd.1	+							NM_139209	NP_631948			G-protein-coupled receptor kinase 7 precursor						visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142310436	142310437	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142310436_142310437delCA								ATR (12768 upstream) : PLS1 (4792 downstream)																																			---	---	---	---
PCOLCE2	26577	broad.mit.edu	37	3	142544848	142544848	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142544848delT	uc003evd.2	-							NM_013363	NP_037495			procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142981810	142981810	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142981810delT								CHST2 (140000 upstream) : SLC9A9 (2255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143819358	143819359	+	IGR	DEL	TA	-	-	rs113264030		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143819358_143819359delTA								C3orf58 (108149 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144862285	144862285	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144862285delA								None (None upstream) : PLOD2 (924943 downstream)																																			---	---	---	---
PLSCR4	57088	broad.mit.edu	37	3	145951756	145951757	+	Intron	INS	-	TATATT	TATATT	rs150054610	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145951756_145951757insTATATT	uc010huy.2	-						PLSCR4_uc010huz.2_Intron|PLSCR4_uc003evt.3_Intron|PLSCR4_uc010hva.2_Intron|PLSCR4_uc003evu.3_Intron	NM_001128305	NP_001121777			phospholipid scramblase 4 isoform a						blood coagulation|phospholipid scrambling	integral to membrane	calcium ion binding|phospholipid scramblase activity|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	147539949	147539950	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147539949_147539950insT								ZIC1 (405445 upstream) : AGTR1 (875708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148039698	148039698	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148039698delA								ZIC1 (905194 upstream) : AGTR1 (375960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148519662	148519662	+	IGR	DEL	A	-	-	rs139712547		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148519662delA								AGTR1 (58874 upstream) : CPB1 (25926 downstream)																																			---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149340290	149340305	+	Intron	DEL	AAGAAAGAAAGAAAGA	-	-	rs72335546	by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149340290_149340305delAAGAAAGAAAGAAAGA	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron	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)															---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149379214	149379215	+	Intron	DEL	TT	-	-	rs66869057		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149379214_149379215delTT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	150206044	150206045	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150206044_150206045delTT								TSC22D2 (28431 upstream) : SERP1 (53736 downstream)																																			---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151117619	151117619	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151117619delT	uc003eyp.2	+						MED12L_uc011bnz.1_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	151298464	151298465	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151298464_151298465delAA								IGSF10 (121967 upstream) : AADACL2 (153239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	151378037	151378038	+	IGR	DEL	TT	-	-	rs10552593		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151378037_151378038delTT								IGSF10 (201540 upstream) : AADACL2 (73666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	151709347	151709347	+	IGR	DEL	T	-	-	rs11310514		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151709347delT								SUCNR1 (109697 upstream) : LOC401093 (271066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152747455	152747456	+	IGR	DEL	TT	-	-	rs149119380		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152747455_152747456delTT								P2RY1 (191614 upstream) : RAP2B (132573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154649000	154649000	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154649000delA								GPR149 (501496 upstream) : MME (92913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	155472425	155472426	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155472425_155472426insA								PLCH1 (50428 upstream) : C3orf33 (7975 downstream)																																			---	---	---	---
C3orf33	285315	broad.mit.edu	37	3	155488751	155488752	+	Intron	INS	-	TGTGTGTG	TGTGTGTG	rs148925987	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155488751_155488752insTGTGTGTG	uc003fal.1	-						C3orf33_uc003fam.1_Intron	NM_173657	NP_775928			hypothetical protein LOC285315								hydrolase activity, acting on ester bonds|nucleic acid binding				0			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	155727479	155727480	+	IGR	INS	-	AACAC	AACAC	rs141224478	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155727479_155727480insAACAC								GMPS (71961 upstream) : KCNAB1 (110857 downstream)																																			---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	155859322	155859322	+	Intron	DEL	T	-	-	rs111355824		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155859322delT	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_5'Flank	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)															---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	155967350	155967350	+	Intron	DEL	A	-	-	rs11366404		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155967350delA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_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)															---	---	---	---
LEKR1	389170	broad.mit.edu	37	3	156654255	156654256	+	Intron	DEL	CC	-	-	rs71931633		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156654255_156654256delCC	uc003fba.1	+							NM_001004316	NP_001004316			leucine, glutamate and lysine rich 1												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156895730	156895730	+	IGR	DEL	T	-	-	rs68141839		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156895730delT								CCNL1 (17248 upstream) : VEPH1 (82968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	156959499	156959499	+	IGR	DEL	A	-	-	rs67187100		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156959499delA								CCNL1 (81017 upstream) : VEPH1 (19199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158342640	158342642	+	IGR	DEL	AGA	-	-	rs78270190		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158342640_158342642delAGA								MLF1 (18388 upstream) : GFM1 (19675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	158778065	158778066	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158778065_158778066delTT								MFSD1 (230561 upstream) : SCHIP1 (9051 downstream)																																			---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159303921	159303921	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159303921delA	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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159383336	159383337	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159383336_159383337delTG	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)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	159989730	159989731	+	Intron	DEL	AA	-	-	rs10708967		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159989730_159989731delAA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160146393	160146393	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160146393delT	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_Intron	NM_001002800	NP_001002800			SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	160427083	160427083	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160427083delA								ARL14 (30850 upstream) : PPM1L (46913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161452762	161452763	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161452762_161452763delTT								OTOL1 (231034 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161532256	161532256	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161532256delT								OTOL1 (310528 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162440671	162440685	+	5'Flank	DEL	CTGGGTGCAGGCAGG	-	-	rs113977945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162440671_162440685delCTGGGTGCAGGCAGG	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162500642	162500645	+	Intron	DEL	GGGT	-	-	rs56824069		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162500642_162500645delGGGT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	163538984	163538984	+	IGR	DEL	A	-	-	rs112594748		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163538984delA								None (None upstream) : MIR1263 (350275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165755176	165755177	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165755176_165755177insT								BCHE (199923 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165921379	165921380	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165921379_165921380insT								BCHE (366126 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166054900	166054902	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166054900_166054902delAAA								BCHE (499647 upstream) : ZBBX (903179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166517468	166517468	+	IGR	DEL	T	-	-	rs72136358		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166517468delT								BCHE (962215 upstream) : ZBBX (440613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166767601	166767602	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166767601_166767602insA								None (None upstream) : ZBBX (190479 downstream)																																			---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167369383	167369383	+	Intron	DEL	T	-	-	rs34523707		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167369383delT	uc003fev.1	-						WDR49_uc003few.1_Intron	NM_178824	NP_849146			WD repeat domain 49											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
PDCD10	11235	broad.mit.edu	37	3	167442174	167442174	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167442174delA	uc003fex.2	-						PDCD10_uc003fez.2_Intron|PDCD10_uc003fey.2_Intron	NM_007217	NP_009148			programmed cell death 10						angiogenesis|apoptosis|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of MAP kinase activity	cytosol|Golgi membrane|plasma membrane	protein homodimerization activity|protein N-terminus binding			lung(1)|central_nervous_system(1)	2														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
Unknown	0	broad.mit.edu	37	3	167869509	167869510	+	IGR	DEL	TC	-	-	rs112503151		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167869509_167869510delTC								GOLIM4 (56092 upstream) : MIR551B (400132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	167917079	167917079	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167917079delC								GOLIM4 (103662 upstream) : MIR551B (352563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168133108	168133108	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168133108delT								GOLIM4 (319691 upstream) : MIR551B (136534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172119931	172119932	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172119931_172119932delTT								FNDC3B (1441 upstream) : GHSR (43019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172874043	172874043	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172874043delG								SPATA16 (15011 upstream) : NLGN1 (242201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	173045026	173045026	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173045026delT								SPATA16 (185994 upstream) : NLGN1 (71218 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173768189	173768189	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173768189delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174534204	174534205	+	IGR	DEL	GT	-	-	rs72019233		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174534204_174534205delGT								NLGN1 (533088 upstream) : NAALADL2 (42906 downstream)																																			---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174744445	174744446	+	Intron	INS	-	A	A	rs112697779		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174744445_174744446insA	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	175431526	175431526	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175431526delT	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	176487539	176487542	+	IGR	DEL	AGGA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176487539_176487542delAGGA								NAALADL2 (964113 upstream) : TBL1XR1 (251001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176520937	176520937	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176520937delA								NAALADL2 (997511 upstream) : TBL1XR1 (217606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176661716	176661717	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176661716_176661717insA								None (None upstream) : TBL1XR1 (76826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177412385	177412387	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177412385_177412387delAAA								TBL1XR1 (497337 upstream) : KCNMB2 (841837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177874529	177874529	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177874529delA								TBL1XR1 (959481 upstream) : KCNMB2 (379695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	178229792	178229792	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178229792delA								None (None upstream) : KCNMB2 (24432 downstream)																																			---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178541702	178541702	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178541702delA	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_Intron|KCNMB2_uc011bqa.1_Intron|KCNMB2_uc011bqb.1_Intron	NM_181361	NP_852006			calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)															---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178898344	178898344	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178898344delA	uc003fjk.2	+							NM_006218	NP_006209			phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)				57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			---	---	---	---
KCNMB3	27094	broad.mit.edu	37	3	178984772	178984773	+	5'UTR	INS	-	TC	TC	rs138080982	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178984772_178984773insTC	uc003fjp.1	-	1					KCNMB3_uc011bqc.1_5'UTR	NM_171828	NP_741979			calcium-activated potassium channel beta 3						detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179861116	179861116	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179861116delA								PEX5L (106599 upstream) : TTC14 (458802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180162086	180162086	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180162086delT								PEX5L (407569 upstream) : TTC14 (157832 downstream)																																			---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180349039	180349040	+	Intron	INS	-	TATAGAATG	TATAGAATG	rs138343088	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180349039_180349040insTATAGAATG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180599215	180599215	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180599215delT								CCDC39 (143553 upstream) : FXR1 (31237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181236066	181236067	+	IGR	DEL	TC	-	-	rs1382698		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181236066_181236067delTC								DNAJC19 (528536 upstream) : SOX2OT (45442 downstream)																																			---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181307010	181307010	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181307010delT	uc003fkv.2	+											Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181360634	181360634	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181360634delA	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	181486646	181486646	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181486646delA								SOX2OT (27643 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181789181	181789181	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181789181delT								SOX2OT (330178 upstream) : ATP11B (722110 downstream)																																			---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	183015430	183015431	+	Intron	INS	-	CCTTCCTT	CCTTCCTT	rs138473795	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183015430_183015431insCCTTCCTT	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc011bqr.1_Intron|uc003fln.1_RNA|uc003flo.2_5'Flank	NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	183101333	183101333	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183101333delT	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc003flp.1_Intron	NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183280528	183280529	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183280528_183280529insA								KLHL6 (7029 upstream) : KLHL24 (72882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183290161	183290161	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183290161delA								KLHL6 (16662 upstream) : KLHL24 (63250 downstream)																																			---	---	---	---
HTR3C	170572	broad.mit.edu	37	3	183773500	183773501	+	Intron	DEL	CA	-	-	rs10561752		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183773500_183773501delCA	uc003fmk.2	+							NM_130770	NP_570126			5-hydroxytryptamine receptor 3 subunit C							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183778476	183778479	+	IGR	DEL	GTTT	-	-	rs111532443		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183778476_183778479delGTTT								HTR3C (17 upstream) : HTR3E (36373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184392646	184392647	+	IGR	DEL	AA	-	-	rs147642659		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184392646_184392647delAA								EPHB3 (92451 upstream) : MAGEF1 (35509 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184619906	184619907	+	Intron	INS	-	G	G	rs10937191	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184619906_184619907insG	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118			vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186015636	186015636	+	Intron	DEL	G	-	-	rs76693402		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186015636delG	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	186083447	186083447	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186083447delA								DGKG (3424 upstream) : CRYGS (172786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	186241882	186241882	+	IGR	DEL	T	-	-	rs77208820	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186241882delT								DGKG (161859 upstream) : CRYGS (14351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	186375495	186375496	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186375495_186375496delAA								FETUB (4699 upstream) : HRG (8302 downstream)																																			---	---	---	---
RTP4	64108	broad.mit.edu	37	3	187087217	187087217	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187087217delG	uc003frm.2	+							NM_022147	NP_071430			28kD interferon responsive protein						detection of chemical stimulus involved in sensory perception of bitter taste|protein targeting to membrane	cytoplasm|integral to membrane	protein binding				0	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	187238397	187238397	+	IGR	DEL	T	-	-	rs145082651		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187238397delT								RTP4 (149030 upstream) : SST (148299 downstream)																																			---	---	---	---
LPP	4026	broad.mit.edu	37	3	188295546	188295549	+	Intron	DEL	TTCG	-	-	rs72048204		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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								---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	189025662	189025662	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189025662delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	189046530	189046530	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189046530delT								TPRG1 (5260 upstream) : TP63 (302686 downstream)																																			---	---	---	---
TP63	8626	broad.mit.edu	37	3	189496774	189496775	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189496774_189496775delGT	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
TP63	8626	broad.mit.edu	37	3	189555581	189555582	+	Intron	INS	-	T	T	rs138345891	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189555581_189555582insT	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_Intron|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189697589	189697589	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189697589delA	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)													---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189749167	189749168	+	Intron	INS	-	TGT	TGT	rs148645669	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189749167_189749168insTGT	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)													---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189749230	189749231	+	Intron	DEL	GA	-	-	rs140059756		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189749230_189749231delGA	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	190829749	190829750	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190829749_190829750delCA								SNAR-I (233910 upstream) : OSTN (100572 downstream)																																			---	---	---	---
OSTN	344901	broad.mit.edu	37	3	190938224	190938224	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190938224delA	uc011bsn.1	+							NM_198184	NP_937827			osteocrin precursor						cell differentiation|multicellular organismal development|ossification		hormone activity			pancreas(1)|skin(1)	2	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	191752711	191752711	+	IGR	DEL	T	-	-	rs11328285		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191752711delT								PYDC2 (573468 upstream) : FGF12 (106973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191763051	191763051	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191763051delA								PYDC2 (583808 upstream) : FGF12 (96633 downstream)																																			---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192587115	192587116	+	Intron	INS	-	AGGGAAAA	AGGGAAAA	rs6778683		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192587115_192587116insAGGGAAAA	uc011bsp.1	-							NM_178496	NP_848591			hypothetical protein LOC151963												0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	193652806	193652809	+	IGR	DEL	TTTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193652806_193652809delTTTG								OPA1 (237207 upstream) : LOC100128023 (58075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193684037	193684037	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193684037delA								OPA1 (268438 upstream) : LOC100128023 (26847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193931517	193931518	+	IGR	DEL	TT	-	-	rs80116718		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193931517_193931518delTT								HES1 (75121 upstream) : LOC100131551 (85906 downstream)																																			---	---	---	---
TMEM44	93109	broad.mit.edu	37	3	194337418	194337418	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194337418delC	uc010hzn.2	-						TMEM44_uc010hzm.2_5'Flank|TMEM44_uc003fuc.2_Intron|TMEM44_uc003fue.2_Intron|TMEM44_uc003fud.2_Intron|TMEM44_uc003fuf.2_Intron|TMEM44_uc011bsv.1_Intron|TMEM44_uc003fuh.1_Intron	NM_001011655	NP_001011655			transmembrane protein 44 isoform b							integral to membrane					0	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194672854	194672857	+	IGR	DEL	AAAG	-	-	rs72197243		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194672854_194672857delAAAG								FAM43A (263090 upstream) : C3orf21 (116158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194712128	194712130	+	IGR	DEL	TCC	-	-	rs9838410		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194712128_194712130delTCC								FAM43A (302364 upstream) : C3orf21 (76885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195323012	195323014	+	IGR	DEL	AAA	-	-	rs112691827		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195323012_195323014delAAA								APOD (11936 upstream) : SDHAP2 (61896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195436325	195436326	+	Intron	INS	-	G	G	rs144844794		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195436325_195436326insG	uc003fux.1	+											Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195557472	195557472	+	IGR	DEL	A	-	-	rs139076899	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195557472delA								MUC4 (18324 upstream) : TNK2 (32764 downstream)																																			---	---	---	---
ZDHHC19	131540	broad.mit.edu	37	3	195937292	195937293	+	Intron	INS	-	GAAA	GAAA	rs149833656	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195937292_195937293insGAAA	uc003fwc.2	-						ZDHHC19_uc010hzz.2_Intron|ZDHHC19_uc010iaa.2_Intron|ZDHHC19_uc010iab.2_Intron	NM_001039617	NP_001034706			zinc finger, DHHC domain containing 19							integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)														---	---	---	---
TCTEX1D2	255758	broad.mit.edu	37	3	196035786	196035787	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196035786_196035787delAA	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)														---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196161166	196161166	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196161166delA	uc003fwm.3	-						UBXN7_uc003fwn.3_5'Flank|UBXN7_uc010iae.2_5'Flank|UBXN7_uc010iaf.2_5'Flank	NM_015562	NP_056377			UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196655003	196655003	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196655003delG	uc003fwz.3	+						SENP5_uc011bty.1_Intron	NM_152699	NP_689912			SUMO1/sentrin specific peptidase 5						cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)														---	---	---	---
NCBP2	22916	broad.mit.edu	37	3	196664216	196664216	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196664216delA	uc003fxd.1	-						NCBP2_uc003fxb.1_Intron|NCBP2_uc011btz.1_Intron|NCBP2_uc003fxc.1_Intron|NCBP2_uc003fxe.1_Intron|NCBP2_uc003fxf.2_3'UTR	NM_007362	NP_031388			nuclear cap binding protein subunit 2, 20kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of RNA export from nucleus|positive regulation of viral transcription|regulation of translational initiation|snRNA export from nucleus|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm	nucleotide binding|protein binding|RNA 7-methylguanosine cap binding				0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	29172	29172	+	IGR	DEL	A	-	-	rs145707628		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29172delA								None (None upstream) : ZNF595 (24055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29239	29239	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29239delT								None (None upstream) : ZNF595 (23988 downstream)																																			---	---	---	---
ZNF595	152687	broad.mit.edu	37	4	67784	67784	+	Intron	DEL	T	-	-	rs146895580		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67784delT	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330			zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)														---	---	---	---
PIGG	54872	broad.mit.edu	37	4	515274	515275	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:515274_515275delAA	uc003gak.3	+						PIGG_uc003gaj.3_Intron|PIGG_uc011bux.1_Intron|PIGG_uc010ibf.2_Intron|PIGG_uc003gal.3_Intron|PIGG_uc003gai.2_Intron|PIGG_uc011buw.1_Intron|PIGG_uc003gam.2_Intron|PIGG_uc003gan.2_Intron	NM_001127178	NP_001120650			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	609854	609858	+	IGR	DEL	TTTTT	-	-	rs142617762	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:609854_609858delTTTTT								PIGG (76535 upstream) : PDE6B (9505 downstream)																																			---	---	---	---
PCGF3	10336	broad.mit.edu	37	4	718750	718752	+	Intron	DEL	AAA	-	-	rs150783610		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:718750_718752delAAA	uc011bva.1	+						PCGF3_uc003gbc.1_Intron|PCGF3_uc003gbd.1_Intron|PCGF3_uc003gbe.2_Intron|PCGF3_uc010ibh.2_Intron|uc003gbf.2_5'Flank	NM_006315	NP_006306			ring finger protein 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	1028823	1028823	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1028823delA								FGFRL1 (8138 upstream) : RNF212 (21220 downstream)																																			---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1919853	1919853	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1919853delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geh.1_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								---	---	---	---
Unknown	0	broad.mit.edu	37	4	2022139	2022140	+	IGR	INS	-	TC	TC	rs147820362	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2022139_2022140insTC								WHSC2 (11180 upstream) : C4orf48 (21549 downstream)																																			---	---	---	---
POLN	353497	broad.mit.edu	37	4	2186889	2186889	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2186889delG	uc003ger.2	-						POLN_uc010ich.1_Intron|POLN_uc011bvi.1_Intron	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2958218	2958218	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2958218delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694			probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
GRK4	2868	broad.mit.edu	37	4	3016524	3016524	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3016524delA	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
GRK4	2868	broad.mit.edu	37	4	3038811	3038812	+	Intron	DEL	TG	-	-	rs34216391		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3038811_3038812delTG	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3470790	3470791	+	Intron	INS	-	GT	GT	rs146996008		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3470790_3470791insGT	uc003ghd.2	+						DOK7_uc003ghe.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3600454	3600455	+	IGR	DEL	GT	-	-	rs66734766		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3600454_3600455delGT								LRPAP1 (66230 upstream) : ADRA2C (167620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3604083	3604084	+	IGR	INS	-	A	A	rs35405998		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3604083_3604084insA								LRPAP1 (69859 upstream) : ADRA2C (163991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3608308	3608311	+	IGR	DEL	TGAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3608308_3608311delTGAA								LRPAP1 (74084 upstream) : ADRA2C (159764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3624355	3624356	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3624355_3624356delCT								LRPAP1 (90131 upstream) : ADRA2C (143719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3632892	3632893	+	IGR	INS	-	GT	GT	rs144601290	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3632892_3632893insGT								LRPAP1 (98668 upstream) : ADRA2C (135182 downstream)																																			---	---	---	---
D4S234E	27065	broad.mit.edu	37	4	4353663	4353664	+	Intron	DEL	TG	-	-	rs142488078	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4353663_4353664delTG	uc011bvz.1	+							NM_014392	NP_055207			brain neuron cytoplasmic protein 1						dopamine receptor signaling pathway	Golgi membrane|integral to membrane|nucleus	dopamine receptor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4571309	4571309	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4571309delG	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4639954	4639954	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4639954delC	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	6251065	6251066	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6251065_6251066insT								JAKMIP1 (48747 upstream) : WFS1 (20511 downstream)																																			---	---	---	---
PPP2R2C	5522	broad.mit.edu	37	4	6556658	6556661	+	Intron	DEL	GAAA	-	-	rs71889314	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6556658_6556661delGAAA	uc011bwd.1	-						PPP2R2C_uc011bwe.1_Intron	NM_181876	NP_870991			gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6925986	6925990	+	Intron	DEL	AATCC	-	-	rs57881179		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6925986_6925990delAATCC	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron	NM_001113361	NP_001106832			TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7353436	7353437	+	Intron	INS	-	CAT	CAT	rs113163287		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7353436_7353437insCAT	uc003gkb.3	+							NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7450332	7450335	+	Intron	DEL	CCTT	-	-	rs10531260		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7450332_7450335delCCTT	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7678444	7678445	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7678444_7678445delTC	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7892814	7892815	+	Intron	INS	-	A	A	rs75603065		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7892814_7892815insA	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	8187063	8187064	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8187063_8187064insA								ABLIM2 (26504 upstream) : SH3TC1 (13996 downstream)																																			---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9982876	9982878	+	Intron	DEL	ATG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9982876_9982878delATG	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9990375	9990375	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9990375delA	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	10127994	10127996	+	IGR	DEL	AGG	-	-	rs10532684		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10127994_10127996delAGG								WDR1 (9421 upstream) : ZNF518B (313509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	10422882	10422883	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10422882_10422883insT								WDR1 (304309 upstream) : ZNF518B (18622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	10727477	10727477	+	IGR	DEL	A	-	-	rs34959920		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10727477delA								CLNK (41091 upstream) : MIR572 (642974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11198713	11198713	+	IGR	DEL	A	-	-	rs35388345		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11198713delA								CLNK (512327 upstream) : MIR572 (171738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12780999	12780999	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12780999delT								None (None upstream) : HSP90AB2P (554038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	15173401	15173402	+	IGR	INS	-	T	T	rs142552903	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15173401_15173402insT								CPEB2 (101627 upstream) : C1QTNF7 (168158 downstream)																																			---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16825119	16825119	+	Intron	DEL	T	-	-	rs112467730		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16825119delT	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16889322	16889323	+	Intron	INS	-	A	A	rs138636395	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16889322_16889323insA	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	16975918	16975919	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16975918_16975919insA								LDB2 (75494 upstream) : QDPR (512101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	17031286	17031298	+	IGR	DEL	ACTGGAACCCAAG	-	-	rs6148320		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17031286_17031298delACTGGAACCCAAG								LDB2 (130862 upstream) : QDPR (456722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	17130238	17130238	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17130238delT								LDB2 (229814 upstream) : QDPR (357782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18215246	18215246	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18215246delG								LCORL (191861 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18688564	18688564	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18688564delA								LCORL (665179 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18816496	18816496	+	IGR	DEL	A	-	-	rs75230309		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18816496delA								LCORL (793111 upstream) : None (None downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	20813134	20813139	+	Intron	DEL	GTGTGC	-	-	rs35065714		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20813134_20813139delGTGTGC	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	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)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21513788	21513811	+	Intron	DEL	GGAGGGAGGAAGGAAGGAACGAAC	-	-	rs68124536		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	21731146	21731146	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21731146delA	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)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21953135	21953135	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21953135delA	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	22628732	22628733	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22628732_22628733insT								GPR125 (111060 upstream) : GBA3 (65815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23632440	23632441	+	IGR	DEL	TT	-	-	rs34521737		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23632440_23632441delTT								GBA3 (811249 upstream) : PPARGC1A (161204 downstream)																																			---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23804836	23804836	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23804836delA	uc003gqs.2	-						PPARGC1A_uc003gqt.2_Intron	NM_013261	NP_037393			peroxisome proliferator-activated receptor						androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	24126293	24126294	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24126293_24126294delTT								PPARGC1A (234593 upstream) : MIR573 (395521 downstream)																																			---	---	---	---
PI4K2B	55300	broad.mit.edu	37	4	25261983	25261983	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25261983delT	uc003grk.2	+						PI4K2B_uc011bxs.1_Intron	NM_018323	NP_060793			phosphatidylinositol 4-kinase type 2 beta							cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	25300656	25300656	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25300656delA								PI4K2B (19825 upstream) : ZCCHC4 (13740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25547235	25547236	+	IGR	DEL	TT	-	-	rs71639883		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25547235_25547236delTT								ANAPC4 (127116 upstream) : SLC34A2 (110199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26208952	26208953	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26208952_26208953delTG								C4orf52 (277452 upstream) : RBPJ (112379 downstream)																																			---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26362670	26362671	+	Intron	INS	-	GT	GT	rs71899348		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26362670_26362671insGT	uc003grx.1	+						RBPJ_uc003gry.1_Intron|RBPJ_uc003grz.1_Intron|RBPJ_uc011bxt.1_Intron|RBPJ_uc003gsa.1_Intron|RBPJ_uc003gsb.1_Intron|RBPJ_uc003gsc.1_5'Flank	NM_005349	NP_005340			recombining binding protein suppressor of						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)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	26860027	26860031	+	5'Flank	DEL	AAGGA	-	-	rs147233613		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26860027_26860031delAAGGA	uc003gsh.3	+						STIM2_uc003gsg.3_5'Flank|STIM2_uc010iex.2_5'Flank	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	27039406	27039407	+	IGR	INS	-	TT	TT	rs144483064	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27039406_27039407insTT								STIM2 (13598 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27614726	27614726	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27614726delT								STIM2 (588918 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27922778	27922779	+	IGR	DEL	GA	-	-	rs61793889		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27922778_27922779delGA								STIM2 (896970 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28053683	28053684	+	IGR	DEL	CG	-	-	rs142677562		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28053683_28053684delCG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28110740	28110741	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28110740_28110741delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28143298	28143298	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28143298delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28470750	28470750	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28470750delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28998727	28998728	+	IGR	DEL	TT	-	-	rs111418732		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28998727_28998728delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29529491	29529491	+	IGR	DEL	C	-	-	rs33957259		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29529491delC								None (None upstream) : None (None downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30840118	30840118	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30840118delT	uc011bxx.1	+						PCDH7_uc011bxw.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	31197684	31197684	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31197684delA								PCDH7 (49263 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31800356	31800356	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31800356delG								PCDH7 (651935 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33027008	33027008	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33027008delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33843839	33843840	+	IGR	DEL	TA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33843839_33843840delTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34008934	34008936	+	Intron	DEL	CAT	-	-	rs111757710		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34008934_34008936delCAT	uc003gsn.2	-											Homo sapiens, clone IMAGE:5172449, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	34414581	34414582	+	IGR	DEL	TT	-	-	rs35331101		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34414581_34414582delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35140164	35140166	+	IGR	DEL	CTC	-	-	rs149704500	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35140164_35140166delCTC								None (None upstream) : ARAP2 (809678 downstream)																																			---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37431687	37431687	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37431687delT	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
KLF3	51274	broad.mit.edu	37	4	38686163	38686165	+	Intron	DEL	TTT	-	-	rs10542788		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38686163_38686165delTTT	uc003gth.3	+						KLF3_uc003gtg.2_Intron	NM_016531	NP_057615			Kruppel-like factor 3 (basic)						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39139752	39139753	+	IGR	INS	-	AGG	AGG	rs76849230		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39139752_39139753insAGG								KLHL5 (15924 upstream) : WDR19 (44271 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39187514	39187516	+	Intron	DEL	TTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39187514_39187516delTTG	uc003gtv.2	+						WDR19_uc010ifl.1_Intron|WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39226487	39226489	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39226487_39226489delTTT	uc003gtv.2	+						WDR19_uc003gtu.1_Intron|WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
KLB	152831	broad.mit.edu	37	4	39413145	39413147	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39413145_39413147delTTT	uc003gua.2	+						KLB_uc011byj.1_Intron	NM_175737	NP_783864			klotho beta						carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1																		---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39916103	39916104	+	Intron	INS	-	G	G	rs148438975	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39916103_39916104insG	uc003guv.3	-						PDS5A_uc010ifo.2_Intron|PDS5A_uc003guw.3_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	40674393	40674396	+	IGR	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40674393_40674396delAAAA								RBM47 (41753 upstream) : NSUN7 (77518 downstream)																																			---	---	---	---
APBB2	323	broad.mit.edu	37	4	40932464	40932471	+	Intron	DEL	GTGCGCGC	-	-	rs145872032		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40932464_40932471delGTGCGCGC	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc011byt.1_Intron	NM_173075	NP_775098			amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	41244813	41244814	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41244813_41244814delAA								APBB2 (28178 upstream) : UCHL1 (14084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42328471	42328474	+	IGR	DEL	GGAG	-	-	rs34833590		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42328471_42328474delGGAG								BEND4 (173576 upstream) : SHISA3 (71382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42734633	42734633	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42734633delT								ATP8A1 (75511 upstream) : GRXCR1 (160651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43273977	43273980	+	IGR	DEL	ATAC	-	-	rs138300822		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43273977_43273980delATAC								GRXCR1 (241304 upstream) : KCTD8 (901942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43275239	43275239	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43275239delT								GRXCR1 (242566 upstream) : KCTD8 (900683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43867888	43867889	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43867888_43867889delAC								GRXCR1 (835215 upstream) : KCTD8 (308033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45680008	45680009	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45680008_45680009delCA								GNPDA2 (951396 upstream) : GABRG1 (357780 downstream)																																			---	---	---	---
ATP10D	57205	broad.mit.edu	37	4	47551968	47551971	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47551968_47551971delTTTT	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186			ATPase, class V, type 10D						ATP biosynthetic process|cation transport	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(2)|pancreas(1)	3																		---	---	---	---
ATP10D	57205	broad.mit.edu	37	4	47571412	47571413	+	Intron	INS	-	CAGACCC	CAGACCC	rs138298566	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47571412_47571413insCAGACCC	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186			ATPase, class V, type 10D						ATP biosynthetic process|cation transport	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(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48041039	48041039	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48041039delA								NIPAL1 (1961 upstream) : TXK (27373 downstream)																																			---	---	---	---
TEC	7006	broad.mit.edu	37	4	48233774	48233774	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48233774delA	uc003gxz.2	-							NM_003215	NP_003206			tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48655700	48655700	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48655700delT	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron|FRYL_uc003gyn.3_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	49099749	49099753	+	IGR	DEL	TCCGG	-	-	rs60947727		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	49221428	49221428	+	IGR	DEL	T	-	-	rs111806399		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49221428delT								CWH43 (157335 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49246088	49246088	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49246088delA								CWH43 (181995 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49634016	49634020	+	IGR	DEL	GGAAG	-	-	rs57378837		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49634016_49634020delGGAAG								CWH43 (569923 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52935036	52935037	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52935036_52935037insT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53242671	53242671	+	IGR	DEL	T	-	-	rs34449125		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53242671delT								SPATA18 (279214 upstream) : USP46 (214458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53423101	53423102	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53423101_53423102delTC								SPATA18 (459644 upstream) : USP46 (34027 downstream)																																			---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	54123275	54123276	+	Intron	INS	-	AC	AC	rs137988703	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54123275_54123276insAC	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753			sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54539972	54539972	+	Intron	DEL	G	-	-	rs1477880	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54539972delG	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)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	55027132	55027132	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55027132delT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58020058	58020059	+	Intron	DEL	AG	-	-	rs71208987		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58020058_58020059delAG	uc003hco.2	+											Homo sapiens, clone IMAGE:5722917, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	58414330	58414330	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58414330delT								IGFBP7 (437791 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58717883	58717883	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58717883delA								IGFBP7 (741344 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59075980	59075980	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59075980delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60570655	60570655	+	IGR	DEL	A	-	-	rs35063204		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60570655delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61045184	61045186	+	IGR	DEL	TGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61045184_61045186delTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61397911	61397911	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61397911delT								None (None upstream) : LPHN3 (669063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61429593	61429593	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61429593delT								None (None upstream) : LPHN3 (637381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61438535	61438536	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61438535_61438536delTG								None (None upstream) : LPHN3 (628438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61564903	61564904	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61564903_61564904insT								None (None upstream) : LPHN3 (502070 downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62217463	62217463	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62217463delA	uc003hcq.3	+						LPHN3_uc010ihg.1_Intron					RecName: Full=Latrophilin-3; AltName: Full=Calcium-independent alpha-latrotoxin receptor 3; AltName: Full=Lectomedin-3; Flags: Precursor;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62362818	62362818	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62362818delT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62602790	62602791	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62602790_62602791delTT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62766020	62766020	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62766020delT	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	65870168	65870169	+	IGR	INS	-	C	C	rs150874227	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65870168_65870169insC								TECRL (594990 upstream) : EPHA5 (315113 downstream)																																			---	---	---	---
EPHA5	2044	broad.mit.edu	37	4	66500870	66500871	+	Intron	DEL	CA	-	-	rs139625901		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66500870_66500871delCA	uc003hcy.2	-						EPHA5_uc003hcx.2_Intron|EPHA5_uc003hcz.2_Intron|EPHA5_uc011cah.1_Intron|EPHA5_uc011cai.1_Intron|EPHA5_uc003hda.2_Intron	NM_004439	NP_004430			ephrin receptor EphA5 isoform a precursor						cAMP-mediated signaling|neuron development	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(19)|stomach(2)|ovary(2)|central_nervous_system(1)	24															TSP Lung(17;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66770911	66770912	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66770911_66770912insT								EPHA5 (235258 upstream) : MIR1269 (371630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66777310	66777310	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66777310delC								EPHA5 (241657 upstream) : MIR1269 (365232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67731335	67731338	+	IGR	DEL	TGTC	-	-	rs76474299		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67731335_67731338delTGTC								MIR1269 (588689 upstream) : CENPC1 (606651 downstream)																																			---	---	---	---
CENPC1	1060	broad.mit.edu	37	4	68340422	68340422	+	Intron	DEL	A	-	-	rs75737176		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68340422delA	uc003hdd.1	-						CENPC1_uc010ihj.1_Intron|CENPC1_uc010ihk.1_Intron|CENPC1_uc010ihl.2_3'UTR	NM_001812	NP_001803			centromere protein C 1						mitotic prometaphase	condensed chromosome kinetochore|condensed nuclear chromosome, centromeric region|cytosol	DNA binding			urinary_tract(1)|lung(1)	2																		---	---	---	---
UBA6	55236	broad.mit.edu	37	4	68531151	68531152	+	Intron	INS	-	TG	TG	rs60372702		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68531151_68531152insTG	uc003hdg.3	-						UBA6_uc003hdi.2_Intron|UBA6_uc003hdj.2_Intron	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																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68965762	68965762	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68965762delA	uc003hdt.1	-							NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69262933	69262933	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69262933delA								YTHDC1 (47109 upstream) : UGT2B15 (249383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70246731	70246731	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70246731delT								UGT2B28 (85964 upstream) : UGT2B4 (99153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70249075	70249075	+	IGR	DEL	T	-	-	rs77582319		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70249075delT								UGT2B28 (88308 upstream) : UGT2B4 (96809 downstream)																																			---	---	---	---
UGT2A1	10941	broad.mit.edu	37	4	70462252	70462252	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70462252delT	uc003hem.3	-						UGT2A1_uc011caq.1_Intron|UGT2A1_uc010ihu.2_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Intron	NM_006798	NP_006789			UDP glucuronosyltransferase 2 family,						detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
AMBN	258	broad.mit.edu	37	4	71465157	71465157	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71465157delA	uc003hfl.2	+							NM_016519	NP_057603			ameloblastin precursor						bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)|skin(1)	4			Lung(101;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	71755487	71755490	+	IGR	DEL	TCCC	-	-	rs4343698		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71755487_71755490delTCCC								GRSF1 (49860 upstream) : MOBKL1A (12574 downstream)																																			---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72112463	72112464	+	Intron	INS	-	T	T	rs147204315	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72112463_72112464insT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72211024	72211024	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72211024delT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hgc.3_Intron|SLC4A4_uc003hga.2_Intron|SLC4A4_uc003hgb.3_Intron	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	72465613	72465613	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72465613delT								SLC4A4 (27810 upstream) : GC (141800 downstream)																																			---	---	---	---
COX18	285521	broad.mit.edu	37	4	73930892	73930893	+	Intron	INS	-	G	G	rs79402424		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73930892_73930893insG	uc003hgm.1	-						COX18_uc003hgn.1_Intron|COX18_uc011cbc.1_Intron|COX18_uc010iih.1_Intron	NM_173827	NP_776188			mitochondrial COX18 precursor						protein insertion into mitochondrial membrane|respiratory chain complex IV assembly	integral to mitochondrial inner membrane	protein transporter activity				0	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	74125732	74125735	+	5'Flank	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74125732_74125735delTTTT	uc003hgp.2	-						ANKRD17_uc003hgq.2_5'Flank|ANKRD17_uc003hgr.2_5'Flank	NM_032217	NP_115593			ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
IL8	3576	broad.mit.edu	37	4	74654422	74654422	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74654422delT	uc011cbh.1	+							NM_000584	NP_000575			interleukin 8 precursor						angiogenesis|calcium-mediated signaling|cell cycle arrest|cellular response to lipopolysaccharide|embryonic digestive tract development|G-protein coupled receptor protein signaling pathway|immune response|induction of positive chemotaxis|inflammatory response|negative regulation of cell proliferation|neutrophil activation|neutrophil chemotaxis|positive regulation of neutrophil chemotaxis|regulation of cell adhesion|regulation of retroviral genome replication	extracellular space|intracellular	chemokine activity|interleukin-8 receptor binding			ovary(2)	2	Breast(15;0.00102)		all cancers(17;0.00169)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)	LUSC - Lung squamous cell carcinoma(721;0.008)	Ketoprofen(DB01009)|Salbutamol(DB01001)|Simvastatin(DB00641)|Zileuton(DB00744)													---	---	---	---
IL8	3576	broad.mit.edu	37	4	74677886	74677887	+	Intron	INS	-	A	A	rs140572781	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74677886_74677887insA	uc011cbh.1	+							NM_000584	NP_000575			interleukin 8 precursor						angiogenesis|calcium-mediated signaling|cell cycle arrest|cellular response to lipopolysaccharide|embryonic digestive tract development|G-protein coupled receptor protein signaling pathway|immune response|induction of positive chemotaxis|inflammatory response|negative regulation of cell proliferation|neutrophil activation|neutrophil chemotaxis|positive regulation of neutrophil chemotaxis|regulation of cell adhesion|regulation of retroviral genome replication	extracellular space|intracellular	chemokine activity|interleukin-8 receptor binding			ovary(2)	2	Breast(15;0.00102)		all cancers(17;0.00169)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)	LUSC - Lung squamous cell carcinoma(721;0.008)	Ketoprofen(DB01009)|Salbutamol(DB01001)|Simvastatin(DB00641)|Zileuton(DB00744)													---	---	---	---
BTC	685	broad.mit.edu	37	4	75703793	75703793	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75703793delA	uc003hig.2	-							NM_001729	NP_001720			betacellulin precursor						positive regulation of cell division|positive regulation of cell proliferation	extracellular space|integral to membrane|plasma membrane|soluble fraction	epidermal growth factor receptor binding|growth factor activity			central_nervous_system(1)|skin(1)	2			Lung(101;0.219)															---	---	---	---
ART3	419	broad.mit.edu	37	4	77031734	77031735	+	Intron	DEL	AA	-	-	rs34864947		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77031734_77031735delAA	uc003hjo.2	+						ART3_uc003hjk.2_Intron|ART3_uc003hjn.2_Intron|ART3_uc003hjp.2_Intron|ART3_uc010ijb.2_Intron|ART3_uc003hjq.2_Intron|ART3_uc003hjr.2_Intron|ART3_uc010ijc.2_Intron|ART3_uc010ijd.2_Intron	NM_001130016	NP_001123488			ADP-ribosyltransferase 3 isoform a						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77470529	77470529	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77470529delT	uc011cbx.1	+							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	77744220	77744221	+	IGR	DEL	CC	-	-	rs13102047		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77744220_77744221delCC								SHROOM3 (39817 upstream) : ANKRD56 (71862 downstream)																																			---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79217229	79217229	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79217229delT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc003hky.1_Intron|FRAS1_uc003hkz.2_Intron|FRAS1_uc003hla.1_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	80204427	80204427	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80204427delT	uc003hlr.1	+						uc003hls.2_Intron					Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80571824	80571824	+	IGR	DEL	T	-	-	rs113983067		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80571824delT								GK2 (242452 upstream) : GDEP (176801 downstream)																																			---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81769365	81769366	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81769365_81769366delAA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82353175	82353175	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82353175delT	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron	NM_152545	NP_689758			RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
ENOPH1	58478	broad.mit.edu	37	4	83378359	83378359	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83378359delA	uc003hmv.2	+						ENOPH1_uc003hmw.2_Intron|ENOPH1_uc003hmx.2_Intron	NM_021204	NP_067027			enolase-phosphatase 1						L-methionine salvage from methylthioadenosine	cytoplasm|nucleus	2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity|2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity|acireductone synthase activity|magnesium ion binding|phosphoglycolate phosphatase activity				0																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83792991	83792991	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83792991delA	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	84699579	84699579	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84699579delA								AGPAT9 (172554 upstream) : NKX6-1 (714857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84861246	84861246	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84861246delT	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85769410	85769410	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85769410delA	uc003hpd.2	-						WDFY3_uc003hpf.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	86332343	86332376	+	IGR	DEL	TATCTGAGGATGTGAGGCTGGATTCAAACCCAGT	-	-	rs59483602		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86332343_86332376delTATCTGAGGATGTGAGGCTGGATTCAAACCCAGT								C4orf12 (404175 upstream) : ARHGAP24 (63908 downstream)																																			---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87349233	87349233	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87349233delA	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)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87656211	87656212	+	Intron	INS	-	T	T	rs142916492	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87656211_87656212insT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	87834218	87834218	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87834218delA								C4orf36 (20643 upstream) : AFF1 (21945 downstream)																																			---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87978238	87978238	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87978238delT	uc003hqj.3	+						AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	88040567	88040567	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88040567delA	uc003hqj.3	+						AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
HSD17B11	51170	broad.mit.edu	37	4	88296987	88296988	+	Intron	INS	-	TTTC	TTTC	rs151117303	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88296987_88296988insTTTC	uc003hqp.2	-							NM_016245	NP_057329			estradiol 17-beta-dehydrogenase 11						androgen catabolic process|steroid biosynthetic process	cytoplasm|extracellular region	binding|estradiol 17-beta-dehydrogenase activity			ovary(2)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88590970	88590970	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88590970delA								DMP1 (5460 upstream) : IBSP (129732 downstream)																																			---	---	---	---
ABCG2	9429	broad.mit.edu	37	4	89043422	89043422	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89043422delT	uc003hrg.2	-						ABCG2_uc003hrh.2_Intron|ABCG2_uc003hrf.2_Intron	NM_004827	NP_004818			ATP-binding cassette, sub-family G, member 2						cellular iron ion homeostasis|urate metabolic process	integral to membrane|plasma membrane	ATP binding|heme transporter activity|protein homodimerization activity|xenobiotic-transporting ATPase activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Imatinib(DB00619)|Mitoxantrone(DB01204)|Nicardipine(DB00622)|Nitrendipine(DB01054)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Topotecan(DB01030)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	89223116	89223117	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89223116_89223117delAA	uc003hro.2	+											Homo sapiens, clone IMAGE:5199401, mRNA.																														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89619724	89619761	+	Intron	DEL	CAAGTCTTTCTAAAGCATGGGGCCCAGGGCCAAGGCCC	-	-	rs72009992		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89619724_89619761delCAAGTCTTTCTAAAGCATGGGGCCCAGGGCCAAGGCCC	uc003hrw.1	+						HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron|NAP1L5_uc003hrx.2_5'Flank	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89720802	89720803	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89720802_89720803insT	uc003hse.1	-						FAM13A_uc003hsb.1_Intron|FAM13A_uc003hsd.1_Intron|FAM13A_uc003hsc.1_Intron|FAM13A_uc011cdq.1_Intron|FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsg.1_Intron|FAM13A_uc003hsh.1_Intron|FAM13A_uc010ikr.1_Intron	NM_014883	NP_055698			family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91170876	91170876	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91170876delT	uc003hsv.3	+						FAM190A_uc003hsu.3_Intron|FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91475347	91475348	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91475347_91475348insA	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91824988	91824988	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91824988delA	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93699387	93699387	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93699387delT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.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)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94291628	94291629	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94291628_94291629delAC	uc011cdt.1	+						GRID2_uc011cdu.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)													---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95127782	95127783	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95127782_95127783insT	uc003htc.3	+						SMARCAD1_uc003htb.3_5'Flank|SMARCAD1_uc003htd.3_5'Flank|SMARCAD1_uc010ila.2_5'Flank	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96128054	96128056	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96128054_96128056delTTT	uc003htp.1	-						UNC5C_uc010ilc.1_Intron	NM_003728	NP_003719			unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	96496881	96496882	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96496881_96496882insT								UNC5C (26719 upstream) : PDHA2 (264357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	96694558	96694559	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96694558_96694559insT								UNC5C (224396 upstream) : PDHA2 (66680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97057650	97057650	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97057650delT								PDHA2 (295026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97252249	97252249	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97252249delA	uc003hts.1	+											full-length cDNA clone CS0DI013YE21 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	98192102	98192102	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98192102delT								None (None upstream) : C4orf37 (287932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98328519	98328519	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98328519delT								None (None upstream) : C4orf37 (151515 downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98802243	98802243	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98802243delA	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	98909179	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98909178_98909179delCA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99134271	99134271	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99134271delA								C4orf37 (69880 upstream) : RAP1GDS1 (48256 downstream)																																			---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99393485	99393485	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99393485delT	uc003hub.2	-	8					TSPAN5_uc011cdz.1_3'UTR	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99408390	99408392	+	Intron	DEL	AAA	-	-	rs71588952		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99408390_99408392delAAA	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	99750907	99750908	+	IGR	INS	-	AT	AT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99750907_99750908insAT								TSPAN5 (171180 upstream) : EIF4E (48699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	99788869	99788870	+	IGR	INS	-	CT	CT	rs139507009	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99788869_99788870insCT								TSPAN5 (209142 upstream) : EIF4E (10737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101312207	101312207	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101312207delA								DDIT4L (200594 upstream) : EMCN (4293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101631529	101631530	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101631529_101631530delAC								EMCN (192279 upstream) : PPP3CA (313057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101746046	101746049	+	IGR	DEL	TTGT	-	-	rs34070770		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101746046_101746049delTTGT								EMCN (306796 upstream) : PPP3CA (198538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101760519	101760520	+	IGR	INS	-	GTTT	GTTT	rs149654563	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101760519_101760520insGTTT								EMCN (321269 upstream) : PPP3CA (184067 downstream)																																			---	---	---	---
PPP3CA	5530	broad.mit.edu	37	4	102028515	102028516	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102028515_102028516delCA	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935			protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102839362	102839362	+	Intron	DEL	A	-	-	rs3733198	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	103609544	103609545	+	Intron	DEL	AC	-	-	rs142507327		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103609544_103609545delAC	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)														---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103649712	103649712	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103649712delA	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	103714723	103714724	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103714723_103714724insT								MANBA (32572 upstream) : UBE2D3 (823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	104426002	104426003	+	IGR	INS	-	CTCCTT	CTCCTT	rs137903652	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104426002_104426003insCTCCTT								CENPE (306436 upstream) : TACR3 (84622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	105358857	105358857	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105358857delA								TACR3 (717884 upstream) : CXXC4 (34488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	105755521	105755521	+	IGR	DEL	A	-	-	rs11322824		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105755521delA								CXXC4 (339463 upstream) : TET2 (312422 downstream)																																			---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106754621	106754621	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106754621delA	uc003hxz.3	+						GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890			glutathione S-transferase, C-terminal domain							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	107227770	107227771	+	Intron	INS	-	C	C	rs146683270	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107227770_107227771insC	uc010ilv.2	-						TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	107395402	107395402	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107395402delA								AIMP1 (125023 upstream) : DKK2 (447558 downstream)																																			---	---	---	---
ELOVL6	79071	broad.mit.edu	37	4	110997062	110997062	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110997062delA	uc003hzz.2	-						ELOVL6_uc003iaa.2_Intron	NM_001130721	NP_001124193			elongation of very long chain fatty acids-like						fatty acid elongation, saturated fatty acid|long-chain fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process		fatty acid elongase activity|protein binding			haematopoietic_and_lymphoid_tissue(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00462)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111653615	111653616	+	IGR	INS	-	T	T	rs113030324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111653615_111653616insT								PITX2 (90498 upstream) : MIR297 (128122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111859602	111859603	+	IGR	INS	-	TGTG	TGTG	rs137893125	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111859602_111859603insTGTG								MIR297 (77799 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112247401	112247402	+	IGR	INS	-	CT	CT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112247401_112247402insCT								MIR297 (465598 upstream) : C4orf32 (819151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112247537	112247537	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112247537delA								MIR297 (465734 upstream) : C4orf32 (819016 downstream)																																			---	---	---	---
ALPK1	80216	broad.mit.edu	37	4	113336791	113336791	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113336791delA	uc003iap.3	+						ALPK1_uc011cfw.1_Intron|ALPK1_uc003ian.3_Intron|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Intron|ALPK1_uc010imo.2_Intron	NM_025144	NP_079420			alpha-kinase 1								ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	113650354	113650357	+	IGR	DEL	AAAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113650354_113650357delAAAC								LARP7 (71613 upstream) : ANK2 (88882 downstream)																																			---	---	---	---
ANK2	287	broad.mit.edu	37	4	114182342	114182342	+	Intron	DEL	T	-	-	rs79077724		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114182342delT	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc003ibc.2_Intron|ANK2_uc011cgb.1_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	116191720	116191721	+	IGR	INS	-	GA	GA	rs139567780	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116191720_116191721insGA								NDST4 (156688 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117618963	117618963	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117618963delT								MIR1973 (398039 upstream) : TRAM1L1 (385753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117850877	117850877	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117850877delT								MIR1973 (629953 upstream) : TRAM1L1 (153839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118076974	118076974	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118076974delA								TRAM1L1 (70238 upstream) : NDST3 (877799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118144488	118144488	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118144488delA								TRAM1L1 (137752 upstream) : NDST3 (810285 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119168362	119168363	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119168362_119168363delAA	uc003ibx.2	+							NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119229054	119229055	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119229054_119229055delAA	uc003ica.1	-							NM_003619	NP_003610			neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119239769	119239769	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119239769delT	uc003ica.1	-							NM_003619	NP_003610			neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	119305587	119305587	+	IGR	DEL	A	-	-	rs66473115		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119305587delA								PRSS12 (31665 upstream) : CEP170L (131908 downstream)																																			---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119659245	119659245	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119659245delA	uc003ici.3	-						SEC24D_uc003ich.3_Intron|SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_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																		---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120076025	120076026	+	Intron	DEL	CG	-	-	rs113489330		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120076025_120076026delCG	uc003icp.3	+							NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	121505049	121505050	+	IGR	DEL	AT	-	-	rs3085704	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121505049_121505050delAT								MAD2L1 (517036 upstream) : PRDM5 (110880 downstream)																																			---	---	---	---
QRFPR	84109	broad.mit.edu	37	4	122300772	122300772	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122300772delT	uc010inj.1	-						QRFPR_uc010ink.1_Intron|QRFPR_uc003ids.2_Intron|QRFPR_uc010inl.1_Intron	NM_198179	NP_937822			G protein-coupled receptor 103							plasma membrane	neuropeptide Y receptor activity				0																		---	---	---	---
TRPC3	7222	broad.mit.edu	37	4	122871628	122871628	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122871628delA	uc003ieg.2	-							NM_001130698	NP_001124170			transient receptor potential cation channel,						axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																OREG0016312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123164876	123164876	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123164876delA	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	125123506	125123506	+	IGR	DEL	G	-	-	rs112447742		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125123506delG								LOC285419 (271988 upstream) : ANKRD50 (461962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125248135	125248135	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125248135delA								LOC285419 (396617 upstream) : ANKRD50 (337333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125261510	125261510	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125261510delT								LOC285419 (409992 upstream) : ANKRD50 (323958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125665253	125665254	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125665253_125665254delGT								ANKRD50 (31366 upstream) : FAT4 (572313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129279951	129279965	+	IGR	DEL	ATCAGATGGTGCCAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129279951_129279965delATCAGATGGTGCCAT								PGRMC2 (71003 upstream) : PHF17 (450814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129666419	129666419	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129666419delG								PGRMC2 (457471 upstream) : PHF17 (64360 downstream)																																			---	---	---	---
SCLT1	132320	broad.mit.edu	37	4	129869491	129869491	+	Intron	DEL	A	-	-	rs145196324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129869491delA	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	130042314	130042315	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130042314_130042315delAA								C4orf33 (8472 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130147868	130147868	+	IGR	DEL	C	-	-	rs58663258		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130147868delC								C4orf33 (114026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131271265	131271266	+	IGR	INS	-	TTCC	TTCC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131271265_131271266insTTCC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131348483	131348483	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131348483delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132711161	132711161	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132711161delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132954804	132954805	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132954804_132954805insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133086496	133086499	+	IGR	DEL	TTTT	-	-	rs141948612		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133086496_133086499delTTTT								None (None upstream) : PCDH10 (983971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133753139	133753139	+	IGR	DEL	A	-	-	rs71593097		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133753139delA								None (None upstream) : PCDH10 (317331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134494858	134494858	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134494858delT								PCDH10 (382127 upstream) : PABPC4L (622633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134866293	134866293	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134866293delA								PCDH10 (753562 upstream) : PABPC4L (251198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135960778	135960783	+	IGR	DEL	GTGTGC	-	-	rs67748649		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135960778_135960783delGTGTGC								PABPC4L (837875 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136759177	136759178	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136759177_136759178insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136770585	136770586	+	IGR	DEL	TG	-	-	rs113815696		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136770585_136770586delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137400625	137400626	+	IGR	INS	-	CCTTCCTT	CCTTCCTT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137400625_137400626insCCTTCCTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137437814	137437814	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137437814delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138705783	138705783	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138705783delA								PCDH18 (252135 upstream) : SLC7A11 (379465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139213520	139213521	+	IGR	INS	-	AC	AC	rs146582130	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139213520_139213521insAC								SLC7A11 (50017 upstream) : CCRN4L (723422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139364952	139364953	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139364952_139364953insA								SLC7A11 (201449 upstream) : CCRN4L (571990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	140510182	140510182	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140510182delA								SETD7 (32605 upstream) : MGST2 (76740 downstream)																																			---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140990971	140990972	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140990971_140990972delAA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	141512284	141512285	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141512284_141512285delTG								UCP1 (22325 upstream) : TBC1D9 (29652 downstream)																																			---	---	---	---
RNF150	57484	broad.mit.edu	37	4	141867831	141867832	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141867831_141867832insT	uc003iio.1	-						RNF150_uc010iok.1_Intron|RNF150_uc003iip.1_Intron	NM_020724	NP_065775			ring finger protein 150 precursor							integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	142479329	142479329	+	IGR	DEL	G	-	-	rs35485275		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142479329delG								ZNF330 (323481 upstream) : IL15 (78425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142679138	142679139	+	IGR	DEL	AT	-	-	rs146789824	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142679138_142679139delAT								IL15 (24527 upstream) : INPP4B (270045 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143142760	143142760	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143142760delT	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)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143642974	143642974	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143642974delA	uc003iix.3	-						INPP4B_uc003iiw.3_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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144054553	144054554	+	IGR	DEL	AG	-	-	rs78763922		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144054553_144054554delAG								INPP4B (286949 upstream) : USP38 (51516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145774716	145774716	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145774716delA	uc003ijt.2	+											Homo sapiens cDNA clone IMAGE:5268539.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	145814040	145814041	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145814040_145814041delAG								HHIP (154159 upstream) : ANAPC10 (102273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	146338536	146338537	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146338536_146338537delAG								OTUD4 (237704 upstream) : SMAD1 (64414 downstream)																																			---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146834762	146834762	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146834762delA	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157			zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147167098	147167098	+	IGR	DEL	A	-	-	rs113103281		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147167098delA								LSM6 (55886 upstream) : SLC10A7 (8039 downstream)																																			---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148657271	148657272	+	Intron	INS	-	TG	TG	rs144442370	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148657271_148657272insTG	uc003ilf.2	+						ARHGAP10_uc003ile.1_Intron	NM_024605	NP_078881			Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148802420	148802421	+	Intron	DEL	AA	-	-	rs112175265		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148802420_148802421delAA	uc003ilf.2	+						ARHGAP10_uc003ilg.2_5'Flank	NM_024605	NP_078881			Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	149781932	149781933	+	IGR	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149781932_149781933insTG								NR3C2 (418289 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150933099	150933099	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150933099delA								None (None upstream) : DCLK2 (66981 downstream)																																			---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151042223	151042223	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151042223delA	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350			doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151726753	151726757	+	Intron	DEL	GAAAA	-	-	rs10549548	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151726753_151726757delGAAAA	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151739714	151739717	+	Intron	DEL	GTGC	-	-	rs67072803		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151739714_151739717delGTGC	uc010ipj.2	-						LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152059689	152059689	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152059689delA	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|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)																---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152089547	152089548	+	Intron	INS	-	TTTC	TTTC	rs148678625	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152089547_152089548insTTTC	uc010ipl.1	-						SH3D19_uc003imb.2_5'Flank|SH3D19_uc003imc.2_Intron|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)																---	---	---	---
FAM160A1	729830	broad.mit.edu	37	4	152519231	152519231	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152519231delA	uc003imj.2	+							NM_001109977	NP_001103447			hypothetical protein LOC729830												0																		---	---	---	---
PET112L	5188	broad.mit.edu	37	4	152657172	152657172	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152657172delA	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555			PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154529298	154529298	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154529298delA	uc003inm.3	+						KIAA0922_uc010ipp.2_Intron|KIAA0922_uc010ipq.2_Intron	NM_015196	NP_056011			hypothetical protein LOC23240 isoform 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154664697	154664697	+	Intron	DEL	T	-	-	rs11099896	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154664697delT	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)																---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158027744	158027744	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158027744delT	uc003ipj.2	+							NM_000824	NP_000815			glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
GRIA2	2891	broad.mit.edu	37	4	158142152	158142152	+	5'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158142152delA	uc003ipm.3	+	1					GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_5'UTR|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_5'Flank	NM_001083619	NP_001077088			glutamate receptor, ionotropic, AMPA 2 isoform 2						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	158947631	158947632	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158947631_158947632insT								LOC340017 (450336 upstream) : FAM198B (98101 downstream)																																			---	---	---	---
ETFDH	2110	broad.mit.edu	37	4	159593988	159593988	+	Intron	DEL	A	-	-	rs111870477		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159593988delA	uc003iqb.2	+						C4orf46_uc003iqa.2_5'Flank|C4orf46_uc010iqp.1_5'Flank|ETFDH_uc010iqq.2_Intron|ETFDH_uc011cjg.1_Intron|ETFDH_uc010iqr.2_Intron	NM_004453	NP_004444			electron-transferring-flavoprotein dehydrogenase						fatty acid beta-oxidation using acyl-CoA dehydrogenase|respiratory electron transport chain|response to oxidative stress|transport	integral to mitochondrial inner membrane|mitochondrial matrix	4 iron, 4 sulfur cluster binding|electron carrier activity|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity, oxidizing metal ions with flavin as acceptor|ubiquinone binding			large_intestine(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)												OREG0016379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FNIP2	57600	broad.mit.edu	37	4	159793157	159793157	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159793157delT	uc003iqe.3	+							NM_020840	NP_065891			folliculin interacting protein 2						DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	160367929	160367929	+	IGR	DEL	G	-	-	rs5863362		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160367929delG								RAPGEF2 (86630 upstream) : None (None downstream)																																	OREG0016383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	4	160969203	160969205	+	IGR	DEL	AAC	-	-	rs112582181		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160969203_160969205delAAC								RAPGEF2 (687904 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161655327	161655327	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161655327delT								None (None upstream) : FSTL5 (649724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	164097171	164097171	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164097171delG								NAF1 (9098 upstream) : NPY1R (147946 downstream)																																			---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	165089635	165089636	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165089635_165089636insA	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	165419861	165419862	+	IGR	INS	-	A	A	rs149564713	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165419861_165419862insA								MARCH1 (114659 upstream) : TRIM61 (455738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165808434	165808434	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165808434delC	uc003iqv.1	+											Homo sapiens cDNA FLJ35259 fis, clone PROST2004251.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	166469229	166469236	+	IGR	DEL	AATGTTAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166469229_166469236delAATGTTAT								CPE (49748 upstream) : TLL1 (325174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	166664756	166664757	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166664756_166664757insA								CPE (245275 upstream) : TLL1 (129653 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166942375	166942376	+	Intron	INS	-	A	A	rs148764346	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166942375_166942376insA	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	167473088	167473090	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167473088_167473090delAAA								TLL1 (448095 upstream) : SPOCK3 (181446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	167631909	167631910	+	IGR	INS	-	TAACT	TAACT	rs140159906	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167631909_167631910insTAACT								TLL1 (606916 upstream) : SPOCK3 (22626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168310748	168310748	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168310748delA								SPOCK3 (155007 upstream) : ANXA10 (702959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168402039	168402040	+	IGR	INS	-	T	T	rs71604497		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168402039_168402040insT								SPOCK3 (246298 upstream) : ANXA10 (611667 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169179590	169179590	+	Intron	DEL	T	-	-	rs112601793		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169179590delT	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)														---	---	---	---
DDX60L	91351	broad.mit.edu	37	4	169376423	169376424	+	Intron	INS	-	TGTGTGTGTG	TGTGTGTGTG	rs149946768	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169376423_169376424insTGTGTGTGTG	uc003irq.3	-						DDX60L_uc003irr.1_Intron|DDX60L_uc003irs.1_Intron	NM_001012967	NP_001012985			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169698667	169698669	+	Intron	DEL	CAG	-	-	rs77308434		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169698667_169698669delCAG	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				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169728429	169728430	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169728429_169728430delCA	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				---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170034262	170034263	+	Intron	INS	-	T	T	rs145443375	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170034262_170034263insT	uc003isa.1	-							NM_020870	NP_065921			SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)														---	---	---	---
C4orf27	54969	broad.mit.edu	37	4	170665971	170665972	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170665971_170665972delTT	uc003isl.3	-							NM_017867	NP_060337			hypothetical protein LOC54969							nucleus				ovary(1)|pancreas(1)	2		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170978523	170978523	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170978523delT								MFAP3L (31094 upstream) : AADAT (2851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171533436	171533436	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171533436delT								AADAT (522064 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172414814	172414817	+	IGR	DEL	AAAC	-	-	rs3078076		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172414814_172414817delAAAC								None (None upstream) : GALNTL6 (319758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172519145	172519145	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172519145delA								None (None upstream) : GALNTL6 (215430 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173190411	173190411	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173190411delA	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173661094	173661094	+	Intron	DEL	A	-	-	rs35229715		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173661094delA	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	175116502	175116502	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175116502delA	uc003ito.1	-											Homo sapiens cDNA FLJ43267 fis, clone IMR322007704.																														---	---	---	---
ADAM29	11086	broad.mit.edu	37	4	175884295	175884295	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175884295delA	uc003iuc.2	+						ADAM29_uc003iud.2_Intron|ADAM29_uc010irr.2_Intron|ADAM29_uc011cki.1_Intron	NM_014269	NP_055084			ADAM metallopeptidase domain 29 preproprotein						proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	176968442	176968443	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176968442_176968443delCA								GPM6A (44794 upstream) : WDR17 (18689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178071960	178071960	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178071960delA								VEGFC (358065 upstream) : NEIL3 (159031 downstream)																																			---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178675281	178675284	+	Intron	DEL	TCTG	-	-	rs33952425		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178675281_178675284delTCTG	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	179512187	179512188	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179512187_179512188delGT								LOC285501 (600284 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180316739	180316740	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180316739_180316740insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180655787	180655787	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180655787delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181059560	181059561	+	IGR	INS	-	AC	AC	rs146834444	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181059560_181059561insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181260704	181260707	+	IGR	DEL	CACA	-	-	rs10540749		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181260704_181260707delCACA								None (None upstream) : None (None downstream)																																			---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183226385	183226385	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183226385delC	uc010irv.1	+											Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184082191	184082191	+	Intron	DEL	A	-	-	rs114220084	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184082191delA	uc010irx.2	+							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	184814263	184814263	+	IGR	DEL	T	-	-	rs11347203		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184814263delT								C4orf41 (179519 upstream) : STOX2 (12246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185214013	185214014	+	IGR	INS	-	GA	GA	rs138204534	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185214013_185214014insGA								ENPP6 (74899 upstream) : IRF2 (94864 downstream)																																			---	---	---	---
ACSL1	2180	broad.mit.edu	37	4	185707571	185707572	+	Intron	INS	-	GCAC	GCAC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185707571_185707572insGCAC	uc003iww.2	-						ACSL1_uc011ckm.1_Intron|ACSL1_uc003iwt.1_Intron|ACSL1_uc003iwu.1_Intron|ACSL1_uc011ckn.1_Intron|ACSL1_uc003iwv.1_Intron	NM_001995	NP_001986			acyl-CoA synthetase long-chain family member 1						digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186268598	186268598	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186268598delT	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	NM_031953	NP_114159			sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
C4orf47	441054	broad.mit.edu	37	4	186351009	186351009	+	Intron	DEL	C	-	-	rs4862526	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186351009delC	uc003ixt.2	+						C4orf47_uc003ixs.2_Intron	NM_001114357	NP_001107829			hypothetical protein LOC441054												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	187374560	187374560	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187374560delT	uc003izb.1	-						uc003izc.2_Intron					Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187583996	187583996	+	Intron	DEL	T	-	-	rs139151945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187583996delT	uc003izf.2	-							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)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187600759	187600759	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187600759delA	uc003izf.2	-							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	188050703	188050703	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188050703delA								FAT1 (402853 upstream) : ZFP42 (866222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188346570	188346571	+	IGR	DEL	AA	-	-	rs76134112		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188346570_188346571delAA								FAT1 (698720 upstream) : ZFP42 (570354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189097555	189097572	+	IGR	DEL	GAGAGAGGGAGACAGAGG	-	-	rs36226787		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189097555_189097572delGAGAGAGGGAGACAGAGG								TRIML1 (28906 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189375685	189375686	+	Intron	DEL	AC	-	-	rs33912924		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189375685_189375686delAC	uc003izo.1	+						uc003izp.1_5'Flank					Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189689038	189689039	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189689038_189689039delGA								TRIML1 (620389 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190597992	190597993	+	IGR	INS	-	CA	CA	rs142646698		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190597992_190597993insCA								None (None upstream) : FRG1 (263981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190629252	190629262	+	IGR	DEL	ACCTAAAAGTA	-	-	rs6148862		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190629252_190629262delACCTAAAAGTA								None (None upstream) : FRG1 (232712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190650483	190650484	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190650483_190650484delGA								None (None upstream) : FRG1 (211490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190654659	190654659	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190654659delG								None (None upstream) : FRG1 (207315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190664836	190664836	+	IGR	DEL	G	-	-	rs2318576		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190664836delG								None (None upstream) : FRG1 (197138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190676591	190676592	+	IGR	INS	-	CA	CA	rs148685845		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190676591_190676592insCA								None (None upstream) : FRG1 (185382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190842430	190842431	+	Intron	INS	-	GA	GA	rs77290568		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190842430_190842431insGA	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190853948	190853949	+	Intron	INS	-	AG	AG	rs142792467	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190853948_190853949insAG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	531395	531396	+	IGR	INS	-	GGCT	GGCT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:531395_531396insGGCT								SLC9A3 (6846 upstream) : CEP72 (81009 downstream)																																			---	---	---	---
CEP72	55722	broad.mit.edu	37	5	629050	629050	+	Intron	DEL	G	-	-	rs67151603		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:629050delG	uc003jbf.2	+						CEP72_uc011clz.1_Intron	NM_018140	NP_060610			centrosomal protein 72 kDa						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	1045053	1045054	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1045053_1045054delGT								NKD2 (6128 upstream) : SLC12A7 (5437 downstream)																																			---	---	---	---
LOC728613	728613	broad.mit.edu	37	5	1606183	1606183	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1606183delA	uc003jcq.3	-						LOC728613_uc003jcp.3_Intron|LOC728613_uc003jcr.2_Intron|LOC728613_uc003jcs.2_Intron|LOC728613_uc010ith.1_Intron	NR_003713				Homo sapiens cDNA, FLJ97024.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	1960874	1960875	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1960874_1960875delCA								IRX4 (77994 upstream) : IRX2 (785406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1977040	1977040	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1977040delA								IRX4 (94160 upstream) : IRX2 (769241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2308633	2308633	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2308633delT								IRX4 (425753 upstream) : IRX2 (437648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3278084	3278084	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3278084delT								C5orf38 (522572 upstream) : IRX1 (318084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3538965	3538967	+	IGR	DEL	TTC	-	-	rs67155909		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3538965_3538967delTTC								C5orf38 (783453 upstream) : IRX1 (57201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4375566	4375567	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4375566_4375567insC								IRX1 (774050 upstream) : LOC340094 (658905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4471664	4471665	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4471664_4471665delAG								IRX1 (870148 upstream) : LOC340094 (562807 downstream)																																			---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5231120	5231121	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5231120_5231121insG	uc003jdl.2	+						ADAMTS16_uc003jdk.1_Intron	NM_139056	NP_620687			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	5531070	5531070	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5531070delT								KIAA0947 (40733 upstream) : FLJ33360 (779484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5636849	5636849	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5636849delG								KIAA0947 (146512 upstream) : FLJ33360 (673705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6435837	6435838	+	IGR	INS	-	TTC	TTC	rs138704154	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6435837_6435838insTTC								MED10 (57198 upstream) : UBE2QL1 (12898 downstream)																																			---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9830298	9830299	+	Intron	INS	-	GGAC	GGAC	rs150244702	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9830298_9830299insGGAC	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10489309	10489320	+	IGR	DEL	AGAGAGAGAGAC	-	-	rs71582424		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10489309_10489320delAGAGAGAGAGAC								ROPN1L (24172 upstream) : DAP (190023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10938096	10938096	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10938096delG								DAP (176709 upstream) : CTNND2 (33856 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11304431	11304432	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11304431_11304432delCA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	12734392	12734392	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12734392delA	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	13609764	13609764	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13609764delT								None (None upstream) : DNAH5 (80673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14025974	14025974	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14025974delA								DNAH5 (81385 upstream) : TRIO (117855 downstream)																																			---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16115153	16115153	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16115153delA	uc003jfo.2	-							NM_001102562	NP_001096032			membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17644548	17644549	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17644548_17644549insA								BASP1 (367613 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18406748	18406748	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18406748delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18722538	18722538	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18722538delA								None (None upstream) : CDH18 (750619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20404594	20404594	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20404594delT								CDH18 (416287 upstream) : GUSBP1 (937348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20719223	20719223	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20719223delT	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																														---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21539615	21539616	+	Intron	INS	-	TA	TA	rs143282782	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21539615_21539616insTA	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																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21543501	21543501	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21543501delT	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																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21547416	21547417	+	Intron	INS	-	G	G	rs143671141		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21547416_21547417insG	uc003jgh.3	+							NR_027026				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	21755645	21755645	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21755645delA	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron|uc003jgj.2_Intron	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)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22202275	22202278	+	Intron	DEL	CCTC	-	-	rs72243697		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22202275_22202278delCCTC	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	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)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22486743	22486743	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22486743delG	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)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22651811	22651813	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22651811_22651813delTTT	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)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24516012	24516012	+	Intron	DEL	T	-	-	rs34653438		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24516012delT	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718			cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24668792	24668792	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24668792delT								CDH10 (23881 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26033084	26033087	+	IGR	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26033084_26033087delAAAA								None (None upstream) : CDH9 (847622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26694931	26694931	+	IGR	DEL	A	-	-	rs79310249		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26694931delA								None (None upstream) : CDH9 (185778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26721985	26721986	+	IGR	INS	-	AGA	AGA	rs141888888	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26721985_26721986insAGA								None (None upstream) : CDH9 (158723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30034091	30034091	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30034091delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30656647	30656647	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30656647delA								None (None upstream) : CDH6 (537149 downstream)																																			---	---	---	---
CDH6	1004	broad.mit.edu	37	5	31200675	31200676	+	Intron	DEL	AC	-	-	rs10533381		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31200675_31200676delAC	uc003jhe.1	+						CDH6_uc003jhc.1_Intron|CDH6_uc003jhd.1_Intron	NM_004932	NP_004923			cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7																		---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31551840	31551841	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31551840_31551841insG	uc003jhj.3	+						C5orf22_uc003jhk.3_Intron|C5orf22_uc010iuj.2_Intron	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32206569	32206569	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32206569delT								GOLPH3 (32144 upstream) : MTMR12 (20543 downstream)																																			---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32739289	32739289	+	Intron	DEL	G	-	-	rs58981865		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739289delG	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	32817230	32817231	+	IGR	DEL	AC	-	-	rs35340563		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32817230_32817231delAC								C5orf23 (25411 upstream) : TARS (623571 downstream)																																			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33852008	33852009	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33852008_33852009delCA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
TTC23L	153657	broad.mit.edu	37	5	34880572	34880572	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34880572delT	uc003jiu.2	+							NM_144725	NP_653326			tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1																		---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35664381	35664381	+	Intron	DEL	A	-	-	rs34622548		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35664381delA	uc003jjo.2	+						SPEF2_uc003jjn.1_Intron|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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36528575	36528575	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36528575delA								RANBP3L (226564 upstream) : SLC1A3 (77882 downstream)																																			---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37179347	37179347	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37179347delT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	38028104	38028105	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38028104_38028105insA								GDNF (188322 upstream) : EGFLAM (230428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	38611462	38611462	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38611462delC	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38655341	38655341	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38655341delT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38660049	38660049	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38660049delT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38709114	38709115	+	IGR	INS	-	G	G	rs148054263	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38709114_38709115insG								LIFR (113607 upstream) : OSMR (137013 downstream)																																			---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38958957	38958957	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38958957delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_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)																	---	---	---	---
FYB	2533	broad.mit.edu	37	5	39130175	39130175	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39130175delA	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367			FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
FYB	2533	broad.mit.edu	37	5	39245705	39245707	+	Intron	DEL	TTT	-	-	rs35932165		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39245705_39245707delTTT	uc011cpl.1	-							NM_001465	NP_001456			FYN binding protein (FYB-120/130) isoform 1						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
FYB	2533	broad.mit.edu	37	5	39261408	39261408	+	Intron	DEL	A	-	-	rs34116289		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39261408delA	uc011cpl.1	-							NM_001465	NP_001456			FYN binding protein (FYB-120/130) isoform 1						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	39786293	39786293	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39786293delT								DAB2 (360958 upstream) : PTGER4 (893739 downstream)																																			---	---	---	---
CARD6	84674	broad.mit.edu	37	5	40846119	40846120	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40846119_40846120delTT	uc003jmg.2	+							NM_032587	NP_115976			caspase recruitment domain family, member 6						apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
CARD6	84674	broad.mit.edu	37	5	40852067	40852068	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40852067_40852068delAA	uc003jmg.2	+							NM_032587	NP_115976			caspase recruitment domain family, member 6						apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	42963434	42963434	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42963434delA								SEPP1 (137436 upstream) : C5orf39 (75749 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42972490	42972491	+	IGR	INS	-	G	G	rs149907564	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42972490_42972491insG								SEPP1 (146492 upstream) : C5orf39 (66692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	43071890	43071890	+	Intron	DEL	T	-	-	rs68155609		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43071890delT	uc010ivk.2	+											Homo sapiens cDNA, FLJ18440.																														---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43227090	43227090	+	Intron	DEL	A	-	-	rs116815779	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43227090delA	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
CCL28	56477	broad.mit.edu	37	5	43401185	43401185	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43401185delA	uc003jnu.2	-						CCL28_uc003jns.2_Intron|CCL28_uc003jnt.2_Intron	NM_148672	NP_683513			chemokine (C-C motif) ligand 28 precursor						chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2																		---	---	---	---
CCL28	56477	broad.mit.edu	37	5	43402983	43402983	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43402983delA	uc003jnu.2	-						CCL28_uc003jns.2_Intron|CCL28_uc003jnt.2_Intron	NM_148672	NP_683513			chemokine (C-C motif) ligand 28 precursor						chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2																		---	---	---	---
NNT	23530	broad.mit.edu	37	5	43651679	43651680	+	Intron	INS	-	A	A	rs112687077		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43651679_43651680insA	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	46093820	46093821	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46093820_46093821insA								HCN1 (397600 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51229840	51229840	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51229840delT								ISL1 (539283 upstream) : ITGA1 (853934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51813287	51813287	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51813287delA								None (None upstream) : ITGA1 (270487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51902779	51902780	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51902779_51902780delAA								None (None upstream) : ITGA1 (180994 downstream)																																			---	---	---	---
ITGA1	3672	broad.mit.edu	37	5	52093299	52093299	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52093299delA	uc003jou.2	+						ITGA1_uc003jov.2_Intron|PELO_uc003jos.2_Intron|PELO_uc003jot.1_Intron	NM_181501	NP_852478			integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	52806792	52806792	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52806792delT								FST (24890 upstream) : NDUFS4 (49673 downstream)																																			---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53541969	53541969	+	Intron	DEL	T	-	-	rs11318745		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53541969delT	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	54005419	54005419	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54005419delT								SNX18 (163004 upstream) : ESM1 (268277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	54861589	54861589	+	IGR	DEL	A	-	-	rs79028324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54861589delA								PPAP2A (30716 upstream) : SLC38A9 (60087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55944096	55944097	+	IGR	DEL	CA	-	-	rs67057009		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55944096_55944097delCA								ANKRD55 (414910 upstream) : MAP3K1 (166803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55989059	55989059	+	IGR	DEL	G	-	-	rs35227224		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55989059delG								ANKRD55 (459873 upstream) : MAP3K1 (121841 downstream)																																			---	---	---	---
C5orf35	133383	broad.mit.edu	37	5	56210885	56210885	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56210885delT	uc003jqx.2	+						C5orf35_uc003jqy.2_Intron	NM_153706	NP_714917			hypothetical protein LOC133383											ovary(1)	1		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.173)		OV - Ovarian serous cystadenocarcinoma(10;2.58e-39)														---	---	---	---
GPBP1	65056	broad.mit.edu	37	5	56505447	56505448	+	Intron	INS	-	T	T	rs145185917	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56505447_56505448insT	uc003jrh.3	+						GPBP1_uc010iwg.2_Intron|GPBP1_uc003jri.3_Intron|GPBP1_uc003jrj.3_Intron	NM_022913	NP_075064			GC-rich promoter binding protein 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	57376556	57376556	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57376556delT								ACTBL2 (597920 upstream) : PLK2 (373256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57521188	57521188	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57521188delG								ACTBL2 (742552 upstream) : PLK2 (228624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57802082	57802082	+	IGR	DEL	A	-	-	rs34069555		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57802082delA								GAPT (9897 upstream) : RAB3C (76857 downstream)																																			---	---	---	---
ELOVL7	79993	broad.mit.edu	37	5	60129975	60129975	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60129975delT	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)																---	---	---	---
ERCC8	1161	broad.mit.edu	37	5	60180842	60180843	+	Intron	DEL	TT	-	-	rs149604237		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60180842_60180843delTT	uc003jsm.3	-						ERCC8_uc003jsk.2_Intron|ERCC8_uc003jsl.3_Intron|ERCC8_uc011cqp.1_Intron	NM_000082	NP_000073			excision repair cross-complementing rodent						positive regulation of DNA repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein polyubiquitination|response to oxidative stress|response to UV|response to UV|transcription-coupled nucleotide-excision repair	Cul4A-RING ubiquitin ligase complex|nuclear matrix|nucleoplasm|nucleotide-excision repair complex|soluble fraction	protein binding|protein complex binding				0		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)											Direct_reversal_of_damage|NER					---	---	---	---
ZSWIM6	57688	broad.mit.edu	37	5	60789950	60789951	+	Intron	DEL	CA	-	-	rs34538330		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60789950_60789951delCA	uc003jsr.2	+							NM_020928	NP_065979			zinc finger, SWIM-type containing 6								zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	61233089	61233089	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61233089delT								FLJ37543 (230727 upstream) : KIF2A (368900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61257989	61257990	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61257989_61257990delTT								FLJ37543 (255627 upstream) : KIF2A (343999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61370248	61370248	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61370248delA								FLJ37543 (367886 upstream) : KIF2A (231741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61412199	61412199	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61412199delT								FLJ37543 (409837 upstream) : KIF2A (189790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61948818	61948818	+	IGR	DEL	C	-	-	rs78170917		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61948818delC								IPO11 (24403 upstream) : ISCA1P1 (122384 downstream)																																			---	---	---	---
RNF180	285671	broad.mit.edu	37	5	63494646	63494646	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63494646delT	uc003jti.2	+						RNF180_uc003jth.3_Intron|RNF180_uc010iws.2_Intron	NM_001113561	NP_001107033			ring finger protein 180 isoform 1							integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)														---	---	---	---
RGS7BP	401190	broad.mit.edu	37	5	63805383	63805383	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63805383delT	uc003jtj.2	+							NM_001029875	NP_001025046			regulator of G-protein signaling 7 binding						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane					0		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)														---	---	---	---
SFRS12IP1	285672	broad.mit.edu	37	5	64023941	64023941	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64023941delT	uc003jtk.2	-	4	423	c.271delA	c.(271-273)AGGfs	p.R91fs		NM_173829	NP_776190	Q8N9Q2	SR1IP_HUMAN	P18SRP protein	91	Lys-rich.				mRNA processing|RNA splicing		nucleic acid binding|zinc ion binding				0		Lung NSC(167;1.66e-05)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.119)														---	---	---	---
SGTB	54557	broad.mit.edu	37	5	65001368	65001368	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65001368delC	uc003jud.2	-							NM_019072	NP_061945			small glutamine-rich tetratricopeptide repeat								binding				0		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65095745	65095745	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65095745delA	uc003juf.2	+						NLN_uc003jug.2_Intron|NLN_uc010iww.2_Intron	NM_020726	NP_065777			neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65495568	65495568	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65495568delA								SFRS12 (18856 upstream) : MAST4 (396608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	65520224	65520224	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65520224delT								SFRS12 (43512 upstream) : MAST4 (371952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	65701658	65701659	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65701658_65701659insT								SFRS12 (224946 upstream) : MAST4 (190517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66879364	66879364	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66879364delT								CD180 (386747 upstream) : PIK3R1 (632240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67269911	67269911	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67269911delT								CD180 (777294 upstream) : PIK3R1 (241693 downstream)																																			---	---	---	---
PIK3R1	5295	broad.mit.edu	37	5	67592579	67592580	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67592579_67592580delAA	uc003jva.2	+						PIK3R1_uc003jvb.2_Intron|PIK3R1_uc003jvc.2_Intron|PIK3R1_uc003jvd.2_Intron|PIK3R1_uc003jve.2_Intron	NM_181523	NP_852664			phosphoinositide-3-kinase, regulatory subunit 1						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			---	---	---	---
SLC30A5	64924	broad.mit.edu	37	5	68423678	68423679	+	Intron	INS	-	GG	GG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68423678_68423679insGG	uc003jvh.2	+						SLC30A5_uc003jvj.2_Intron|SLC30A5_uc003jvk.2_Intron	NM_022902	NP_075053			solute carrier family 30 (zinc transporter),						cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity			central_nervous_system(1)	1		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70761707	70761707	+	Intron	DEL	A	-	-	rs71612562		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70761707delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72561354	72561354	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72561354delG								TMEM174 (90386 upstream) : FOXD1 (180733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72608843	72608845	+	IGR	DEL	TCT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72608843_72608845delTCT								TMEM174 (137875 upstream) : FOXD1 (133242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72838168	72838168	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72838168delT								BTF3 (36720 upstream) : ANKRA2 (9995 downstream)																																			---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74135799	74135799	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74135799delA	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	74250028	74250028	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74250028delG								FAM169A (58240 upstream) : GCNT4 (73262 downstream)																																			---	---	---	---
ANKRD31	256006	broad.mit.edu	37	5	74464561	74464561	+	Intron	DEL	A	-	-	rs34439861		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74464561delA	uc003kdo.1	-											Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.												0																		---	---	---	---
ANKRD31	256006	broad.mit.edu	37	5	74533259	74533259	+	5'Flank	DEL	T	-	-	rs76548666		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74533259delT	uc003kdo.1	-											Homo sapiens cDNA FLJ40191 fis, clone TESTI2019280, weakly similar to Homo sapiens nasopharyngeal carcinoma susceptibility protein LZ16 mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	75302626	75302626	+	IGR	DEL	T	-	-	rs34151061		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75302626delT								POC5 (289313 upstream) : SV2C (76679 downstream)																																			---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75531599	75531599	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75531599delT	uc003kei.1	+							NM_014979	NP_055794			synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	75671610	75671611	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75671610_75671611delAG								SV2C (50194 upstream) : IQGAP2 (27538 downstream)																																			---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75787809	75787809	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75787809delT	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)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75908636	75908636	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75908636delC	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	76229737	76229738	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76229737_76229738insT								S100Z (12682 upstream) : CRHBP (18942 downstream)																																			---	---	---	---
LOC728723	728723	broad.mit.edu	37	5	76388578	76388579	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76388578_76388579delAA	uc010izz.2	+						LOC728723_uc011csx.1_Intron|LOC728723_uc003key.2_Intron|LOC728723_uc003kez.2_Intron|LOC728723_uc003kex.2_Intron					Homo sapiens cDNA FLJ30582 fis, clone BRAWH2007308.												0																		---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76523233	76523233	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76523233delT	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)														---	---	---	---
DMGDH	29958	broad.mit.edu	37	5	78294993	78294993	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78294993delA	uc003kfs.2	-							NM_013391	NP_037523			dimethylglycine dehydrogenase precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	78508495	78508496	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78508495_78508496delAA								BHMT (80383 upstream) : JMY (23458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79190793	79190794	+	IGR	INS	-	G	G	rs147424041	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79190793_79190794insG								CMYA5 (94745 upstream) : MTX3 (81747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79405423	79405425	+	IGR	DEL	AAG	-	-	rs35038295	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79405423_79405425delAAG								THBS4 (26318 upstream) : SERINC5 (2049 downstream)																																			---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79809324	79809324	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79809324delT	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	79850424	79850424	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79850424delG								FAM151B (12218 upstream) : ANKRD34B (2151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	80248526	80248526	+	IGR	DEL	A	-	-	rs72429792		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80248526delA								MSH3 (75893 upstream) : RASGRF2 (8032 downstream)																																			---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80443093	80443093	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80443093delT	uc003kha.1	+						RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840			Ras protein-specific guanine						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81064651	81064651	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81064651delA								SSBP2 (17579 upstream) : ATG10 (203193 downstream)																																			---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81463889	81463889	+	Intron	DEL	T	-	-	rs34095396		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81463889delT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81953447	81953447	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81953447delT								ATP6AP1L (339301 upstream) : TMEM167A (395220 downstream)																																			---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82865856	82865856	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82865856delA	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Intron	NM_004385	NP_004376			versican isoform 1 precursor						cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
HAPLN1	1404	broad.mit.edu	37	5	83003138	83003138	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83003138delC	uc003kin.2	-							NM_001884	NP_001875			hyaluronan and proteoglycan link protein 1						cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding			large_intestine(3)|ovary(1)|skin(1)	5		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	84159381	84159381	+	IGR	DEL	C	-	-	rs116388363	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84159381delC								EDIL3 (478770 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84160377	84160378	+	IGR	INS	-	A	A	rs151258630	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84160377_84160378insA								EDIL3 (479766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84585005	84585005	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84585005delA								EDIL3 (904394 upstream) : NBPF22P (993257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84997162	84997163	+	IGR	DEL	AC	-	-	rs5869294		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84997162_84997163delAC								None (None upstream) : NBPF22P (581099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85820370	85820370	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85820370delT								NBPF22P (227008 upstream) : COX7C (93414 downstream)																																			---	---	---	---
RASA1	5921	broad.mit.edu	37	5	86671080	86671080	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86671080delT	uc003kiw.2	+						RASA1_uc010jav.2_Intron|RASA1_uc003kix.2_Intron|RASA1_uc011ctv.1_Intron|RASA1_uc011ctw.1_Intron|RASA1_uc010jaw.2_Intron	NM_002890	NP_002881			RAS p21 protein activator 1 isoform 1						cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(3)|ovary(1)|lung(1)	5		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	86891382	86891382	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86891382delT								CCNH (182546 upstream) : TMEM161B (599642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87103655	87103655	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87103655delA								CCNH (394819 upstream) : TMEM161B (387369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87128799	87128799	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87128799delT								CCNH (419963 upstream) : TMEM161B (362225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87457066	87457066	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87457066delA								CCNH (748230 upstream) : TMEM161B (33958 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87507233	87507234	+	Intron	INS	-	A	A	rs141333825	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87507233_87507234insA	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)														---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87842333	87842333	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87842333delA	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	88238277	88238277	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88238277delA	uc003kjn.1	+											Homo sapiens mRNA; cDNA DKFZp586I041 (from clone DKFZp586I041).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	88570176	88570177	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88570176_88570177delCA								MEF2C (370307 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88591601	88591601	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88591601delA								MEF2C (391732 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89103502	89103502	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89103502delT								MEF2C (903633 upstream) : CETN3 (586029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89419602	89419602	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89419602delT								None (None upstream) : CETN3 (269929 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90406703	90406704	+	Intron	INS	-	G	G	rs144178227	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90406703_90406704insG	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91098139	91098139	+	IGR	DEL	A	-	-	rs36010568		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91098139delA								LOC100129716 (381608 upstream) : None (None downstream)																																			---	---	---	---
ARSK	153642	broad.mit.edu	37	5	94938845	94938845	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94938845delA	uc003kld.2	+						ARSK_uc010jbg.2_Intron|ARSK_uc011cum.1_Intron	NM_198150	NP_937793			arylsulfatase K precursor							extracellular region	arylsulfatase activity|metal ion binding			pancreas(1)	1		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	95203949	95203950	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95203949_95203950insA								C5orf27 (8115 upstream) : ELL2 (16854 downstream)																																			---	---	---	---
LNPEP	4012	broad.mit.edu	37	5	96319154	96319154	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96319154delT	uc003kmv.1	+						LNPEP_uc003kmw.1_Intron	NM_005575	NP_005566			leucyl/cystinyl aminopeptidase isoform 1						cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	99055053	99055054	+	IGR	INS	-	CA	CA	rs143133859	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99055053_99055054insCA								CHD1 (792815 upstream) : LOC100133050 (660155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99753074	99753074	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99753074delA								LOC100133050 (29116 upstream) : FAM174A (118050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99839937	99839938	+	Intron	INS	-	AT	AT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99839937_99839938insAT	uc003kni.2	-											full-length cDNA clone CS0DJ013YK21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	100123676	100123676	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100123676delC								FAM174A (201236 upstream) : ST8SIA4 (18964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101320815	101320815	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101320815delT								None (None upstream) : SLCO4C1 (248879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103097322	103097325	+	IGR	DEL	TGTG	-	-	rs148129896		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103097322_103097325delTGTG								NUDT12 (198832 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103311351	103311351	+	IGR	DEL	A	-	-	rs74827938		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103311351delA								NUDT12 (412861 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104255866	104255866	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104255866delA	uc003koj.1	-											full-length cDNA clone CS0DI081YP23 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	105455614	105455615	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105455614_105455615delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105614320	105614323	+	IGR	DEL	TGTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105614320_105614323delTGTG								None (None upstream) : None (None downstream)																																			---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107641190	107641190	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107641190delA	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	107896561	107896562	+	IGR	INS	-	T	T	rs137877781	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107896561_107896562insT								FBXL17 (178762 upstream) : FER (186961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108605207	108605208	+	IGR	INS	-	AAG	AAG	rs147392120	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108605207_108605208insAAG								FER (81834 upstream) : PJA2 (65203 downstream)																																			---	---	---	---
PJA2	9867	broad.mit.edu	37	5	108726032	108726032	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108726032delT	uc003kos.3	-							NM_014819	NP_055634			praja 2, RING-H2 motif containing						long-term memory|regulation of protein kinase A signaling cascade	cell junction|endoplasmic reticulum membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	ligase activity|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108989076	108989077	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108989076_108989077insT								PJA2 (243401 upstream) : MAN2A1 (36079 downstream)																																			---	---	---	---
CAMK4	814	broad.mit.edu	37	5	110621445	110621445	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110621445delT	uc011cvj.1	+						CAMK4_uc003kpf.2_Intron|CAMK4_uc010jbv.2_Intron	NM_001744	NP_001735			calcium/calmodulin-dependent protein kinase IV						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111240696	111240697	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111240696_111240697delTC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	111472493	111472493	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111472493delA								C5orf13 (159865 upstream) : EPB41L4A (5645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	111947762	111947762	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111947762delA								FLJ11235 (191089 upstream) : APC (95456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	112846078	112846079	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112846078_112846079delAA								MCC (21551 upstream) : YTHDC2 (3331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113306968	113306968	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113306968delA								YTHDC2 (375989 upstream) : KCNN2 (391048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	114181350	114181350	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114181350delA								KCNN2 (349154 upstream) : TRIM36 (279117 downstream)																																			---	---	---	---
TRIM36	55521	broad.mit.edu	37	5	114491759	114491759	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114491759delA	uc003kqs.2	-						TRIM36_uc011cwc.1_Intron|TRIM36_uc003kqt.2_Intron	NM_018700	NP_061170			tripartite motif-containing 36 isoform 1							acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding			ovary(4)|lung(2)|breast(2)	8		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	114639624	114639624	+	IGR	DEL	A	-	-	rs72308188		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114639624delA								CCDC112 (7166 upstream) : FEM1C (216984 downstream)																																			---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115822792	115822792	+	Intron	DEL	A	-	-	rs111384042		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115822792delA	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847			sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	116007267	116007268	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116007267_116007268delAG								SEMA6A (96716 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116040874	116040876	+	IGR	DEL	AAA	-	-	rs75632061		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116040874_116040876delAAA								SEMA6A (130323 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116413968	116413968	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116413968delA								SEMA6A (503417 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117341707	117341707	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117341707delA								None (None upstream) : DTWD2 (830864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	118034347	118034350	+	IGR	DEL	CACA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118034347_118034350delCACA								None (None upstream) : DTWD2 (138221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	118123307	118123308	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118123307_118123308delTT								None (None upstream) : DTWD2 (49263 downstream)																																			---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118544543	118544543	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118544543delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron	NM_005509	NP_005500			Dmx-like 1											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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	119256802	119256802	+	IGR	DEL	T	-	-	rs113161080		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119256802delT								FAM170A (285286 upstream) : PRR16 (543217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119525571	119525571	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119525571delC								FAM170A (554055 upstream) : PRR16 (274448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122025437	122025437	+	Intron	DEL	A	-	-	rs11292537		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122025437delA	uc003ktd.2	-											Homo sapiens, clone IMAGE:5171821, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	122569136	122569137	+	IGR	DEL	AG	-	-	rs150146979	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122569136_122569137delAG								PRDM6 (45392 upstream) : CEP120 (111443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122569136	122569137	+	IGR	INS	-	GG	GG	rs150146979	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122569136_122569137insGG								PRDM6 (45392 upstream) : CEP120 (111443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122790388	122790388	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122790388delT								CEP120 (31136 upstream) : CSNK1G3 (57405 downstream)																																			---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123998505	123998506	+	Intron	INS	-	AC	AC	rs148333298	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123998505_123998506insAC	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Intron|ZNF608_uc003ktt.1_Intron	NM_020747	NP_065798			zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124031881	124031883	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124031881_124031883delAAA	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Intron|ZNF608_uc003ktt.1_Intron	NM_020747	NP_065798			zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124035680	124035680	+	Intron	DEL	C	-	-	rs11289646		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124035680delC	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Intron|ZNF608_uc003ktt.1_Intron	NM_020747	NP_065798			zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	124564046	124564047	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124564046_124564047delTT								ZNF608 (479546 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125632656	125632656	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125632656delA								None (None upstream) : GRAMD3 (63132 downstream)																																			---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125785750	125785750	+	Intron	DEL	T	-	-	rs74504299		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125785750delT	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwu.1_Intron	NM_023927	NP_076416			GRAM domain containing 3 isoform 2											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	125987648	125987655	+	IGR	DEL	AAGGAAGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125987648_125987655delAAGGAAGG								C5orf48 (15674 upstream) : LMNB1 (125178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	126073462	126073462	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126073462delA								C5orf48 (101488 upstream) : LMNB1 (39371 downstream)																																			---	---	---	---
FLJ33630	644873	broad.mit.edu	37	5	127295317	127295317	+	Intron	DEL	T	-	-	rs5871287		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127295317delT	uc003kun.2	-						FLJ33630_uc003kuo.2_Intron					Homo sapiens full length insert cDNA clone ZD74E10.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	128391260	128391261	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128391260_128391261insT								SLC27A6 (21926 upstream) : ISOC1 (39181 downstream)																																			---	---	---	---
CHSY3	337876	broad.mit.edu	37	5	129326070	129326071	+	Intron	INS	-	GT	GT	rs142840698	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129326070_129326071insGT	uc003kvd.2	+							NM_175856	NP_787052			chondroitin sulfate synthase 3							Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	130466607	130466608	+	IGR	DEL	AA	-	-	rs145310143		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130466607_130466608delAA								CHSY3 (944281 upstream) : HINT1 (28267 downstream)																																			---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130850421	130850421	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130850421delA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_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)														---	---	---	---
ACSL6	23305	broad.mit.edu	37	5	131174267	131174268	+	Intron	INS	-	T	T	rs140363823	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131174267_131174268insT	uc003kvv.1	-							NM_015256				acyl-CoA synthetase long-chain family member 6						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	132132298	132132298	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132132298delT								SEPT8 (18737 upstream) : ANKRD43 (16735 downstream)																																			---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132259064	132259067	+	Intron	DEL	GAGA	-	-	rs150967298		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132259064_132259067delGAGA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron	NM_014423	NP_055238			ALL1 fused gene from 5q31						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)															---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132262051	132262051	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132262051delA	uc003kyd.2	-						AFF4_uc011cxk.1_Intron|AFF4_uc003kye.1_Intron	NM_014423	NP_055238			ALL1 fused gene from 5q31						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	132381506	132381506	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132381506delA								ZCCHC10 (19266 upstream) : HSPA4 (6156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	133014253	133014254	+	IGR	INS	-	GT	GT	rs145518575	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133014253_133014254insGT								FSTL4 (66030 upstream) : C5orf15 (276945 downstream)																																			---	---	---	---
SEC24A	10802	broad.mit.edu	37	5	134017933	134017934	+	Intron	DEL	AA	-	-	rs79922505		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134017933_134017934delAA	uc003kzs.2	+						SEC24A_uc011cxu.1_Intron	NM_021982	NP_068817			SEC24 related gene family, member A						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			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	134500797	134500798	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134500797_134500798delTT	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	134777090	134777091	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134777090_134777091delGT								H2AFY (41513 upstream) : C5orf20 (2814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	134867718	134867718	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134867718delC								TIFAB (79629 upstream) : NEUROG1 (2262 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136658655	136658656	+	Intron	INS	-	AG	AG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136658655_136658656insAG	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
CDC23	8697	broad.mit.edu	37	5	137528539	137528539	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137528539delA	uc003lcl.2	-							NM_004661	NP_004652			cell division cycle protein 23						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1 phase of mitotic cell cycle|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase plate congression|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination|regulation of exit from mitosis	anaphase-promoting complex|cytosol|nucleoplasm	binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	137884087	137884098	+	IGR	DEL	GTGTGTGTGTGT	-	-	rs71941272		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137884087_137884098delGTGTGTGTGTGT								ETF1 (5155 upstream) : HSPA9 (6927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	138040185	138040187	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138040185_138040187delTTT								HSPA9 (129070 upstream) : CTNNA1 (48920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	138920579	138920580	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138920579_138920580delAA								TMEM173 (58287 upstream) : UBE2D2 (20171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	139135142	139135143	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139135142_139135143delTG								CXXC5 (72462 upstream) : PSD2 (40263 downstream)																																			---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139406737	139406737	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139406737delA	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874			neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139535361	139535361	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139535361delA								C5orf53 (26970 upstream) : C5orf32 (19292 downstream)																																			---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140191637	140191638	+	Intron	INS	-	T	T	rs10064118		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140191637_140191638insT	uc003lhb.2	+						PCDHA1_uc003lha.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron	NM_018900	NP_061723			protocadherin alpha 1 isoform 1 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	140495863	140495863	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140495863delA								PCDHB3 (12458 upstream) : PCDHB4 (5718 downstream)																																			---	---	---	---
PCDHGA2	56113	broad.mit.edu	37	5	140757172	140757173	+	Intron	INS	-	A	A	rs71576112		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140757172_140757173insA	uc003ljk.1	+						PCDHGA1_uc003lji.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	NM_018915	NP_061738			protocadherin gamma subfamily A, 2 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	142652510	142652510	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142652510delT								ARHGAP26 (43939 upstream) : NR3C1 (4987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	145110254	145110254	+	IGR	DEL	A	-	-	rs75894060		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145110254delA								None (None upstream) : PRELID2 (28328 downstream)																																			---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146148452	146148452	+	Intron	DEL	T	-	-	rs66618231		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146148452delT	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567			beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147302992	147302992	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147302992delT								C5orf46 (16891 upstream) : SPINK5 (140543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	147408035	147408035	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147408035delT								C5orf46 (121934 upstream) : SPINK5 (35500 downstream)																																			---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148210598	148210598	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148210598delT	uc003lpp.1	-							NM_024577				SH3 domain and tetratricopeptide repeats 2								binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
GRPEL2	134266	broad.mit.edu	37	5	148729782	148729782	+	Intron	DEL	C	-	-	rs78081934	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148729782delC	uc003lqj.2	+						GRPEL2_uc011dca.1_Intron	NM_152407	NP_689620			GrpE-like 2, mitochondrial precursor						protein folding	mitochondrial matrix	adenyl-nucleotide exchange factor activity|chaperone binding|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	149078117	149078125	+	IGR	DEL	GAAATGGTT	-	-	rs72107553		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149078117_149078125delGAAATGGTT								ARHGEF37 (63590 upstream) : PPARGC1B (31739 downstream)																																			---	---	---	---
HMGXB3	22993	broad.mit.edu	37	5	149409151	149409152	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149409151_149409152insT	uc003lrk.3	+							NM_014983	NP_055798			HMG box domain containing 3							nucleus	DNA binding|kinase activity			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	149721514	149721515	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149721514_149721515delTC								ARSI (38989 upstream) : TCOF1 (15687 downstream)																																			---	---	---	---
SYNPO	11346	broad.mit.edu	37	5	150008132	150008132	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150008132delA	uc003lsn.2	+							NM_001109974	NP_001103444			synaptopodin isoform B						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)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150788561	150788561	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150788561delT	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	151639270	151639270	+	Intron	DEL	C	-	-	rs67720382		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151639270delC	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	153819551	153819552	+	Intron	INS	-	T	T	rs137875046	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153819551_153819552insT	uc003lvi.2	-											Homo sapiens cDNA FLJ38109 fis, clone D3OST2001788.																														---	---	---	---
MRPL22	29093	broad.mit.edu	37	5	154342287	154342287	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154342287delG	uc003lvy.3	+						MRPL22_uc003lvz.3_Intron	NM_014180	NP_054899			mitochondrial ribosomal protein L22 isoform a						translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155226739	155226740	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155226739_155226740delTT	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	155230547	155230548	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155230547_155230548insA	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	155407816	155407816	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155407816delA	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	155635909	155635909	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155635909delT	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	156063254	156063255	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156063254_156063255insA	uc003lwd.3	+						SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
HAVCR2	84868	broad.mit.edu	37	5	156537810	156537810	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156537810delT	uc003lwk.1	-						HAVCR2_uc003lwl.2_5'Flank	NM_032782	NP_116171			T cell immunoglobulin mucin 3 precursor							integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156772458	156772458	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156772458delT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron|C5orf40_uc003lwu.2_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156777885	156777885	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156777885delT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157472364	157472364	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157472364delA								CLINT1 (186196 upstream) : EBF1 (650560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159334942	159334943	+	IGR	DEL	TC	-	-	rs112786409		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159334942_159334943delTC								LOC285627 (441658 upstream) : ADRA1B (8797 downstream)																																			---	---	---	---
SLU7	10569	broad.mit.edu	37	5	159839544	159839545	+	Intron	DEL	AG	-	-	rs67184721	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159839544_159839545delAG	uc003lyg.2	-							NM_006425	NP_006416			step II splicing factor SLU7						alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding			ovary(1)	1	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	160578625	160578625	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160578625delA								LOC285629 (212992 upstream) : GABRB2 (136811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161097475	161097475	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161097475delG								GABRB2 (122345 upstream) : GABRA6 (15183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161922280	161922280	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161922280delA								GABRG2 (339736 upstream) : CCNG1 (942297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162427327	162427327	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162427327delA								GABRG2 (844783 upstream) : CCNG1 (437250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162696400	162696401	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162696400_162696401insT								None (None upstream) : CCNG1 (168176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163517806	163517807	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163517806_163517807delAC								MAT2B (571473 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164521242	164521242	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164521242delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164817419	164817419	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164817419delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166627161	166627162	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166627161_166627162delTG								None (None upstream) : ODZ2 (84681 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167402458	167402460	+	Intron	DEL	TTT	-	-	rs113523777		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167402458_167402460delTTT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168217738	168217738	+	Intron	DEL	A	-	-	rs74475404	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168217738delA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|SLIT3_uc003mac.1_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)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169262764	169262764	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169262764delT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	169525857	169525858	+	IGR	INS	-	GTGA	GTGA	rs140953286	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169525857_169525858insGTGA								DOCK2 (15473 upstream) : FOXI1 (7059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	170261080	170261082	+	IGR	DEL	CAT	-	-	rs111380690		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170261080_170261082delCAT								GABRP (20032 upstream) : RANBP17 (27940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	170945683	170945683	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170945683delA								FGF18 (61521 upstream) : FBXW11 (342873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171446083	171446083	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171446083delT								FBXW11 (12206 upstream) : STK10 (22991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172178243	172178244	+	IGR	INS	-	AAGG	AAGG	rs28532090		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172178243_172178244insAAGG								NEURL1B (59712 upstream) : DUSP1 (16858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172226606	172226608	+	IGR	DEL	AGA	-	-	rs138985222		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172226606_172226608delAGA								DUSP1 (28403 upstream) : ERGIC1 (34615 downstream)																																			---	---	---	---
ERGIC1	57222	broad.mit.edu	37	5	172316409	172316409	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172316409delA	uc003mbw.3	+							NM_001031711	NP_001026881			endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	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	173638214	173638214	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173638214delA								HMP19 (102033 upstream) : MSX2 (513361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173701282	173701289	+	IGR	DEL	CATCCATC	-	-	rs111262696		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173701282_173701289delCATCCATC								HMP19 (165101 upstream) : MSX2 (450286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173949583	173949586	+	IGR	DEL	TATA	-	-	rs11134851		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173949583_173949586delTATA								HMP19 (413402 upstream) : MSX2 (201989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174226861	174226862	+	IGR	INS	-	TA	TA	rs140271141	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174226861_174226862insTA								MSX2 (68960 upstream) : DRD1 (640814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174321866	174321866	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174321866delA								MSX2 (163965 upstream) : DRD1 (545810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174659269	174659270	+	IGR	INS	-	GGC	GGC	rs58764676	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174659269_174659270insGGC								MSX2 (501368 upstream) : DRD1 (208406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174731905	174731907	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174731905_174731907delAAA								MSX2 (574004 upstream) : DRD1 (135769 downstream)																																			---	---	---	---
C5orf25	375484	broad.mit.edu	37	5	175763071	175763072	+	Intron	INS	-	AGGG	AGGG	rs151279591	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175763071_175763072insAGGG	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc003mdv.2_Intron					RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)														---	---	---	---
C5orf25	375484	broad.mit.edu	37	5	175771971	175771971	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175771971delT	uc003mds.3	+						C5orf25_uc003mdt.3_Intron|C5orf25_uc003mdr.3_Intron|C5orf25_uc003mdv.2_Intron					RecName: Full=Uncharacterized protein C5orf25;												0	all_cancers(89;0.00381)|Renal(175;0.000269)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	175802286	175802287	+	IGR	INS	-	CCAC	CCAC	rs142545417		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175802286_175802287insCCAC								ARL10 (1783 upstream) : NOP16 (8663 downstream)																																			---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175894332	175894332	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175894332delT	uc003mej.3	+							NM_014613	NP_055428			UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
UNC5A	90249	broad.mit.edu	37	5	176246370	176246370	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176246370delA	uc003mey.2	+						UNC5A_uc003mex.1_Intron	NM_133369	NP_588610			netrin receptor Unc5h1 precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane				skin(1)	1	all_cancers(89;0.000119)|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)															---	---	---	---
LMAN2	10960	broad.mit.edu	37	5	176763857	176763859	+	Intron	DEL	AGG	-	-	rs143120422		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176763857_176763859delAGG	uc003mge.2	-						LMAN2_uc003mgd.2_Intron	NM_006816	NP_006807			lectin, mannose-binding 2 precursor						protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	metal ion binding|sugar binding				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)															---	---	---	---
FAM153A	285596	broad.mit.edu	37	5	177167589	177167589	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177167589delT	uc010jkp.1	-						FAM153A_uc011dgd.1_Intron|FAM153A_uc003mib.1_Intron|FAM153A_uc003mic.2_Intron	NM_173663	NP_775934			hypothetical protein LOC285596											skin(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	177533775	177533775	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177533775delC								FAM153C (57687 upstream) : N4BP3 (6781 downstream)																																			---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177834808	177834808	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177834808delA	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)														---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	178990682	178990682	+	Intron	DEL	T	-	-	rs34656379		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178990682delT	uc003mka.1	+						RUFY1_uc003mkb.1_Intron|RUFY1_uc003mkc.1_Intron	NM_025158	NP_079434			RUN and FYVE domain-containing 1 isoform a						endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
MGAT1	4245	broad.mit.edu	37	5	180233285	180233285	+	Intron	DEL	A	-	-	rs78979266		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180233285delA	uc003mmh.3	-						MGAT1_uc010jlf.2_5'Flank|MGAT1_uc010jlg.2_5'Flank|MGAT1_uc010jlh.2_Intron|MGAT1_uc003mmi.3_Intron	NM_001114618	NP_001108090			mannosyl (alpha-1,3-)-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(1)	1	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	180322338	180322339	+	IGR	INS	-	GG	GG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180322338_180322339insGG								ZFP62 (34053 upstream) : BTNL8 (3738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	180708776	180708777	+	IGR	INS	-	G	G	rs140221514		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180708776_180708777insG								TRIM52 (20657 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	783712	783712	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:783712delC								EXOC2 (90603 upstream) : LOC285768 (177530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	805629	805629	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:805629delA								EXOC2 (112520 upstream) : LOC285768 (155613 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1800864	1800864	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1800864delT	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)														---	---	---	---
RIPK1	8737	broad.mit.edu	37	6	3079143	3079143	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3079143delT	uc010jni.2	+						RIPK1_uc003muv.3_Intron|RIPK1_uc003muw.3_Intron|RIPK1_uc011dhs.1_Intron|RIPK1_uc003mux.2_Intron	NM_003804	NP_003795			receptor (TNFRSF)-interacting serine-threonine						activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)																---	---	---	---
BPHL	670	broad.mit.edu	37	6	3143456	3143459	+	Intron	DEL	AAAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3143456_3143459delAAAC	uc003mva.2	+						BPHL_uc003muz.2_Intron|BPHL_uc011dht.1_Intron|BPHL_uc003muy.2_Intron	NM_004332	NP_004323			biphenyl hydrolase-like precursor						cellular amino acid metabolic process|response to toxin	mitochondrion	hydrolase activity				0	Ovarian(93;0.0386)	all_hematologic(90;0.108)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	3188827	3188827	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3188827delT	uc003mve.2	-						uc003mvf.2_Intron					Homo sapiens, clone IMAGE:4998578, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	3237301	3237301	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3237301delA	uc003mvi.1	+											Homo sapiens cDNA FLJ38900 fis, clone NT2NE2001021.																														---	---	---	---
SLC22A23	63027	broad.mit.edu	37	6	3290216	3290216	+	Intron	DEL	T	-	-	rs35568219		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3290216delT	uc003mvm.3	-						SLC22A23_uc003mvn.3_Intron|SLC22A23_uc003mvo.3_Intron|SLC22A23_uc003mvp.1_Intron|SLC22A23_uc010jnn.2_Intron|SLC22A23_uc003mvq.1_5'Flank	NM_015482	NP_056297			solute carrier family 22, member 23 isoform a						ion transport	integral to membrane	transmembrane transporter activity			ovary(1)	1	Ovarian(93;0.0493)	all_hematologic(90;0.0905)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	4259267	4259267	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4259267delT								PECI (123436 upstream) : CDYL (447126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4672580	4672580	+	IGR	DEL	A	-	-	rs59960469	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4672580delA								PECI (536749 upstream) : CDYL (33813 downstream)																																			---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5311640	5311641	+	Intron	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5311640_5311641insGT	uc010jnv.1	+						FARS2_uc003mwr.2_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	5893116	5893116	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5893116delC								FARS2 (121300 upstream) : NRN1 (105119 downstream)																																			---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6353435	6353436	+	Intron	INS	-	TC	TC	rs140899215	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6353435_6353436insTC	uc003mww.3	-							NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6410275	6410283	+	Intron	DEL	GCACAGGCA	-	-	rs113809379		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6410275_6410283delGCACAGGCA	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	7013357	7013358	+	IGR	INS	-	AGG	AGG	rs141496783	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7013357_7013358insAGG								LY86 (358141 upstream) : RREB1 (94830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7073433	7073433	+	IGR	DEL	C	-	-	rs575187	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7073433delC								LY86 (418217 upstream) : RREB1 (34755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7506850	7506850	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7506850delA								RIOK1 (88582 upstream) : DSP (35020 downstream)																																			---	---	---	---
BMP6	654	broad.mit.edu	37	6	7846027	7846027	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7846027delT	uc003mxu.3	+							NM_001718	NP_001709			bone morphogenetic protein 6 preproprotein						BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity			large_intestine(2)|ovary(1)	3	Ovarian(93;0.0721)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8336639	8336640	+	IGR	INS	-	T	T	rs140204831		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8336639_8336640insT								EEF1E1 (233811 upstream) : SLC35B3 (75093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9810843	9810844	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9810843_9810844insA	uc003myg.1	-						uc010jog.1_Intron|uc003myh.1_Intron|uc003myi.2_Intron|uc003myj.1_Intron|uc003myk.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	10269034	10269035	+	IGR	INS	-	C	C	rs138831738	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10269034_10269035insC								None (None upstream) : TFAP2A (127882 downstream)																																			---	---	---	---
PAK1IP1	55003	broad.mit.edu	37	6	10702474	10702474	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10702474delA	uc003mzg.2	+							NM_017906	NP_060376			PAK1 interacting protein 1						negative regulation of signal transduction	nucleolus|plasma membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.117)																---	---	---	---
TMEM14C	51522	broad.mit.edu	37	6	10728061	10728061	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10728061delA	uc003mzh.2	+						TMEM14C_uc010joq.1_Intron|TMEM14C_uc003mzi.2_Intron	NM_016462	NP_057546			transmembrane protein 14C						heme biosynthetic process	integral to membrane|mitochondrial membrane					0	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)	Epithelial(50;0.246)															---	---	---	---
GCM2	9247	broad.mit.edu	37	6	10876680	10876681	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10876680_10876681insA	uc003mzn.3	-	3	525_526	c.453_454insT	c.(451-456)TTTCAGfs	p.F151fs	SYCP2L_uc011dim.1_Intron	NM_004752	NP_004743	O75603	GCM2_HUMAN	glial cells missing homolog 2	151_152	GCM.				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	11739275	11739275	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11739275delA	uc003nab.2	-						C6orf105_uc003naa.2_5'Flank|C6orf105_uc011dip.1_Intron	NM_032744	NP_116133			hypothetical protein LOC84830 isoform 2							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)															---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12130980	12130981	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12130980_12130981insT	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)																---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13231348	13231349	+	Intron	DEL	AG	-	-	rs35635704		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13231348_13231349delAG	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	13278490	13278490	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13278490delT	uc010jpc.2	+						PHACTR1_uc003nah.1_Intron|TBC1D7_uc003naj.2_Intron|TBC1D7_uc011dis.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)															---	---	---	---
NOL7	51406	broad.mit.edu	37	6	13617256	13617256	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13617256delT	uc003naz.2	+							NM_016167	NP_057251			nucleolar protein 7, 27kDa							mitochondrion|nucleolus					0	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	14498945	14498946	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14498945_14498946delTT								CD83 (361799 upstream) : JARID2 (746788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14773078	14773079	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14773078_14773079insT								CD83 (635932 upstream) : JARID2 (472655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14799346	14799346	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14799346delT								CD83 (662200 upstream) : JARID2 (446388 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15392301	15392310	+	Intron	DEL	GTGTGTGTGC	-	-	rs71789239		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15392301_15392310delGTGTGTGTGC	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron	NM_004973	NP_004964			jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	15708084	15708084	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15708084delA								DTNBP1 (44813 upstream) : MYLIP (421233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15813598	15813598	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15813598delA								DTNBP1 (150327 upstream) : MYLIP (315719 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16581454	16581457	+	Intron	DEL	GTGC	-	-	rs72001198		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16581454_16581457delGTGC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	17271021	17271022	+	IGR	DEL	GT	-	-	rs71884980		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17271021_17271022delGT								ATXN1 (509300 upstream) : RBM24 (10787 downstream)																																			---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17436298	17436299	+	Intron	INS	-	TCTT	TCTT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17436298_17436299insTCTT	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	17536717	17536717	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17536717delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	17732826	17732828	+	IGR	DEL	CTT	-	-	rs60688187		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17732826_17732828delCTT								NUP153 (26008 upstream) : KIF13A (27757 downstream)																																			---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17823269	17823269	+	Intron	DEL	T	-	-	rs10708452		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17823269delT	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003ncj.2_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	18088663	18088663	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18088663delG								KIF13A (100864 upstream) : NHLRC1 (32055 downstream)																																			---	---	---	---
DEK	7913	broad.mit.edu	37	6	18263751	18263751	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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								---	---	---	---
RNF144B	255488	broad.mit.edu	37	6	18448448	18448448	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18448448delG	uc003ncs.2	+							NM_182757	NP_877434			IBR domain containing 2						apoptosis|positive regulation of anti-apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	19591426	19591427	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19591426_19591427delAA								None (None upstream) : ID4 (246190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19855465	19855466	+	IGR	INS	-	A	A	rs113041334	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19855465_19855466insA								ID4 (14551 upstream) : MBOAT1 (245469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20055527	20055530	+	IGR	DEL	GAGA	-	-	rs56294314	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20055527_20055530delGAGA								ID4 (214613 upstream) : MBOAT1 (45405 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20538462	20538464	+	Intron	DEL	TTT	-	-	rs10612082		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20538462_20538464delTTT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc010jpo.1_Intron|CDKAL1_uc003ndb.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	21132753	21132753	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21132753delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	21523092	21523093	+	RNA	DEL	AC	-	-	rs35794055		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21523092_21523093delAC	uc003ndh.2	-	1		c.922_923delGT								full-length cDNA clone CS0DF017YB01 of Fetal brain of Homo sapiens (human).																														---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22108290	22108301	+	Intron	DEL	ACACACACACAC	-	-	rs72120835		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22108290_22108301delACACACACACAC	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22123867	22123870	+	Intron	DEL	TTTT	-	-	rs35201539		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22123867_22123870delTTTT	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	22399731	22399731	+	IGR	DEL	G	-	-	rs2744130	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22399731delG								PRL (96649 upstream) : HDGFL1 (169947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23283265	23283265	+	IGR	DEL	T	-	-	rs35562183		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23283265delT								HDGFL1 (712516 upstream) : NRSN1 (843149 downstream)																																			---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24842997	24842997	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24842997delT	uc003neo.1	-						FAM65B_uc011djs.1_Intron|FAM65B_uc011dju.1_Intron|FAM65B_uc003nep.2_Intron|FAM65B_uc011djt.1_Intron	NM_014722	NP_055537			hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25279840	25279840	+	5'UTR	DEL	T	-	-	rs72361376		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25279840delT	uc011djw.1	+	1					LRRC16A_uc010jpx.2_5'UTR|LRRC16A_uc010jpy.2_5'UTR	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																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25479028	25479030	+	Intron	DEL	AAA	-	-	rs111562802		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25479028_25479030delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	25647375	25647376	+	IGR	INS	-	A	A	rs145288424	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25647375_25647376insA								LRRC16A (26619 upstream) : SCGN (5053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26698238	26698240	+	IGR	DEL	CTA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26698238_26698240delCTA								ZNF322A (38275 upstream) : GUSBL1 (141026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26818444	26818444	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26818444delA								ZNF322A (158481 upstream) : GUSBL1 (20822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27489210	27489211	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27489210_27489211delAG								ZNF184 (48313 upstream) : HIST1H2BL (286047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	27548420	27548421	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27548420_27548421delAA								ZNF184 (107523 upstream) : HIST1H2BL (226837 downstream)																																			---	---	---	---
ZKSCAN4	387032	broad.mit.edu	37	6	28217831	28217831	+	Intron	DEL	G	-	-	rs115815993	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28217831delG	uc003nks.1	-						ZKSCAN4_uc011dlb.1_Intron	NM_019110	NP_061983			zinc finger with KRAB and SCAN domains 4						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ZKSCAN4	387032	broad.mit.edu	37	6	28220485	28220485	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28220485delT	uc003nks.1	-						ZKSCAN4_uc011dlb.1_Intron	NM_019110	NP_061983			zinc finger with KRAB and SCAN domains 4						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	28609437	28609437	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28609437delG								SCAND3 (54325 upstream) : TRIM27 (261343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28619653	28619653	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28619653delA								SCAND3 (64541 upstream) : TRIM27 (251127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	29620289	29620290	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29620289_29620290delAA								GABBR1 (19327 upstream) : MOG (4519 downstream)																																			---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29865448	29865448	+	Intron	DEL	G	-	-	rs9278416		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29865448delG	uc011dmb.1	+						HCG2P7_uc003nof.2_5'Flank	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																		---	---	---	---
RNF39	80352	broad.mit.edu	37	6	30039567	30039568	+	Intron	DEL	TG	-	-	rs35559353		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30039567_30039568delTG	uc003npe.2	-						RNF39_uc003npd.2_Intron	NM_025236	NP_079512			ring finger protein 39 isoform 1							cytoplasm	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30249025	30249025	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30249025delT								HLA-L (14297 upstream) : HCG18 (6149 downstream)																																			---	---	---	---
ABCF1	23	broad.mit.edu	37	6	30543385	30543386	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30543385_30543386insT	uc003nql.2	+						ABCF1_uc003nqk.2_Intron|ABCF1_uc003nqm.2_Intron|ABCF1_uc010jsb.2_Intron	NM_001025091	NP_001020262			ATP-binding cassette, sub-family F, member 1						inflammatory response|translational initiation	nuclear envelope|nuclear envelope|nucleoplasm|nucleoplasm|polysomal ribosome	ATP binding|ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
MRPS18B	28973	broad.mit.edu	37	6	30591558	30591558	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30591558delT	uc003nqo.2	+						MRPS18B_uc011dml.1_Intron|MRPS18B_uc010jsd.1_Intron	NM_014046	NP_054765			mitochondrial ribosomal protein S18B precursor						translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome			ovary(1)	1																		---	---	---	---
C6orf136	221545	broad.mit.edu	37	6	30620236	30620236	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30620236delA	uc003nqw.3	+						C6orf136_uc003nqx.3_Intron|C6orf136_uc011dmn.1_Intron	NM_001109938	NP_001103408			hypothetical protein LOC221545 isoform 1												0																		---	---	---	---
VARS2	57176	broad.mit.edu	37	6	30893244	30893244	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30893244delC	uc003nsc.1	+						VARS2_uc011dmx.1_Intron|VARS2_uc011dmy.1_Intron|VARS2_uc011dmz.1_Intron|VARS2_uc011dna.1_Intron|VARS2_uc011dnb.1_Intron|VARS2_uc011dnc.1_Intron|VARS2_uc011dnd.1_Intron|VARS2_uc010jsg.1_Intron|VARS2_uc010jsh.1_Intron	NM_020442	NP_065175			valyl-tRNA synthetase 2, mitochondrial						valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
MUC21	394263	broad.mit.edu	37	6	30957120	30957120	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30957120delT	uc003nsh.2	+	3					MUC21_uc003nsi.1_RNA	NM_001010909	NP_001010909			mucin 21 precursor							integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31254547	31254547	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31254547delT	uc003ntf.2	-						HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_Intron|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Intron					SubName: Full=MHC class I antigen;						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31594336	31594337	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31594336_31594337delAA	uc003nvb.3	+						BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Intron	NM_080686	NP_542417			HLA-B associated transcript-2							cytoplasm|nucleus	protein binding				0																		---	---	---	---
LY6G6F	259215	broad.mit.edu	37	6	31681009	31681009	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31681009delA	uc003nwb.1	+						BAT5_uc011dnz.1_Intron|LY6G6E_uc011dob.1_Intron|LY6G6E_uc003nwc.2_Intron|LY6G6E_uc003nwd.2_Intron|LY6G6E_uc003nwe.2_Intron|LY6G6D_uc003nwf.1_5'Flank|LY6G6D_uc003nwg.1_5'Flank	NM_001003693	NP_001003693			G6f protein precursor							integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	31816882	31816882	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31816882delA								C6orf48 (9343 upstream) : NEU1 (9948 downstream)																																			---	---	---	---
CFB	629	broad.mit.edu	37	6	31917557	31917558	+	Intron	INS	-	AT	AT	rs147267186	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31917557_31917558insAT	uc003nyj.3	+						CFB_uc011dor.1_Intron|CFB_uc003nyi.2_Intron	NM_001710	NP_001701			complement factor B preproprotein						complement activation, alternative pathway|proteolysis	extracellular region|plasma membrane	complement binding|serine-type endopeptidase activity			skin(1)	1																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32335020	32335021	+	Intron	INS	-	AGAGAGAGAGAGAGAG	AGAGAGAGAGAGAGAG	rs145251971	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32335020_32335021insAGAGAGAGAGAGAGAG	uc011dpy.1	-						C6orf10_uc011dpz.1_Intron	NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
BTNL2	56244	broad.mit.edu	37	6	32374720	32374730	+	Intron	DEL	TTGGCCCCAGA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32374720_32374730delTTGGCCCCAGA	uc003obg.1	-						BTNL2_uc010jty.1_Intron|BTNL2_uc010jtz.1_Intron|BTNL2_uc010jua.1_Intron	NM_019602	NP_062548			butyrophilin-like 2							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32417794	32417795	+	IGR	INS	-	T	T	rs6937167		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32417794_32417795insT								HLA-DRA (4973 upstream) : HLA-DRB1 (67368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32439504	32439504	+	IGR	DEL	A	-	-	rs111871467		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32439504delA								HLA-DRA (26683 upstream) : HLA-DRB1 (45659 downstream)																																			---	---	---	---
VPS52	6293	broad.mit.edu	37	6	33222455	33222455	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33222455delT	uc003odm.1	-						VPS52_uc003odn.1_Intron	NM_022553	NP_072047			vacuolar protein sorting 52						protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5																		---	---	---	---
VPS52	6293	broad.mit.edu	37	6	33226690	33226690	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33226690delA	uc003odm.1	-						VPS52_uc003odn.1_Intron	NM_022553	NP_072047			vacuolar protein sorting 52						protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33347283	33347284	+	IGR	INS	-	A	A	rs111462606		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33347283_33347284insA								LYPLA2P1 (13144 upstream) : KIFC1 (12029 downstream)																																			---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33406897	33406899	+	Intron	DEL	AAA	-	-	rs72093601		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33406897_33406899delAAA	uc011dri.1	+						SYNGAP1_uc010juy.2_Intron|SYNGAP1_uc010juz.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33850411	33850412	+	5'Flank	INS	-	GTTTT	GTTTT	rs71770463		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33850411_33850412insGTTTT	uc003ofx.1	-						uc003ofy.2_5'Flank|uc003ofz.2_5'Flank|uc003oga.2_5'Flank					DQ601334																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	33918367	33918368	+	IGR	INS	-	GTTTGT	GTTTGT	rs149677721	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33918367_33918368insGTTTGT								MLN (146574 upstream) : MIR1275 (49381 downstream)																																			---	---	---	---
FKBP5	2289	broad.mit.edu	37	6	35669630	35669630	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35669630delT	uc003oky.2	-							NM_001145775	NP_001139247			FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
ETV7	51513	broad.mit.edu	37	6	36338562	36338562	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36338562delT	uc003omb.2	-						ETV7_uc003olz.1_Intron|ETV7_uc003oma.1_Intron|ETV7_uc010jwg.2_Intron|ETV7_uc003omc.2_Intron|ETV7_uc010jwj.2_Intron|ETV7_uc010jwh.2_Intron|ETV7_uc010jwi.2_Intron|ETV7_uc011dtl.1_Intron	NM_016135	NP_057219			ets variant 7						organ morphogenesis|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36459554	36459556	+	IGR	DEL	TTG	-	-	rs35453626		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36459554_36459556delTTG								KCTD20 (1241 upstream) : STK38 (2118 downstream)																																			---	---	---	---
SFRS3	6428	broad.mit.edu	37	6	36561061	36561061	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36561061delT	uc003omj.2	+						SFRS3_uc003omk.2_5'Flank|SFRS3_uc011dtp.1_5'Flank	NM_003017	NP_003008			splicing factor, arginine/serine-rich 3						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0								T	BCL6	follicular lymphoma								---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39399734	39399737	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39399734_39399737delTTTT	uc003oot.2	-						KIF6_uc003oos.2_5'Flank|KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40504161	40504162	+	Intron	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40504161_40504162delAT	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	40705119	40705119	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40705119delA								LRFN2 (149993 upstream) : UNC5CL (289653 downstream)																																			---	---	---	---
PGC	5225	broad.mit.edu	37	6	41712724	41712729	+	Intron	DEL	TCTGTC	-	-	rs72336731		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41712724_41712729delTCTGTC	uc003ora.1	-							NM_002630	NP_002621			progastricsin (pepsinogen C) precursor						digestion|proteolysis	extracellular space	aspartic-type endopeptidase activity				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)															---	---	---	---
FRS3	10817	broad.mit.edu	37	6	41746363	41746364	+	Intron	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41746363_41746364insC	uc003orc.1	-						PRICKLE4_uc011duf.1_5'Flank|PRICKLE4_uc003ord.2_5'Flank	NM_006653	NP_006644			fibroblast growth factor receptor substrate 3						fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding			ovary(2)	2	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42877380	42877380	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42877380delT								C6orf226 (18826 upstream) : PTCRA (6347 downstream)																																			---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42932348	42932348	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42932348delT	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)															---	---	---	---
PPP2R5D	5528	broad.mit.edu	37	6	42977807	42977807	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42977807delA	uc003oth.2	+						MEA1_uc010jyc.1_Intron|PPP2R5D_uc003otg.2_Intron|PPP2R5D_uc010jyd.2_Intron|PPP2R5D_uc011dva.1_Intron|PPP2R5D_uc003oti.2_Intron|PPP2R5D_uc003otj.2_Intron	NM_006245	NP_006236			delta isoform of regulatory subunit B56, protein						nervous system development|signal transduction	cytoplasm|nucleus|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			breast(1)|central_nervous_system(1)	2			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
CRIP3	401262	broad.mit.edu	37	6	43273379	43273379	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43273379delA	uc003ouu.1	-	8						NM_206922	NP_996805			cysteine-rich protein 3							cytoplasm	zinc ion binding			skin(1)	1			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)															---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43295354	43295354	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43295354delT	uc003ouw.2	-							NM_014345				zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
TJAP1	93643	broad.mit.edu	37	6	43448719	43448719	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43448719delT	uc003ovd.2	+						TJAP1_uc003ovf.2_Intron|TJAP1_uc003ove.2_Intron|TJAP1_uc003ovc.2_Intron|TJAP1_uc010jyp.2_Intron|TJAP1_uc011dvh.1_Intron	NM_001146016	NP_001139488			tight junction associated protein 1 isoform a							Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43616935	43616936	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43616935_43616936insT	uc003ovw.1	+						RSPH9_uc003ovx.1_Intron	NM_152732	NP_689945			radial spoke head 9 homolog						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2														Kartagener_syndrome				---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44820742	44820742	+	Intron	DEL	G	-	-	rs146269074		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44820742delG	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																		---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44906324	44906324	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44906324delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	46169127	46169127	+	IGR	DEL	C	-	-	rs12661960	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46169127delC								ENPP5 (30410 upstream) : RCAN2 (19342 downstream)																																			---	---	---	---
GPR116	221395	broad.mit.edu	37	6	46836932	46836932	+	Intron	DEL	A	-	-	rs75249218		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46836932delA	uc003oyo.3	-						GPR116_uc011dwj.1_5'UTR|GPR116_uc011dwk.1_Intron|GPR116_uc003oyp.3_Intron|GPR116_uc003oyq.3_Intron|GPR116_uc010jzi.1_Intron	NM_001098518	NP_001091988			G-protein coupled receptor 116 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)|skin(1)	2			Lung(136;0.192)															---	---	---	---
GPR110	266977	broad.mit.edu	37	6	46990723	46990723	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46990723delT	uc003oyt.2	-						GPR110_uc011dwl.1_Intron|GPR110_uc003oyu.1_Intron	NM_153840	NP_722582			G-protein coupled receptor 110 isoform 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	47744337	47744337	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47744337delT								GPR115 (54580 upstream) : OPN5 (5461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	47832422	47832423	+	IGR	DEL	TG	-	-	rs141622612		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47832422_47832423delTG								OPN5 (38308 upstream) : C6orf138 (13617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49085933	49085934	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49085933_49085934delAA								None (None upstream) : MUT (313060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	49090096	49090096	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49090096delA								None (None upstream) : MUT (308898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50047767	50047767	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50047767delA								DEFB112 (31403 upstream) : TFAP2D (633490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50195565	50195565	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50195565delT								DEFB112 (179201 upstream) : TFAP2D (485692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50957179	50957179	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50957179delT								TFAP2B (141854 upstream) : PKHD1 (522966 downstream)																																			---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51670156	51670157	+	Intron	INS	-	AG	AG	rs75384368		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51670156_51670157insAG	uc003pah.1	-						PKHD1_uc010jzn.1_Intron|PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51854697	51854699	+	Intron	DEL	GGG	-	-	rs72417168	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51854697_51854699delGGG	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	51990366	51990366	+	IGR	DEL	A	-	-	rs11357374		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51990366delA								PKHD1 (37943 upstream) : MIR206 (18781 downstream)																																			---	---	---	---
TMEM14A	28978	broad.mit.edu	37	6	52548282	52548284	+	Intron	DEL	AAA	-	-	rs71799754	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52548282_52548284delAAA	uc003pax.2	+							NM_014051	NP_054770			transmembrane protein 14A							integral to membrane					0	Lung NSC(77;0.118)																	---	---	---	---
GSTA2	2939	broad.mit.edu	37	6	52617144	52617144	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52617144delA	uc003pay.2	-							NM_000846	NP_000837			glutathione S-transferase alpha 2						glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			ovary(1)	1	Lung NSC(77;0.118)				Aminophenazone(DB01424)|Amsacrine(DB00276)|Busulfan(DB01008)|Chlorambucil(DB00291)|Chloroquine(DB00608)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Mechlorethamine(DB00888)|Praziquantel(DB01058)|Vitamin E(DB00163)													---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53688923	53688925	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53688923_53688925delTTT	uc003pcd.1	+							NM_018214	NP_060684			leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56125454	56125457	+	Intron	DEL	GAAT	-	-	rs10570199		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56125454_56125457delGAAT	uc003pcu.1	-							NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
DST	667	broad.mit.edu	37	6	56675511	56675513	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56675511_56675513delAAA	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
DST	667	broad.mit.edu	37	6	56778069	56778069	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56778069delT	uc003pdf.2	-							NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
ZNF451	26036	broad.mit.edu	37	6	56997610	56997610	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56997610delA	uc003pdm.1	+						ZNF451_uc003pdl.2_Intron|ZNF451_uc003pdn.1_Intron|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Intron	NM_001031623	NP_001026794			zinc finger protein 451 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57227093	57227094	+	Intron	INS	-	ACTT	ACTT	rs142617330	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57227093_57227094insACTT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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	57230872	57230872	+	Intron	DEL	A	-	-	rs67809122		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57230872delA	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	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	57272214	57272214	+	Intron	DEL	T	-	-	rs11352940		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57272214delT	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	57307820	57307820	+	Intron	DEL	T	-	-	rs77086258		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57307820delT	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	57324548	57324550	+	Intron	DEL	CTT	-	-	rs142446807		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57324548_57324550delCTT	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	57339799	57339801	+	Intron	DEL	CGA	-	-	rs11306040		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57339799_57339801delCGA	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	57366676	57366676	+	Intron	DEL	A	-	-	rs11337169		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57366676delA	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	57397342	57397342	+	Intron	DEL	G	-	-	rs5876596		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57397342delG	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	57455348	57455349	+	Intron	DEL	GA	-	-	rs144561408		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57455348_57455349delGA	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	57534160	57534161	+	IGR	INS	-	AT	AT	rs112386427		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57534160_57534161insAT								PRIM2 (20785 upstream) : GUSBL2 (711998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57540898	57540899	+	IGR	INS	-	CA	CA	rs58468150		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57540898_57540899insCA								PRIM2 (27523 upstream) : GUSBL2 (705260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57542931	57542931	+	IGR	DEL	G	-	-	rs112793267		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57542931delG								PRIM2 (29556 upstream) : GUSBL2 (703228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57566382	57566382	+	IGR	DEL	A	-	-	rs147917443		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57566382delA								PRIM2 (53007 upstream) : GUSBL2 (679777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57576631	57576632	+	IGR	INS	-	TGT	TGT	rs139864615	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57576631_57576632insTGT								PRIM2 (63256 upstream) : GUSBL2 (669527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57591634	57591636	+	IGR	DEL	TTG	-	-	rs36091874		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57591634_57591636delTTG								PRIM2 (78259 upstream) : GUSBL2 (654523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57593384	57593385	+	IGR	INS	-	A	A	rs149184524	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57593384_57593385insA								PRIM2 (80009 upstream) : GUSBL2 (652774 downstream)																																			---	---	---	---
EYS	346007	broad.mit.edu	37	6	65472577	65472578	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65472577_65472578delCA	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	65984803	65984804	+	Intron	DEL	GA	-	-	rs34765036		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65984803_65984804delGA	uc011dxu.1	-							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	66276285	66276285	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66276285delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.1_Intron|EYS_uc010kaj.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	66359266	66359267	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66359266_66359267delAC	uc011dxu.1	-						EYS_uc003peq.2_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	66762037	66762038	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66762037_66762038delAC								MCART3P (262662 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67675418	67675418	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67675418delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	69336655	69336655	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69336655delA								None (None upstream) : BAI3 (8977 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69390174	69390174	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69390174delA	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)																---	---	---	---
BAI3	577	broad.mit.edu	37	6	69810745	69810748	+	Intron	DEL	GGAA	-	-	rs67440362		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69810745_69810748delGGAA	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)																---	---	---	---
FAM135A	57579	broad.mit.edu	37	6	71242634	71242635	+	Intron	INS	-	A	A	rs76625823		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71242634_71242635insA	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_Intron|FAM135A_uc003pfo.1_Intron|FAM135A_uc010kan.1_Intron	NM_001162529	NP_001156001			hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1																		---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71508370	71508370	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71508370delA	uc003pfr.2	+	6	754	c.506delA	c.(505-507)GAAfs	p.E169fs	SMAP1_uc011dxy.1_RNA|SMAP1_uc003pfs.2_Frame_Shift_Del_p.E142fs|SMAP1_uc010kao.2_Frame_Shift_Del_p.E142fs|SMAP1_uc010kap.2_Frame_Shift_Del_p.E159fs	NM_001044305	NP_001037770	Q8IYB5	SMAP1_HUMAN	stromal membrane-associated GTPase-activating	169					regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	72213967	72213968	+	IGR	DEL	CC	-	-	rs59954495		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72213967_72213968delCC								C6orf155 (83519 upstream) : RIMS1 (382682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72450252	72450253	+	IGR	DEL	GC	-	-	rs5000512	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72450252_72450253delGC								C6orf155 (319804 upstream) : RIMS1 (146397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74041640	74041641	+	IGR	DEL	AC	-	-	rs140448926		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74041640_74041641delAC								C6orf147 (21552 upstream) : DPPA5 (21146 downstream)																																			---	---	---	---
OOEP	441161	broad.mit.edu	37	6	74082375	74082375	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74082375delG	uc003pgu.3	-						OOEP_uc003pgv.3_Intron	NM_001080507	NP_001073976			oocyte expressed protein homolog							cytoplasm					0																		---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74152128	74152128	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74152128delT	uc003pgx.1	-							NM_138441	NP_612450			hypothetical protein LOC115004												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74267534	74267534	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74267534delT								EEF1A1 (36243 upstream) : SLC17A5 (35569 downstream)																																			---	---	---	---
CD109	135228	broad.mit.edu	37	6	74456315	74456316	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74456315_74456316delTT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	75339533	75339533	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75339533delA	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75443100	75443101	+	IGR	DEL	AC	-	-	rs10535727		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75443100_75443101delAC								CD109 (905060 upstream) : COL12A1 (350942 downstream)																																			---	---	---	---
TMEM30A	55754	broad.mit.edu	37	6	75965692	75965692	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75965692delT	uc003phw.2	-	7					TMEM30A_uc003phx.2_3'UTR	NM_018247	NP_060717			transmembrane protein 30A isoform 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	77172977	77172977	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77172977delA								IMPG1 (390642 upstream) : HTR1B (998971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77493378	77493378	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77493378delA								IMPG1 (711043 upstream) : HTR1B (678570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79237140	79237140	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79237140delG								None (None upstream) : IRAK1BP1 (340049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79373950	79373951	+	IGR	INS	-	AC	AC	rs62426811	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79373950_79373951insAC								None (None upstream) : IRAK1BP1 (203238 downstream)																																			---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79708254	79708254	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79708254delA	uc003pir.2	-						PHIP_uc011dyp.1_Intron	NM_017934	NP_060404			pleckstrin homology domain interacting protein						insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
SH3BGRL2	83699	broad.mit.edu	37	6	80386357	80386358	+	Intron	DEL	TA	-	-	rs71714945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80386357_80386358delTA	uc003piz.1	+							NM_031469	NP_113657			SH3 domain binding glutamic acid-rich protein							nucleus	SH3 domain binding				0		all_cancers(76;0.00188)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.174)		BRCA - Breast invasive adenocarcinoma(397;0.0278)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	82095705	82095706	+	IGR	DEL	AC	-	-	rs141658651		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82095705_82095706delAC								None (None upstream) : FAM46A (359742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82201006	82201006	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82201006delT								None (None upstream) : FAM46A (254442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83525824	83525826	+	IGR	DEL	AAC	-	-	rs140419025		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83525824_83525826delAAC								TPBG (449210 upstream) : UBE2CBP (76360 downstream)																																			---	---	---	---
UBE2CBP	90025	broad.mit.edu	37	6	83647339	83647339	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83647339delA	uc003pjp.2	-						UBE2CBP_uc011dyx.1_Intron	NM_198920	NP_944602			ubiquitin-conjugating enzyme E2C binding							cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83840469	83840469	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83840469delT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron	NM_015018	NP_055833			dopey family member 1						protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)														---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83900377	83900377	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83900377delA	uc003pjv.2	-						PGM3_uc003pjw.2_Intron|PGM3_uc011dyz.1_Intron|RWDD2A_uc003pjx.3_5'Flank|RWDD2A_uc011dza.1_5'Flank	NM_015599	NP_056414			phosphoglucomutase 3						dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	84813152	84813153	+	IGR	INS	-	T	T	rs138462917	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84813152_84813153insT								MRAP2 (12549 upstream) : KIAA1009 (20808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85141655	85141658	+	IGR	DEL	TCCT	-	-	rs10569726		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85141655_85141658delTCCT								KIAA1009 (204320 upstream) : TBX18 (255423 downstream)																																			---	---	---	---
NT5E	4907	broad.mit.edu	37	6	86189463	86189464	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86189463_86189464delTC	uc003pko.3	+						NT5E_uc010kbr.2_Intron	NM_002526	NP_002517			5' nucleotidase, ecto precursor						DNA metabolic process|purine base metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	5'-nucleotidase activity|nucleotide binding			ovary(3)|central_nervous_system(1)	4		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Pentoxifylline(DB00806)													---	---	---	---
SYNCRIP	10492	broad.mit.edu	37	6	86329254	86329255	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86329254_86329255delAA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363			synaptotagmin binding, cytoplasmic RNA						CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	86562503	86562503	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86562503delT								SNHG5 (174052 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86881884	86881884	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86881884delA								SNHG5 (493433 upstream) : HTR1E (765140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87473861	87473861	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87473861delT								None (None upstream) : HTR1E (173163 downstream)																																			---	---	---	---
CGA	1081	broad.mit.edu	37	6	87797955	87797956	+	Intron	DEL	AC	-	-	rs71944433		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87797955_87797956delAC	uc003plj.1	-							NM_000735	NP_000726			glycoprotein hormones, alpha polypeptide						hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity			ovary(1)	1		all_cancers(76;5.98e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000102)		BRCA - Breast invasive adenocarcinoma(108;0.0484)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87892312	87892312	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87892312delA	uc003plm.3	+						ZNF292_uc003pll.1_Intron	NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
C6orf165	154313	broad.mit.edu	37	6	88125702	88125702	+	Intron	DEL	A	-	-	rs34892535		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88125702delA	uc003plv.2	+						C6orf165_uc003plw.2_Intron|C6orf165_uc010kbv.1_Intron|C6orf165_uc003plu.1_Intron	NM_001031743	NP_001026913			hypothetical protein LOC154313 isoform 1											central_nervous_system(1)	1		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;0.0419)														---	---	---	---
SLC35A1	10559	broad.mit.edu	37	6	88220956	88220956	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88220956delT	uc011dzj.1	+						SLC35A1_uc003plx.2_Intron|SLC35A1_uc010kbw.2_Intron|SLC35A1_uc003plz.2_Intron|SLC35A1_uc011dzi.1_Intron|SLC35A1_uc003ply.2_Intron|SLC35A1_uc010kbx.2_Intron|SLC35A1_uc010kby.2_Intron	NM_006416	NP_006407			solute carrier family 35 (CMP-sialic acid						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)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88311735	88311735	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88311735delA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	89281653	89281654	+	IGR	INS	-	T	T	rs140464655	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89281653_89281654insT								CNR1 (405886 upstream) : RNGTT (38335 downstream)																																			---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89649489	89649489	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89649489delT	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	89769092	89769093	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89769092_89769093delTT								RNGTT (95744 upstream) : PNRC1 (21336 downstream)																																			---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90472434	90472434	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90472434delA	uc003pnn.1	-						MDN1_uc003pno.1_Intron	NM_014611	NP_055426			MDN1, midasin homolog						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)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90654400	90654401	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90654400_90654401delTC	uc011eab.1	-						BACH2_uc003pnw.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)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90917763	90917763	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90917763delA	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)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90929683	90929683	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90929683delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91145558	91145558	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91145558delT								BACH2 (138996 upstream) : MAP3K7 (79795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91329059	91329061	+	IGR	DEL	CCC	-	-	rs67246887		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91329059_91329061delCCC								MAP3K7 (32152 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91747078	91747079	+	IGR	INS	-	A	A	rs140549726	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91747078_91747079insA								MAP3K7 (450171 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92037647	92037648	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92037647_92037648delTT								MAP3K7 (740740 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92157061	92157061	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92157061delT								MAP3K7 (860154 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92907493	92907496	+	IGR	DEL	GAGA	-	-	rs138238353		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92907493_92907496delGAGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93295800	93295800	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93295800delA								None (None upstream) : EPHA7 (653942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	95404115	95404116	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95404115_95404116insC								TSG1 (917916 upstream) : MANEA (621297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98715362	98715377	+	IGR	DEL	TCCTTCCTTCCTTCCT	-	-	rs72178118		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98715362_98715377delTCCTTCCTTCCTTCCT								MIR2113 (242865 upstream) : POU3F2 (567203 downstream)																																			---	---	---	---
POU3F2	5454	broad.mit.edu	37	6	99279672	99279672	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99279672delG	uc003ppe.2	+							NM_005604	NP_005595			POU domain, class 3, transcription factor 2						positive regulation of cell proliferation		identical protein binding|sequence-specific DNA binding transcription factor activity				0		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;0.0355)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	99626045	99626046	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99626045_99626046insA								FBXL4 (230196 upstream) : C6orf168 (94748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100463474	100463474	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100463474delA								MCHR2 (21360 upstream) : SIM1 (373277 downstream)																																			---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100848857	100848857	+	Intron	DEL	A	-	-	rs74999406		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100848857delA	uc003pqj.3	-						SIM1_uc010kcu.2_Intron	NM_005068	NP_005059			single-minded homolog 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101670570	101670570	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101670570delT								ASCC3 (341346 upstream) : GRIK2 (176335 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102212587	102212587	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102212587delT	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	102775903	102775903	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102775903delG								GRIK2 (257946 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	102871845	102871845	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102871845delA								GRIK2 (353888 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103197319	103197321	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103197319_103197321delAAA								GRIK2 (679362 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103415226	103415227	+	IGR	DEL	TG	-	-	rs62429097		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103415226_103415227delTG								GRIK2 (897269 upstream) : None (None downstream)																																			---	---	---	---
LIN28B	389421	broad.mit.edu	37	6	105451395	105451395	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105451395delT	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)																---	---	---	---
LIN28B	389421	broad.mit.edu	37	6	105485560	105485560	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105485560delT	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)																---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107484805	107484806	+	Intron	DEL	TT	-	-	rs76746262		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107484805_107484806delTT	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
OSTM1	28962	broad.mit.edu	37	6	108387177	108387178	+	Intron	DEL	TA	-	-	rs5878959		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108387177_108387178delTA	uc003psd.2	-							NM_014028	NP_054747			osteopetrosis associated transmembrane protein 1							integral to membrane				central_nervous_system(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108690819	108690819	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108690819delT	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)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108700205	108700205	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108700205delT	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)														---	---	---	---
SESN1	27244	broad.mit.edu	37	6	109358992	109358992	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109358992delA	uc003psu.2	-							NM_014454	NP_055269			sestrin 1						cell cycle arrest|negative regulation of cell proliferation|response to DNA damage stimulus	nucleus				ovary(1)	1		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	110554988	110554988	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110554988delT								CDC40 (1568 upstream) : C6orf186 (12161 downstream)																																			---	---	---	---
C6orf186	728464	broad.mit.edu	37	6	110687340	110687340	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110687340delA	uc003pub.2	-											Homo sapiens cDNA FLJ45203 fis, clone BRCAN2008701.							extracellular region					0																		---	---	---	---
SLC16A10	117247	broad.mit.edu	37	6	111411835	111411836	+	Intron	DEL	CA	-	-	rs112280068		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111411835_111411836delCA	uc003pus.2	+						SLC16A10_uc003pur.3_Intron	NM_018593	NP_061063			solute carrier family 16, member 10						aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)														---	---	---	---
FYN	2534	broad.mit.edu	37	6	112110249	112110251	+	Intron	DEL	GAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112110249_112110251delGAG	uc003pvj.2	-						FYN_uc003pvk.2_Intron	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
C6orf225	619208	broad.mit.edu	37	6	112412380	112412380	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112412380delG	uc003pvs.2	+							NM_001033564	NP_001028736			hypothetical protein LOC619208												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	113126415	113126415	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113126415delT								RFPL4B (453917 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113586137	113586137	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113586137delG								RFPL4B (913639 upstream) : MARCKS (592390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115956143	115956143	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115956143delA								None (None upstream) : FRK (306550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116062565	116062566	+	IGR	INS	-	AC	AC	rs140815681	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116062565_116062566insAC								None (None upstream) : FRK (200127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116068299	116068299	+	IGR	DEL	A	-	-	rs76986902		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116068299delA								None (None upstream) : FRK (194394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116073471	116073471	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116073471delA								None (None upstream) : FRK (189222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116080226	116080226	+	IGR	DEL	T	-	-	rs146555923		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116080226delT								None (None upstream) : FRK (182467 downstream)																																			---	---	---	---
RFX6	222546	broad.mit.edu	37	6	117229853	117229860	+	Intron	DEL	ACACACAC	-	-	rs36156236	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117229853_117229860delACACACAC	uc003pxm.2	+							NM_173560	NP_775831			regulatory factor X, 6						glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	protein binding|transcription regulatory region DNA binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	117968828	117968828	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117968828delA								GOPC (45147 upstream) : NUS1 (27789 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118285632	118285633	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118285632_118285633insT	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	118873791	118873791	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118873791delA	uc003pxz.1	-						C6orf204_uc003pya.1_Intron|C6orf204_uc003pyb.2_Intron|C6orf204_uc011ebj.1_Intron|C6orf204_uc003pyc.2_Intron|PLN_uc003pye.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119815441	119815441	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119815441delT	uc003pyn.1	-											Homo sapiens cDNA FLJ39782 fis, clone SPLEN2002175.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119848187	119848189	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119848187_119848189delTTT								MAN1A1 (177261 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120486238	120486239	+	IGR	INS	-	TG	TG	rs141220788	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120486238_120486239insTG								MAN1A1 (815312 upstream) : C6orf170 (914388 downstream)																																			---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121612296	121612296	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121612296delA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122723279	122723279	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122723279delA	uc003pyu.2	+						HSF2_uc003pyt.3_Intron|HSF2_uc003pyv.2_Intron	NM_004506	NP_004497			heat shock transcription factor 2 isoform a						response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122736732	122736732	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122736732delT	uc003pyu.2	+						HSF2_uc003pyt.3_Intron|HSF2_uc003pyv.2_Intron	NM_004506	NP_004497			heat shock transcription factor 2 isoform a						response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	126493741	126493741	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126493741delT								TRMT11 (133323 upstream) : CENPW (167512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127561397	127561397	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127561397delT								RSPO3 (42487 upstream) : RNF146 (26623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127751410	127751410	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127751410delA								ECHDC1 (86656 upstream) : C6orf174 (8142 downstream)																																			---	---	---	---
THEMIS	387357	broad.mit.edu	37	6	128034785	128034785	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128034785delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	128894058	128894058	+	IGR	DEL	T	-	-	rs113066313		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128894058delT								PTPRK (52188 upstream) : LAMA2 (310228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	129854377	129854377	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129854377delC	uc003qbq.2	-											Homo sapiens cDNA clone IMAGE:4822830.																														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129947817	129947818	+	Intron	INS	-	AC	AC	rs145243254	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129947817_129947818insAC	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130044322	130044322	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130044322delT								ARHGAP18 (12952 upstream) : C6orf191 (108069 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131290358	131290358	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131290358delA	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131682087	131682088	+	IGR	DEL	TT	-	-	rs148819047		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131682087_131682088delTT								AKAP7 (77414 upstream) : ARG1 (212277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132395575	132395575	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132395575delT								CTGF (123057 upstream) : MOXD1 (221620 downstream)																																			---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132633738	132633738	+	Intron	DEL	T	-	-	rs10710763		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132633738delT	uc003qdf.2	-						MOXD1_uc003qde.2_Intron	NM_015529	NP_056344			monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	132922064	132922091	+	IGR	DEL	GAGGGAAGGAGGGAAGGAGGGAAAGAAA	-	-	rs142824503	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132922064_132922091delGAGGGAAGGAGGGAAGGAGGGAAAGAAA								TAAR5 (11187 upstream) : TAAR2 (16198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	133321774	133321775	+	IGR	DEL	CA	-	-	rs68006526		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133321774_133321775delCA								RPS12 (183072 upstream) : LOC285735 (87444 downstream)																																			---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133702214	133702214	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133702214delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135158129	135158130	+	IGR	INS	-	C	C	rs146877102	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135158129_135158130insC								SGK1 (518933 upstream) : ALDH8A1 (80399 downstream)																																			---	---	---	---
PDE7B	27115	broad.mit.edu	37	6	136345515	136345515	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136345515delT	uc003qgp.2	+						uc003qgq.1_Intron	NM_018945	NP_061818			phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
MAP7	9053	broad.mit.edu	37	6	136773698	136773698	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136773698delT	uc003qgz.2	-						MAP7_uc011edf.1_Intron|MAP7_uc011edg.1_Intron|MAP7_uc010kgu.2_Intron|MAP7_uc011edh.1_Intron|MAP7_uc010kgv.2_Intron|MAP7_uc010kgs.2_Intron|MAP7_uc011edi.1_Intron|MAP7_uc010kgq.1_Intron|MAP7_uc003qha.1_Intron|MAP7_uc010kgr.2_Intron|MAP7_uc010kgt.2_Intron	NM_003980	NP_003971			microtubule-associated protein 7						establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	137252567	137252567	+	IGR	DEL	T	-	-	rs115322187	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137252567delT								SLC35D3 (5793 upstream) : NHEG1 (47805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138469218	138469219	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138469218_138469219delTT								PERP (40558 upstream) : KIAA1244 (14005 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138483154	138483155	+	5'Flank	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138483154_138483155insG	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	139126449	139126449	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139126449delT								CCDC28A (11995 upstream) : ECT2L (7860 downstream)																																			---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139172313	139172314	+	Intron	INS	-	T	T	rs77192617		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139172313_139172314insT	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174			epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	139452848	139452849	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139452848_139452849delTC								C6orf115 (88409 upstream) : HECA (3400 downstream)																																			---	---	---	---
HECA	51696	broad.mit.edu	37	6	139492974	139492974	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139492974delT	uc003qin.2	+							NM_016217	NP_057301			headcase						respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139662182	139662182	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139662182delT								TXLNB (48974 upstream) : CITED2 (31215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140371811	140371811	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140371811delT	uc003qis.2	+											Homo sapiens, clone IMAGE:3451765, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140400930	140400930	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140400930delT	uc003qis.2	+											Homo sapiens, clone IMAGE:3451765, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142062842	142062842	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142062842delA	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142189311	142189311	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142189311delG	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142719045	142719045	+	Intron	DEL	A	-	-	rs111787190		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142719045delA	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	143693719	143693721	+	IGR	DEL	AAT	-	-	rs72269738		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143693719_143693721delAAT								AIG1 (32280 upstream) : ADAT2 (50249 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144799006	144799009	+	Intron	DEL	TCTA	-	-	rs71769416		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144799006_144799009delTCTA	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	145052834	145052835	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145052834_145052835delAC	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	145348269	145348270	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145348269_145348270insT								UTRN (174101 upstream) : EPM2A (598176 downstream)																																			---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146244679	146244679	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146244679delA	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148			SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146425676	146425677	+	Intron	INS	-	G	G	rs149840958	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146425676_146425677insG	uc010khw.1	+						GRM1_uc010khu.1_Intron|GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146514614	146514614	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146514614delA	uc010khw.1	+						GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	146795612	146795612	+	IGR	DEL	T	-	-	rs67054719		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146795612delT								GRM1 (36881 upstream) : RAB32 (69216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148146791	148146791	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148146791delT								SAMD5 (255634 upstream) : SASH1 (516938 downstream)																																			---	---	---	---
UST	10090	broad.mit.edu	37	6	149369264	149369264	+	Intron	DEL	T	-	-	rs71942705		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149369264delT	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						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)														---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149656234	149656234	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149656234delT	uc003qmj.2	+						TAB2_uc011eec.1_Intron|TAB2_uc010kia.1_Intron|TAB2_uc010kib.1_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	149862317	149862319	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149862317_149862319delTTT	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311			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)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150112120	150112122	+	Intron	DEL	CAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150112120_150112122delCAA	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	150681207	150681208	+	IGR	DEL	TT	-	-	rs66734182		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150681207_150681208delTT								PPP1R14C (109681 upstream) : IYD (8820 downstream)																																			---	---	---	---
PLEKHG1	57480	broad.mit.edu	37	6	150948646	150948646	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150948646delA	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	151270577	151270577	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151270577delA	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|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)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152179717	152179717	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152179717delT	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron	NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						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	152478453	152478453	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152478453delC	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	153678885	153678885	+	IGR	DEL	T	-	-	rs58580110		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153678885delT								RGS17 (226496 upstream) : OPRM1 (652751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154195707	154195708	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154195707_154195708delAA								RGS17 (743318 upstream) : OPRM1 (135928 downstream)																																			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154673284	154673284	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154673284delA	uc003qpx.2	-						IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
NOX3	50508	broad.mit.edu	37	6	155754775	155754777	+	Intron	DEL	AGC	-	-	rs72479937		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155754775_155754777delAGC	uc003qqm.2	-							NM_015718	NP_056533			NADPH oxidase 3								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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	156072889	156072889	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156072889delA								NOX3 (295852 upstream) : MIR1202 (195042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	158130960	158130961	+	IGR	INS	-	AA	AA	rs147328587	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158130960_158130961insAA								ZDHHC14 (35984 upstream) : SNX9 (113333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	158156285	158156285	+	IGR	DEL	A	-	-	rs68128730		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158156285delA								ZDHHC14 (61309 upstream) : SNX9 (88009 downstream)																																			---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158299463	158299464	+	Intron	INS	-	T	T	rs77119884	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158299463_158299464insT	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)														---	---	---	---
TMEM181	57583	broad.mit.edu	37	6	159026190	159026191	+	Intron	INS	-	TATATATA	TATATATA	rs71756533		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159026190_159026191insTATATATA	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron	NM_020823	NP_065874			G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)														---	---	---	---
TMEM181	57583	broad.mit.edu	37	6	159030352	159030352	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159030352delT	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron	NM_020823	NP_065874			G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)														---	---	---	---
WTAP	9589	broad.mit.edu	37	6	160176798	160176798	+	3'UTR	DEL	T	-	-	rs5881337		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160176798delT	uc003qsl.2	+	8					WTAP_uc003qso.2_3'UTR	NM_004906	NP_004897			Wilms' tumour 1-associating protein isoform 1						cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160381300	160381300	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160381300delT								MAS1 (52195 upstream) : IGF2R (8831 downstream)																																			---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160443046	160443047	+	Intron	DEL	AC	-	-	rs35691140		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160443046_160443047delAC	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)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160443052	160443053	+	Intron	INS	-	CACACC	CACACC	rs139403451	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160443052_160443053insCACACC	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)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160524765	160524765	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160633579	160633580	+	Intron	INS	-	C	C	rs2448296	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160633579_160633580insC	uc003qte.1	-							NM_003058	NP_003049			solute carrier family 22 member 2						body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)														---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160645587	160645587	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160645587delT	uc003qtf.2	-						SLC22A2_uc003qte.1_Intron	NM_003058	NP_003049			solute carrier family 22 member 2						body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	161326648	161326648	+	IGR	DEL	T	-	-	rs112724223		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161326648delT								PLG (152303 upstream) : MAP3K4 (86174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164372941	164372943	+	IGR	DEL	TTT	-	-	rs11371868		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164372941_164372943delTTT								QKI (378049 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165259951	165259952	+	IGR	DEL	TG	-	-	rs150031748		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165259951_165259952delTG								None (None upstream) : C6orf118 (433203 downstream)																																			---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165763033	165763033	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165763033delA	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)													---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167148154	167148154	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167148154delC	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)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167238290	167238295	+	Intron	DEL	TGTCTA	-	-	rs112811891		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167238290_167238295delTGTCTA	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)														---	---	---	---
FGFR1OP	11116	broad.mit.edu	37	6	167447490	167447491	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167447490_167447491delTT	uc003qvj.2	+						CCR6_uc003qvl.2_Intron|FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvk.2_Intron	NM_007045	NP_008976			FGFR1 oncogene partner isoform a						G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation	centrosome|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(1)	1		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)				T	FGFR1	MPD|NHL								---	---	---	---
Unknown	0	broad.mit.edu	37	6	167672461	167672462	+	IGR	INS	-	C	C	rs115674032	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167672461_167672462insC								TCP10L2 (76066 upstream) : UNC93A (32341 downstream)																																			---	---	---	---
UNC93A	54346	broad.mit.edu	37	6	167725388	167725389	+	Intron	INS	-	TC	TC	rs147774750	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167725388_167725389insTC	uc003qvq.2	+						UNC93A_uc003qvr.2_Intron	NM_018974	NP_061847			unc-93 homolog A isoform 1							integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168593229	168593230	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168593229_168593230insA								FRMD1 (113390 upstream) : DACT2 (114356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168701667	168701670	+	IGR	DEL	AAAC	-	-	rs111937043		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168701667_168701670delAAAC								FRMD1 (221828 upstream) : DACT2 (5916 downstream)																																			---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168876515	168876515	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168876515delC	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	168919898	168919899	+	Intron	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168919898_168919899insGT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	169180893	169180893	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169180893delT								SMOC2 (112222 upstream) : THBS2 (434983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63521	63521	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63521delA								None (None upstream) : FAM20C (129448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	566234	566234	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:566234delC								PDGFA (6753 upstream) : PRKAR1B (23153 downstream)																																			---	---	---	---
ADAP1	11033	broad.mit.edu	37	7	946142	946143	+	Intron	DEL	GA	-	-	rs58373074		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:946142_946143delGA	uc003sjo.3	-						ADAP1_uc003sjm.3_5'Flank|ADAP1_uc011jvs.1_Intron|ADAP1_uc003sjn.3_Intron|ADAP1_uc010ksc.2_Intron	NM_006869	NP_006860			centaurin, alpha 1						cell surface receptor linked signaling pathway|regulation of ARF GTPase activity	cytoplasm|nucleus|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|protein binding|zinc ion binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	1308935	1308936	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1308935_1308936delTT								UNCX (32323 upstream) : MICALL2 (165060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1386818	1386818	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1386818delT								UNCX (110206 upstream) : MICALL2 (87178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1444069	1444070	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1444069_1444070delCA								UNCX (167457 upstream) : MICALL2 (29926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1718810	1718811	+	IGR	DEL	CG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1718810_1718811delCG								TFAMP1 (62483 upstream) : ELFN1 (29987 downstream)																																			---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2318254	2318257	+	Intron	DEL	ACTC	-	-	rs71550338		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2318254_2318257delACTC	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	2690214	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2690213_2690214delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	3116378	3116379	+	IGR	DEL	TG	-	-	rs66982715		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3116378_3116379delTG								CARD11 (32799 upstream) : SDK1 (224701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	3290423	3290423	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3290423delA								CARD11 (206844 upstream) : SDK1 (50657 downstream)																																			---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3361468	3361469	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3361468_3361469delTC	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3524355	3524355	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3524355delT	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3783380	3783380	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3783380delA	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4988159	4988159	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4988159delA	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070			monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5280899	5280900	+	IGR	DEL	CA	-	-	rs72378496		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5280899_5280900delCA								WIPI2 (7414 upstream) : SLC29A4 (41661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	5854587	5854587	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5854587delC								RNF216 (33295 upstream) : ZNF815 (8204 downstream)																																			---	---	---	---
ZNF815	401303	broad.mit.edu	37	7	5891220	5891221	+	Intron	INS	-	A	A	rs308074	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5891220_5891221insA	uc003spc.2	+						ZNF815_uc003spd.2_Intron	NR_023382				Homo sapiens cDNA FLJ38969 fis, clone NT2RI2002359.												0																		---	---	---	---
USP42	84132	broad.mit.edu	37	7	6185693	6185693	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6185693delA	uc011jwo.1	+						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)														---	---	---	---
ZNF12	7559	broad.mit.edu	37	7	6743199	6743199	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6743199delG	uc003sqt.1	-						ZNF12_uc011jxa.1_Intron|ZNF12_uc003sqs.1_Intron	NM_016265	NP_057349			zinc finger protein 12 isoform a						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)														---	---	---	---
RSPH10B2	728194	broad.mit.edu	37	7	6835564	6835564	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6835564delA	uc003sqw.1	+						RSPH10B2_uc010ktk.1_Intron|RSPH10B2_uc011jxc.1_Intron|RSPH10B2_uc010ktl.1_Intron	NM_173565	NP_775836			radial spoke head 10 homolog B											ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8243699	8243700	+	Intron	DEL	AA	-	-	rs75029395		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8243699_8243700delAA	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|ICA1_uc011jxg.1_Intron|ICA1_uc003srs.1_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	9036053	9036054	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9036053_9036054insA								NXPH1 (243461 upstream) : PER4 (637846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10952116	10952123	+	IGR	DEL	TTCTTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10952116_10952123delTTCTTTTT								None (None upstream) : NDUFA4 (20692 downstream)																																			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11631745	11631746	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11631745_11631746insG	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	11723356	11723356	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11723356delA	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	12331264	12331264	+	IGR	DEL	T	-	-	rs34806985		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12331264delT								TMEM106B (54375 upstream) : VWDE (39245 downstream)																																			---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12634662	12634663	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12634662_12634663delGA	uc003ssn.3	+						SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Intron	NM_001112706	NP_001106177			scinderin isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	12717227	12717228	+	IGR	DEL	CA	-	-	rs60233257		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12717227_12717228delCA								SCIN (24002 upstream) : ARL4A (9253 downstream)																																			---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14456258	14456258	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14456258delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	17317668	17317669	+	IGR	INS	-	TG	TG	rs138520681	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17317668_17317669insTG								AGR3 (396055 upstream) : AHR (20607 downstream)																																			---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18826403	18826406	+	Intron	DEL	TTTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18826403_18826406delTTTC	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)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18826444	18826463	+	Intron	DEL	TTCCTTCCTTCCTTCATTCC	-	-	rs142730759	by1000genomes;byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18826444_18826463delTTCCTTCCTTCCTTCATTCC	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)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18863711	18863713	+	Intron	DEL	AAC	-	-	rs58871197		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18863711_18863713delAAC	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.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	19083080	19083080	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19083080delT								HDAC9 (46096 upstream) : TWIST1 (72013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20583156	20583158	+	IGR	DEL	TCT	-	-	rs34025520		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20583156_20583158delTCT								ITGB8 (127778 upstream) : ABCB5 (72087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21282453	21282453	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21282453delA								RPL23P8 (415014 upstream) : SP4 (185236 downstream)																																			---	---	---	---
SP4	6671	broad.mit.edu	37	7	21485673	21485674	+	Intron	DEL	TG	-	-	rs5882811		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21485673_21485674delTG	uc003sva.2	+						SP4_uc003svb.2_Intron	NM_003112	NP_003103			Sp4 transcription factor						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22357672	22357672	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22357672delA	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																		---	---	---	---
MGC87042	256227	broad.mit.edu	37	7	22534157	22534157	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22534157delT	uc003svh.2	-						MGC87042_uc010kum.1_Intron					SubName: Full=cDNA FLJ60218, highly similar to Six transmembrane epithelial antigen ofprostate 1;							integral to membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	22978456	22978457	+	IGR	DEL	CA	-	-	rs143658259		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22978456_22978457delCA								SNORD93 (82152 upstream) : FAM126A (2430 downstream)																																			---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23411692	23411693	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23411692_23411693delTT	uc003swg.2	-							NM_006547	NP_006538			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
CCDC126	90693	broad.mit.edu	37	7	23652932	23652932	+	Intron	DEL	A	-	-	rs80237772		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23652932delA	uc003swl.2	+						CCDC126_uc003swm.2_Intron|CCDC126_uc003swn.2_Intron	NM_138771	NP_620126			coiled-coil domain containing 126 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
DFNA5	1687	broad.mit.edu	37	7	24758439	24758440	+	Intron	DEL	TA	-	-	rs137893101		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24758439_24758440delTA	uc010kus.1	-						DFNA5_uc003swz.2_Intron|DFNA5_uc003sxa.1_Intron|DFNA5_uc010kut.1_Intron|DFNA5_uc003sxb.2_Intron	NM_001127453	NP_001120925			deafness, autosomal dominant 5 protein isoform						sensory perception of sound					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25518653	25518653	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25518653delT								NPVF (250548 upstream) : MIR148A (470886 downstream)																																			---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26342092	26342095	+	Intron	DEL	CTCC	-	-	rs35323038		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26342092_26342095delCTCC	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454			sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0																		---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26352404	26352404	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26352404delA	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron	NM_013322	NP_037454			sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27766603	27766604	+	IGR	INS	-	AG	AG	rs145535392	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27766603_27766604insAG								HIBADH (64001 upstream) : TAX1BP1 (12388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	28325580	28325581	+	IGR	DEL	AC	-	-	rs34455244		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28325580_28325581delAC								LOC402644 (6262 upstream) : CREB5 (13359 downstream)																																			---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28390181	28390181	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28390181delA	uc003szo.2	+							NM_182899	NP_878902			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																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29535860	29535861	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29535860_29535861delAA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron|CHN2_uc010kvg.2_Intron|CHN2_uc010kvh.2_Intron|CHN2_uc010kvi.2_Intron|CHN2_uc010kve.2_Intron|CHN2_uc003taa.2_Intron|CHN2_uc010kvf.2_Intron|CHN2_uc010kvj.2_Intron|CHN2_uc010kvk.2_Intron|CHN2_uc010kvl.2_Intron|CHN2_uc010kvm.2_Intron|CHN2_uc011jzv.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29535932	29535932	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29535932delA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron|CHN2_uc010kvg.2_Intron|CHN2_uc010kvh.2_Intron|CHN2_uc010kvi.2_Intron|CHN2_uc010kve.2_Intron|CHN2_uc003taa.2_Intron|CHN2_uc010kvf.2_Intron|CHN2_uc010kvj.2_Intron|CHN2_uc010kvk.2_Intron|CHN2_uc010kvl.2_Intron|CHN2_uc010kvm.2_Intron|CHN2_uc011jzv.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30243729	30243730	+	IGR	INS	-	A	A	rs34072391		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30243729_30243730insA								C7orf41 (41348 upstream) : ZNRF2 (80193 downstream)																																			---	---	---	---
INMT	11185	broad.mit.edu	37	7	30766549	30766549	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30766549delT	uc010kwc.1	+											Homo sapiens indolethylamine N-methyltransferase (INMT) mRNA, INMT-1 allele, complete cds.							cytoplasm	amine N-methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	31031792	31031793	+	IGR	INS	-	CG	CG	rs150056159	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31031792_31031793insCG								GHRHR (12651 upstream) : ADCYAP1R1 (60349 downstream)																																			---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32176159	32176159	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32176159delA	uc003tco.1	-							NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32582583	32582583	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32582583delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_5'Flank	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32691335	32691335	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32691335delA	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32731724	32731725	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32731724_32731725delTT	uc011kai.1	+						uc003tcw.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	33075635	33075635	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33075635delA	uc011kai.1	+						NT5C3_uc003tdi.2_Intron|NT5C3_uc003tdj.2_Intron|NT5C3_uc003tdk.2_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	34940648	34940648	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34940648delG								NPSR1 (22704 upstream) : DPY19L1 (20433 downstream)																																			---	---	---	---
TBX20	57057	broad.mit.edu	37	7	35277221	35277222	+	Intron	INS	-	A	A	rs144542303	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35277221_35277222insA	uc011kas.1	-							NM_001077653	NP_001071121			T-box transcription factor TBX20							nucleus	DNA binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	35451634	35451634	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35451634delA								TBX20 (158392 upstream) : HERPUD2 (220638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35495539	35495539	+	IGR	DEL	A	-	-	rs71870690		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35495539delA								TBX20 (202297 upstream) : HERPUD2 (176733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35597697	35597698	+	IGR	INS	-	TACA	TACA	rs142193902	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35597697_35597698insTACA								TBX20 (304455 upstream) : HERPUD2 (74574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35644591	35644591	+	IGR	DEL	C	-	-	rs35239394		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35644591delC								TBX20 (351349 upstream) : HERPUD2 (27681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36027639	36027639	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36027639delA								SEPT7 (82724 upstream) : EEPD1 (165197 downstream)																																			---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	36975013	36975013	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36975013delA	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																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37287800	37287801	+	Intron	DEL	TG	-	-	rs72014175		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37287800_37287801delTG	uc003tfk.1	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	37609204	37609204	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37609204delA								ELMO1 (120674 upstream) : GPR141 (170792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	38161603	38161603	+	IGR	DEL	C	-	-	rs139222035		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38161603delC								EPDR1 (170064 upstream) : STARD3NL (56330 downstream)																																			---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38766400	38766400	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38766400delT	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron|VPS41_uc003tgx.2_Intron	NM_014396	NP_055211			vacuolar protein sorting 41 isoform 1						Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39036879	39036880	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39036879_39036880insT	uc003tha.1	-											Homo sapiens cDNA FLJ12971 fis, clone NT2RP2005882.																														---	---	---	---
LOC349114	349114	broad.mit.edu	37	7	39825140	39825140	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39825140delA	uc003thf.2	+							NR_026999				Homo sapiens cDNA FLJ40085 fis, clone TESTI2002993.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39927388	39927389	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39927388_39927389insT								LOC349114 (93167 upstream) : CDK13 (62570 downstream)																																			---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40276438	40276438	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40276438delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	41222995	41222998	+	IGR	DEL	CTCC	-	-	rs39776		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41222995_41222998delCTCC								C7orf10 (322638 upstream) : INHBA (505605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41661491	41661492	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41661491_41661492delAG								C7orf10 (761134 upstream) : INHBA (67111 downstream)																																			---	---	---	---
LOC285954	285954	broad.mit.edu	37	7	41772931	41772933	+	Intron	DEL	TTT	-	-	rs79263462		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41772931_41772933delTTT	uc003tht.3	+							NR_027118				Homo sapiens cDNA FLJ38947 fis, clone NT2NE2017792.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	42301791	42301791	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42301791delT								GLI3 (25173 upstream) : C7orf25 (647083 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43405701	43405702	+	Intron	INS	-	A	A	rs76336492		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43405701_43405702insA	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	43405817	43405817	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43405817delA	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	43552506	43552506	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43552506delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron|uc003tig.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																		---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44675307	44675307	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44675307delT	uc003tln.2	+						OGDH_uc003tlm.2_Intron|OGDH_uc011kbx.1_Intron|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Intron|OGDH_uc011kbz.1_Intron	NM_002541	NP_002532			oxoglutarate dehydrogenase isoform 1 precursor						glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45177057	45177058	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45177057_45177058delTT								TBRG4 (25740 upstream) : RAMP3 (20309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45892180	45892180	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45892180delT								SEPT7P2 (83563 upstream) : IGFBP1 (35779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46227005	46227005	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46227005delA								IGFBP3 (266134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46338456	46338457	+	IGR	DEL	CA	-	-	rs71567738		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46338456_46338457delCA								IGFBP3 (377585 upstream) : TNS3 (976296 downstream)																																			---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47420368	47420369	+	Intron	DEL	CA	-	-	rs143205554	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47420368_47420369delCA	uc003tnv.2	-						TNS3_uc003tnw.2_Intron	NM_022748	NP_073585			tensin 3							focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	48179753	48179753	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48179753delG								UPP1 (31424 upstream) : ABCA13 (31304 downstream)																																			---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48477990	48477991	+	Intron	INS	-	GTA	GTA	rs141045774	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48477990_48477991insGTA	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	49500825	49500825	+	IGR	DEL	A	-	-	rs34553685		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49500825delA								CDC14C (533776 upstream) : VWC2 (312432 downstream)																																			---	---	---	---
DDC	1644	broad.mit.edu	37	7	50563794	50563795	+	Intron	DEL	TT	-	-	rs112532220		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50563794_50563795delTT	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	50661671	50661674	+	Intron	DEL	CTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50661671_50661674delCTTT	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				---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50744487	50744487	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50744487delG	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				---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50785148	50785149	+	Intron	DEL	GT	-	-	rs72220792		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50785148_50785149delGT	uc003tpi.2	-						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	51545420	51545423	+	IGR	DEL	GTGT	-	-	rs111599341		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51545420_51545423delGTGT								COBL (160905 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	51633517	51633517	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51633517delA								COBL (249002 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53590210	53590210	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53590210delG								POM121L12 (485593 upstream) : HPVC1 (678707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54171051	54171052	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54171051_54171052delAA								None (None upstream) : HPVC1 (97865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	55405729	55405744	+	IGR	DEL	AAACATGGTGGCCTCC	-	-	rs112128644		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55405729_55405744delAAACATGGTGGCCTCC								EGFR (130699 upstream) : LANCL2 (27397 downstream)																																			---	---	---	---
LANCL2	55915	broad.mit.edu	37	7	55476786	55476786	+	Intron	DEL	T	-	-	rs113959130		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55476786delT	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)															---	---	---	---
VOPP1	81552	broad.mit.edu	37	7	55584386	55584386	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55584386delC	uc003tqs.2	-						VOPP1_uc003tqq.2_Intron|VOPP1_uc010kzh.2_Intron|VOPP1_uc010kzi.2_Intron|VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423			EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0																		---	---	---	---
MRPS17	51373	broad.mit.edu	37	7	56015302	56015303	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56015302_56015303delTT	uc003trb.2	+							NM_015969	NP_057053			mitochondrial ribosomal protein S17 precursor						translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56557369	56557370	+	IGR	INS	-	GTTTCCAT	GTTTCCAT	rs139632643	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56557369_56557370insGTTTCCAT								PSPH (373279 upstream) : DKFZp434L192 (6546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56857032	56857032	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56857032delT								DKFZp434L192 (292055 upstream) : ZNF479 (330296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56903097	56903097	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56903097delA	uc003tsm.2	-											DQ599872																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	56972654	56972656	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56972654_56972656delTTT								DKFZp434L192 (407677 upstream) : ZNF479 (214672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57638851	57638852	+	IGR	INS	-	CT	CT	rs141862684	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57638851_57638852insCT								ZNF716 (105586 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57743617	57743618	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57743617_57743618delAG								ZNF716 (210352 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61547705	61547706	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61547705_61547706insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61759467	61759467	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61759467delA								None (None upstream) : LOC643955 (992205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61886139	61886139	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61886139delT								None (None upstream) : LOC643955 (865533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61913788	61913789	+	IGR	DEL	TT	-	-	rs111262847		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61913788_61913789delTT								None (None upstream) : LOC643955 (837883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62981782	62981783	+	IGR	DEL	TC	-	-	rs62476047		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62981782_62981783delTC								LOC100287704 (169631 upstream) : ZNF727 (524038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63860139	63860139	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63860139delC								ZNF679 (132839 upstream) : ZNF680 (120116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64558919	64558919	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64558919delA								ZNF117 (91798 upstream) : INTS4L1 (42684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64984742	64984742	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64984742delC								ZNF92 (118745 upstream) : INTS4L2 (128035 downstream)																																			---	---	---	---
C7orf42	55069	broad.mit.edu	37	7	66404946	66404946	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66404946delT	uc003tvk.2	+						C7orf42_uc010lah.2_Intron|C7orf42_uc003tvl.2_Intron	NM_017994	NP_060464			hypothetical protein LOC55069							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66440369	66440370	+	IGR	INS	-	G	G	rs143844657	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66440369_66440370insG								C7orf42 (16832 upstream) : SBDS (12320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67030646	67030646	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67030646delG								STAG3L4 (244134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67210264	67210265	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67210264_67210265insT								STAG3L4 (423752 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67459530	67459530	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67459530delT								STAG3L4 (673018 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67983027	67983029	+	IGR	DEL	ACA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67983027_67983029delACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68600432	68600432	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68600432delG								None (None upstream) : AUTS2 (463473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68755220	68755221	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68755220_68755221insA								None (None upstream) : AUTS2 (308684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68833675	68833675	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68833675delA								None (None upstream) : AUTS2 (230230 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69652761	69652762	+	Intron	INS	-	TT	TT	rs71991032		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69652761_69652762insTT	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	70021181	70021182	+	Intron	INS	-	CA	CA	rs35740261		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70021181_70021182insCA	uc003tvw.3	+						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	70117335	70117336	+	Intron	INS	-	T	T	rs144662190	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70117335_70117336insT	uc003tvw.3	+						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	70131639	70131639	+	Intron	DEL	T	-	-	rs71703601		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70131639delT	uc003tvw.3	+						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	70185189	70185189	+	Intron	DEL	T	-	-	rs72373002		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70185189delT	uc003tvw.3	+						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	70630937	70630937	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70630937delT	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	71016755	71016763	+	Intron	DEL	AAAAGAGAG	-	-	rs71531749		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71016755_71016763delAAAAGAGAG	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)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71372225	71372226	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71372225_71372226delAC	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	71878763	71878764	+	Intron	INS	-	AT	AT	rs143606666	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71878763_71878764insAT	uc003twc.3	-						CALN1_uc003twb.3_5'Flank	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)																---	---	---	---
WBSCR26	171022	broad.mit.edu	37	7	73148300	73148302	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73148300_73148302delAAA	uc011kez.1	+							NR_026690				Homo sapiens Williams Beuren syndrome chromosome region 26 (non-protein coding) (WBSCR26), non-coding RNA.												0																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73194486	73194488	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73194486_73194488delAAA	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73223371	73223372	+	Intron	INS	-	C	C	rs139156166	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73223371_73223372insC	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73327868	73327868	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73327868delT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73547615	73547616	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73547615_73547616delTT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|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	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73734154	73734156	+	Intron	DEL	AAG	-	-	rs145476760	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73734154_73734156delAAG	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73969294	73969295	+	Intron	INS	-	G	G	rs34885297		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73969294_73969295insG	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																		---	---	---	---
GTF2IP1	2970	broad.mit.edu	37	7	74776124	74776124	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74776124delA	uc003ubw.2	-						uc003ubz.1_Intron|PMS2L2_uc011kfp.1_Intron|PMS2L2_uc011kfq.1_Intron|uc003ucd.2_Intron|uc010lck.2_Intron					SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0																		---	---	---	---
SPDYE5	442590	broad.mit.edu	37	7	75123852	75123852	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75123852delG	uc011kfy.1	+							NM_001099435	NP_001092905			speedy homolog E5												0																		---	---	---	---
CCL26	10344	broad.mit.edu	37	7	75419475	75419476	+	5'Flank	INS	-	CCTT	CCTT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75419475_75419476insCCTT	uc003udt.1	-							NM_006072	NP_006063			chemokine (C-C motif) ligand 26 precursor						cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75427949	75427949	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75427949delT								CCL26 (8885 upstream) : CCL24 (13167 downstream)																																			---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76070128	76070129	+	Intron	INS	-	T	T	rs11459370		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76070128_76070129insT	uc003ufd.3	+						ZP3_uc003ufc.3_Intron|ZP3_uc003ufe.2_Intron	NM_001110354	NP_001103824			zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77121676	77121676	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77121676delA								PION (75959 upstream) : PTPN12 (45097 downstream)																																			---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77821697	77821697	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77821697delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.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)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78160055	78160055	+	Intron	DEL	T	-	-	rs140671545		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78160055delT	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	79290095	79290096	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79290095_79290096delTG								MAGI2 (207205 upstream) : GNAI1 (474044 downstream)																																			---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79785751	79785752	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79785751_79785752delTT	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	79979195	79979196	+	IGR	DEL	GT	-	-	rs116800981	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79979195_79979196delGT								GNAI1 (130470 upstream) : CD36 (19695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	84034495	84034495	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84034495delA								SEMA3A (210278 upstream) : SEMA3D (590379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	84436709	84436710	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84436709_84436710delTG								SEMA3A (612492 upstream) : SEMA3D (188164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	86167958	86167963	+	IGR	DEL	ACACTT	-	-	rs150603014		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86167958_86167963delACACTT								None (None upstream) : GRM3 (105267 downstream)																																			---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86512337	86512338	+	Intron	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86512337_86512338insGT	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)																	---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86625456	86625456	+	Intron	DEL	T	-	-	rs1767743	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86625456delT	uc011kha.1	-						KIAA1324L_uc003uif.1_Intron|KIAA1324L_uc011kgz.1_Intron	NM_001142749	NP_001136221			hypothetical protein LOC222223 isoform 1							integral to membrane				ovary(6)|skin(1)	7	Esophageal squamous(14;0.0058)																	---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87589690	87589691	+	Intron	INS	-	GTGT	GTGT	rs149434554	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87589690_87589691insGTGT	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87621583	87621583	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87621583delC	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	88184836	88184837	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88184836_88184837insT								STEAP4 (248627 upstream) : ZNF804B (203916 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88768431	88768431	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88768431delT	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)			---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90250977	90250978	+	Intron	INS	-	CCTTCCTG	CCTTCCTG	rs6465274	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90250977_90250978insCCTTCCTG	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.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	90919029	90919030	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90919029_90919030delTT								FZD1 (20898 upstream) : MTERF (512430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91250198	91250199	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91250198_91250199delGA								FZD1 (352067 upstream) : MTERF (181261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	91341666	91341667	+	IGR	INS	-	AGGG	AGGG	rs143993987	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91341666_91341667insAGGG								FZD1 (443535 upstream) : MTERF (89793 downstream)																																			---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91996323	91996324	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91996323_91996324insA	uc003ulw.2	+							NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)															---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94600424	94600424	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94600424delA	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	95384085	95384085	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95384085delT								PDK4 (158160 upstream) : DYNC1I1 (17733 downstream)																																			---	---	---	---
DYNC1I1	1780	broad.mit.edu	37	7	95680461	95680461	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95680461delT	uc003uoc.3	+						DYNC1I1_uc003uod.3_Intron|DYNC1I1_uc003uob.2_Intron|DYNC1I1_uc003uoe.3_Intron|DYNC1I1_uc010lfl.2_Intron	NM_004411	NP_004402			dynein, cytoplasmic 1, intermediate chain 1						vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole|vesicle	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	96268527	96268527	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96268527delG	uc010lfm.1	-											Homo sapiens cDNA, FLJ17342.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96278098	96278098	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96278098delT	uc010lfm.1	-											Homo sapiens cDNA, FLJ17342.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96377119	96377130	+	IGR	DEL	CTTCCTTCCTTT	-	-	rs71956221		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96377119_96377130delCTTCCTTCCTTT								SHFM1 (37916 upstream) : DLX6AS (220698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96396424	96396425	+	IGR	INS	-	AG	AG	rs59991210		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96396424_96396425insAG								SHFM1 (57221 upstream) : DLX6AS (201403 downstream)																																			---	---	---	---
DLX6AS	285987	broad.mit.edu	37	7	96627454	96627454	+	Intron	DEL	A	-	-	rs77045477		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96627454delA	uc003uok.2	-						DLX6AS_uc003uol.2_Intron|DLX6AS_uc010lfo.1_Intron					Homo sapiens cDNA FLJ34048 fis, clone FCBBF3000102.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	97633316	97633319	+	IGR	DEL	CCTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97633316_97633319delCCTT								OCM2 (13900 upstream) : LMTK2 (102878 downstream)																																			---	---	---	---
ZSCAN21	7589	broad.mit.edu	37	7	99661218	99661218	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99661218delA	uc003uso.2	+						ZSCAN21_uc003usn.1_Intron	NM_145914	NP_666019			zinc finger protein 38						positive regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
GATS	352954	broad.mit.edu	37	7	99857383	99857383	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99857383delA	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc010lgu.2_Intron	NM_178831	NP_849153			GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100988355	100988356	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100988355_100988356delTT								RABL5 (23262 upstream) : EMID2 (17766 downstream)																																			---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101178870	101178870	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101178870delG	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101470574	101470574	+	Intron	DEL	T	-	-	rs71106567		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101470574delT	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																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103346848	103346848	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103346848delA	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036			reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	103969195	103969197	+	5'UTR	DEL	AGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103969195_103969197delAGG	uc003vce.2	+	1					LHFPL3_uc003vcf.2_5'UTR	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	104610892	104610892	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104610892delT								LOC723809 (43800 upstream) : LOC100216545 (40097 downstream)																																			---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104694845	104694845	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104694845delA	uc003vcm.2	+						MLL5_uc010lja.1_Intron|MLL5_uc010ljb.1_Intron|MLL5_uc003vcl.2_Intron|MLL5_uc010ljc.2_Intron	NM_182931	NP_891847			myeloid/lymphoid or mixed-lineage leukemia 5						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																		---	---	---	---
PUS7	54517	broad.mit.edu	37	7	105127177	105127177	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105127177delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915			pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1																		---	---	---	---
PUS7	54517	broad.mit.edu	37	7	105146865	105146865	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105146865delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915			pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105249915	105249915	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105249915delA	uc003vde.2	-						ATXN7L1_uc003vdf.2_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105320372	105320373	+	Intron	INS	-	A	A	rs144079213	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105320372_105320373insA	uc003vde.2	-						ATXN7L1_uc003vdf.2_5'Flank|ATXN7L1_uc003vdh.3_5'Flank|ATXN7L1_uc011klr.1_5'Flank	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107573177	107573177	+	Intron	DEL	A	-	-	rs72447555		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107573177delA	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003veu.2_5'Flank	NM_002291	NP_002282			laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107928100	107928101	+	Intron	DEL	AT	-	-	rs139446837		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107928100_107928101delAT	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																		---	---	---	---
PNPLA8	50640	broad.mit.edu	37	7	108138578	108138578	+	Intron	DEL	A	-	-	rs72406388		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108138578delA	uc003vff.1	-						PNPLA8_uc003vfg.1_Intron|PNPLA8_uc003vfh.1_Intron|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Intron|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538			patatin-like phospholipase domain containing 8						fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108193657	108193657	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108193657delT								PNPLA8 (25052 upstream) : THAP5 (9016 downstream)																																			---	---	---	---
DNAJB9	4189	broad.mit.edu	37	7	108213939	108213940	+	3'UTR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108213939_108213940delTT	uc003vfn.2	+	3						NM_012328	NP_036460			DnaJ (Hsp40) homolog, subfamily B, member 9						ER-associated protein catabolic process|protein folding	endoplasmic reticulum|nucleolus	heat shock protein binding|misfolded protein binding|unfolded protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108293842	108293842	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108293842delA								DNAJB9 (78550 upstream) : C7orf66 (230198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108555019	108555019	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108555019delT								C7orf66 (30382 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108605178	108605178	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108605178delT								C7orf66 (80541 upstream) : EIF3IP1 (994106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108621610	108621611	+	IGR	INS	-	G	G	rs148280673	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108621610_108621611insG								C7orf66 (96973 upstream) : EIF3IP1 (977673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109794073	109794073	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109794073delT								EIF3IP1 (193803 upstream) : IMMP2L (509037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110018874	110018875	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110018874_110018875delTC								EIF3IP1 (418604 upstream) : IMMP2L (284235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110035434	110035434	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110035434delT								EIF3IP1 (435164 upstream) : IMMP2L (267676 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110695108	110695110	+	Intron	DEL	TTT	-	-	rs113824921		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110695108_110695110delTTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	112034933	112034933	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112034933delT								ZNF277 (50944 upstream) : IFRD1 (28293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112233361	112233361	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112233361delG								C7orf53 (102426 upstream) : TMEM168 (172428 downstream)																																			---	---	---	---
C7orf60	154743	broad.mit.edu	37	7	112513105	112513106	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112513105_112513106delAA	uc003vgo.1	-						C7orf60_uc011kms.1_Intron	NM_152556	NP_689769			hypothetical protein LOC154743											ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112973041	112973041	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112973041delA								LOC401397 (214404 upstream) : PPP1R3A (543841 downstream)																																			---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114009590	114009590	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114009590delA	uc003vgv.1	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgt.1_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114149981	114149981	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114149981delA	uc003vhb.2	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgz.2_Intron|FOXP2_uc003vha.2_Intron|FOXP2_uc011kmu.1_Intron|FOXP2_uc011kmv.1_Intron|FOXP2_uc003vgt.1_Intron|FOXP2_uc003vgv.1_Intron|FOXP2_uc003vgw.2_Intron|FOXP2_uc003vgx.2_Intron|FOXP2_uc003vhd.2_Intron|FOXP2_uc003vhc.2_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	114468390	114468390	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114468390delA								FOXP2 (137298 upstream) : MDFIC (93819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	114944736	114944736	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114944736delA								MDFIC (285473 upstream) : TFEC (630466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115341016	115341017	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115341016_115341017delAC								MDFIC (681753 upstream) : TFEC (234185 downstream)																																			---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117304011	117304011	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117304011delA	uc003vjd.2	+						CFTR_uc011knq.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				---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119998561	119998561	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119998561delT	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
FAM3C	10447	broad.mit.edu	37	7	121018324	121018324	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121018324delA	uc003vjx.2	-						FAM3C_uc010lkm.2_Intron	NM_014888	NP_055703			family with sequence similarity 3, member C						multicellular organismal development	cytoplasmic membrane-bounded vesicle|extracellular region	cytokine activity				0	all_neural(327;0.117)																	---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122327804	122327805	+	Intron	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122327804_122327805delAT	uc010lkp.2	-						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																		---	---	---	---
IQUB	154865	broad.mit.edu	37	7	123101680	123101681	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123101680_123101681insA	uc003vkn.2	-						IQUB_uc011kny.1_5'Flank|IQUB_uc003vko.2_Intron|IQUB_uc010lkt.2_Intron	NM_178827	NP_849149			IQ motif and ubiquitin domain containing											ovary(3)|large_intestine(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123842624	123842625	+	Intron	INS	-	TAAT	TAAT	rs141946795	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123842624_123842625insTAAT	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124432106	124432107	+	5'Flank	INS	-	AC	AC	rs142678970	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124432106_124432107insAC	uc003vlj.1	-											Homo sapiens cDNA clone IMAGE:40146631.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124455307	124455307	+	IGR	DEL	A	-	-	rs79012367		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124455307delA								GPR37 (49626 upstream) : POT1 (7134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124807930	124807930	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124807930delT	uc003vlq.1	+											Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126599073	126599073	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126599073delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126630005	126630005	+	Intron	DEL	A	-	-	rs68093340		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126630005delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.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)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126996395	126996396	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126996395_126996396insA								GRM8 (103248 upstream) : ZNF800 (13958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127248053	127248054	+	IGR	DEL	AG	-	-	rs144565736		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127248053_127248054delAG								FSCN3 (6210 upstream) : PAX4 (2292 downstream)																																			---	---	---	---
SND1	27044	broad.mit.edu	37	7	127523403	127523403	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127523403delT	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	127865607	127865607	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127865607delA								MIR129-1 (17611 upstream) : LEP (15724 downstream)																																			---	---	---	---
METTL2B	55798	broad.mit.edu	37	7	128129490	128129490	+	Intron	DEL	A	-	-	rs111503975		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128129490delA	uc003vnf.2	+						METTL2B_uc003vng.2_Intron|METTL2B_uc011kop.1_Intron	NM_018396	NP_060866			methyltransferase like 2B								methyltransferase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	128465854	128465854	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128465854delT								CCDC136 (3671 upstream) : FLNC (4629 downstream)																																			---	---	---	---
TNPO3	23534	broad.mit.edu	37	7	128607794	128607795	+	Intron	DEL	AC	-	-	rs35430377		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128607794_128607795delAC	uc003vol.1	-						TNPO3_uc010llx.1_Intron|TNPO3_uc003vom.1_Intron|TNPO3_uc010lly.1_Intron|TNPO3_uc010llz.1_Intron	NM_012470	NP_036602			transportin 3						splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	128950947	128950950	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128950947_128950950delAAAA	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
MEST	4232	broad.mit.edu	37	7	130134991	130134991	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130134991delT	uc003vqg.2	+						MEST_uc003vqc.2_Intron|MEST_uc003vqd.2_Intron|MEST_uc003vqf.2_Intron|MEST_uc011kph.1_Intron|MEST_uc010lmg.2_Intron|uc011kpi.1_5'Flank|MIR335_hsa-mir-335|MI0000816_5'Flank	NM_002402	NP_002393			mesoderm specific transcript isoform a						mesoderm development	endoplasmic reticulum membrane|integral to membrane	hydrolase activity|protein binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130149295	130149295	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130149295delA	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130293581	130293582	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130293581_130293582insT	uc003vqh.1	-							NM_012133	NP_036265			coatomer protein complex, subunit gamma 2						intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132007945	132007945	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132007945delA	uc003vra.3	-							NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132297747	132297747	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132297747delA	uc003vrb.2	-							NM_181775	NP_861440			plexin A4 isoform 2							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132526320	132526320	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132526320delA	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	133169293	133169293	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133169293delA	uc003vrk.2	+						EXOC4_uc011kpo.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	133404657	133404658	+	Intron	INS	-	GGAT	GGAT	rs139837579	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133404657_133404658insGGAT	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	133539162	133539163	+	Intron	DEL	CA	-	-	rs62470395		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133539162_133539163delCA	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)														OREG0018331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133628525	133628526	+	Intron	INS	-	T	T	rs151071428	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133628525_133628526insT	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)																---	---	---	---
LRGUK	136332	broad.mit.edu	37	7	133832188	133832189	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133832188_133832189delAA	uc003vrm.1	+							NM_144648	NP_653249			leucine-rich repeats and guanylate kinase domain								ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	134057497	134057497	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134057497delT								SLC35B4 (55670 upstream) : AKR1B1 (69610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	134655920	134655920	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134655920delA								CALD1 (450 upstream) : AGBL3 (15339 downstream)																																			---	---	---	---
AGBL3	340351	broad.mit.edu	37	7	134795944	134795945	+	Intron	DEL	CT	-	-	rs35535345		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134795944_134795945delCT	uc011kpw.1	+						uc003vsg.2_Intron|C7orf49_uc003vsh.2_Intron	NM_178563	NP_848658			carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135016260	135016260	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135016260delT								STRA8 (73018 upstream) : CNOT4 (30293 downstream)																																			---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135287859	135287860	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135287859_135287860delAC	uc003vsw.2	+							NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135452389	135452390	+	IGR	INS	-	A	A	rs67480230		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135452389_135452390insA								FAM180A (18795 upstream) : LUZP6 (159115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136223176	136223176	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136223176delA								LUZP6 (560972 upstream) : CHRM2 (330223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136547991	136547991	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136547991delA								LUZP6 (885787 upstream) : CHRM2 (5408 downstream)																																			---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137745427	137745427	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137745427delT	uc011kqb.1	+						AKR1D1_uc011kqc.1_Intron|AKR1D1_uc011kqd.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138237376	138237376	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138237376delG	uc003vuc.2	+						TRIM24_uc003vub.2_Intron	NM_015905	NP_056989			transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
ATP6V0A4	50617	broad.mit.edu	37	7	138402947	138402948	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138402947_138402948delGT	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856			ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1																		---	---	---	---
ATP6V0A4	50617	broad.mit.edu	37	7	138424844	138424847	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138424844_138424847delAAAA	uc003vuf.2	-						ATP6V0A4_uc003vug.2_Intron|ATP6V0A4_uc003vuh.2_Intron	NM_130841	NP_570856			ATPase, H+ transporting, lysosomal V0 subunit						cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138542874	138542874	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138542874delT	uc011kql.1	-						KIAA1549_uc011kqi.1_Intron|KIAA1549_uc003vuk.3_Intron|KIAA1549_uc011kqj.1_Intron|KIAA1549_uc011kqk.1_Intron	NM_020910	NP_065961			hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	7	138725979	138725979	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138725979delA								ZC3HAV1L (5204 upstream) : ZC3HAV1 (2289 downstream)																																			---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138935293	138935293	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138935293delA	uc011kqr.1	+							NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138951166	138951166	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138951166delA	uc011kqr.1	+						UBN2_uc003vuv.2_Intron	NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	139118058	139118058	+	IGR	DEL	T	-	-	rs68147840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139118058delT								LUC7L2 (9860 upstream) : KLRG2 (20031 downstream)																																			---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140236158	140236160	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140236158_140236160delAAA	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140241781	140241781	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140241781delT	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140297814	140297815	+	Intron	INS	-	A	A	rs150066723	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140297814_140297815insA	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140370192	140370192	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140370192delT	uc003vvy.1	+						ADCK2_uc003vvz.2_5'Flank	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140677926	140677926	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140677926delT								BRAF (53362 upstream) : MRPS33 (28036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141158808	141158808	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141158808delT								MRPS33 (444027 upstream) : AGK (92270 downstream)																																			---	---	---	---
FLJ40852	285962	broad.mit.edu	37	7	141434606	141434606	+	Intron	DEL	C	-	-	rs5888013		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141434606delC	uc011krh.1	-						FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron	NR_015392				Homo sapiens cDNA FLJ40852 fis, clone TRACH2015381.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	142137388	142137390	+	Intron	DEL	AGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142137388_142137390delAGT	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142465862	142465862	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142465862delT	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|TRY6_uc011kso.1_5'Flank					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	143234544	143234544	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143234544delG								TAS2R41 (58655 upstream) : LOC441294 (34346 downstream)																																			---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144410018	144410018	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144410018delG	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|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	145418395	145418395	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145418395delA								TPK1 (885249 upstream) : CNTNAP2 (395058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145722376	145722377	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145722376_145722377insT								None (None upstream) : CNTNAP2 (91076 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146686633	146686634	+	Intron	INS	-	AAAA	AAAA	rs144452867	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146686633_146686634insAAAA	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	148515750	148515750	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148515750delT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	7	149032258	149032259	+	IGR	INS	-	A	A	rs71531612		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149032258_149032259insA								ZNF212 (79577 upstream) : ZNF777 (96202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	149050755	149050755	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149050755delA								ZNF212 (98074 upstream) : ZNF777 (77706 downstream)																																			---	---	---	---
KRBA1	84626	broad.mit.edu	37	7	149417442	149417442	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149417442delC	uc003wfz.2	+						KRBA1_uc010lpj.2_Intron|KRBA1_uc003wga.2_Intron	NM_032534	NP_115923			KRAB A domain containing 1											ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149775303	149775303	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149775303delT								ATP6V0E2 (197517 upstream) : ACTR3C (168999 downstream)																																			---	---	---	---
ABP1	26	broad.mit.edu	37	7	150538404	150538406	+	Intron	DEL	ATC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150538404_150538406delATC	uc003why.1	+							NM_001091	NP_001082			amiloride binding protein 1 precursor						amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	150869311	150869312	+	IGR	INS	-	AGT	AGT	rs72302325		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150869311_150869312insAGT								GBX1 (4444 upstream) : ASB10 (3473 downstream)																																	OREG0018450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SMARCD3	6604	broad.mit.edu	37	7	150955662	150955663	+	Intron	INS	-	G	G	rs60499090	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150955662_150955663insG	uc003wjt.2	-						SMARCD3_uc003wju.2_Intron	NM_001003802	NP_001003802			SWI/SNF related, matrix associated, actin						cellular lipid metabolic process|chromatin modification|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	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151855607	151855607	+	Intron	DEL	G	-	-	rs77253307		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151855607delG	uc003wla.2	-						MLL3_uc003wkz.2_Intron|MLL3_uc003wkx.2_5'Flank|MLL3_uc003wky.2_Intron	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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151902157	151902157	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151902157delA	uc003wla.2	-						MLL3_uc003wkz.2_Intron	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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151987146	151987148	+	Intron	DEL	AAC	-	-	rs79615696		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151987146_151987148delAAC	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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152110686	152110686	+	Intron	DEL	C	-	-	rs68123937		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152110686delC	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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	152117929	152117929	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152117929delG	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	153560552	153560552	+	IGR	DEL	T	-	-	rs66499204		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153560552delT								None (None upstream) : DPP6 (23867 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154021953	154021953	+	Intron	DEL	T	-	-	rs143944650		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154021953delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc010lqh.1_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154176035	154176036	+	Intron	INS	-	TTTG	TTTG	rs137952062	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154176035_154176036insTTTG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154178429	154178430	+	Intron	DEL	GG	-	-	rs113567023		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154178429_154178430delGG	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154665585	154665586	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154665585_154665586delCA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	154891184	154891186	+	IGR	DEL	AGA	-	-	rs59181235		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154891184_154891186delAGA								HTR5A (13725 upstream) : INSIG1 (198300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155084928	155084928	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155084928delA								HTR5A (207469 upstream) : INSIG1 (4558 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155470846	155470850	+	Intron	DEL	TCATT	-	-	rs5888632		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155470846_155470850delTCATT	uc010lqk.1	+						RBM33_uc003wme.2_Intron	NM_053043	NP_444271			RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155725138	155725139	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155725138_155725139delTG								SHH (120171 upstream) : C7orf4 (608046 downstream)																																			---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156661357	156661357	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156661357delA	uc003wmw.3	-						LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron|LMBR1_uc010lqo.2_Intron	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	156924628	156924628	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156924628delA								MNX1 (121281 upstream) : UBE3C (7027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	157295667	157295667	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157295667delT								DNAJB6 (85535 upstream) : PTPRN2 (36084 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157896561	157896561	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157896561delT	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	157948438	157948446	+	Intron	DEL	CACCATCAC	-	-	rs149426760	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157948438_157948446delCACCATCAC	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	157957046	157957107	+	Intron	DEL	GAAGGGCACGCAGAGCAGGAGGGTGCGTAGGAAGGACACGCAGAGCAGGAGCGCGCGCGTAG	-	-	rs71198576		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157957046_157957107delGAAGGGCACGCAGAGCAGGAGGGTGCGTAGGAAGGACACGCAGAGCAGGAGCGCGCGCGTAG	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	158120067	158120069	+	Intron	DEL	ATT	-	-	rs147532097		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158120067_158120069delATT	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	158415857	158415857	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158415857delT								PTPRN2 (35375 upstream) : NCAPG2 (8146 downstream)																																			---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158683291	158683291	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158683291delT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158711644	158711644	+	Intron	DEL	T	-	-	rs3216979		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158711644delT	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158994822	158994823	+	IGR	INS	-	GG	GG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158994822_158994823insGG								VIPR2 (57173 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	159069685	159069685	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:159069685delT								VIPR2 (132036 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	25964	25964	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25964delA								None (None upstream) : OR4F21 (90124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60374	60374	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60374delT								None (None upstream) : OR4F21 (55714 downstream)																																			---	---	---	---
ZNF596	169270	broad.mit.edu	37	8	185479	185479	+	Intron	DEL	T	-	-	rs34268945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:185479delT	uc003wot.2	+						ZNF596_uc003wou.2_Intron|ZNF596_uc003wov.2_Intron|ZNF596_uc003wow.2_Intron	NM_173539	NP_775810			zinc finger protein 596						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1276214	1276215	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1276214_1276215insT								ERICH1 (594988 upstream) : DLGAP2 (173354 downstream)																																			---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1479406	1479407	+	Intron	DEL	GC	-	-	rs139954503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1479406_1479407delGC	uc003wpl.2	+							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	1724654	1724655	+	Intron	INS	-	A	A	rs141640229	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1724654_1724655insA	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)														---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1884676	1884676	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1884676delA	uc003wpr.2	+						ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc010lre.2_Intron	NM_014629	NP_055444			Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2130434	2130435	+	IGR	INS	-	CG	CG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2130434_2130435insCG								MYOM2 (37055 upstream) : CSMD1 (662441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2596232	2596232	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2596232delA								MYOM2 (502853 upstream) : CSMD1 (196644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2657554	2657554	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2657554delC								MYOM2 (564175 upstream) : CSMD1 (135322 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3777880	3777881	+	Intron	DEL	TT	-	-	rs139461025	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3777880_3777881delTT	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	4059998	4059998	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4059998delT	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	4412803	4412803	+	Intron	DEL	G	-	-	rs34787327	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4412803delG	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	4852349	4852349	+	5'Flank	DEL	G	-	-	rs11359703		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4852349delG	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	5088138	5088139	+	IGR	INS	-	C	C	rs138055173	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5088138_5088139insC								CSMD1 (235810 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5325343	5325345	+	IGR	DEL	TTT	-	-	rs66941724		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5325343_5325345delTTT								CSMD1 (473015 upstream) : MCPH1 (938776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5907642	5907643	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5907642_5907643delAA								None (None upstream) : MCPH1 (356478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6086198	6086199	+	IGR	INS	-	AC	AC	rs34027318		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6086198_6086199insAC								None (None upstream) : MCPH1 (177922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6516689	6516689	+	IGR	DEL	A	-	-	rs113498103		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6516689delA								MCPH1 (10664 upstream) : AGPAT5 (49189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6791544	6791544	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6791544delG								DEFA6 (7946 upstream) : DEFA4 (1801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7385967	7385967	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7385967delG								DEFB107A (19134 upstream) : FAM90A7 (27694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8382963	8382963	+	IGR	DEL	T	-	-	rs35854069		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8382963delT								SGK223 (143706 upstream) : CLDN23 (176703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8584883	8584883	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8584883delA								CLDN23 (23267 upstream) : MFHAS1 (57116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8610513	8610513	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8610513delA								CLDN23 (48897 upstream) : MFHAS1 (31486 downstream)																																			---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8695533	8695534	+	Intron	INS	-	C	C	rs142249621	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8695533_8695534insC	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8709999	8710004	+	Intron	DEL	ACACAT	-	-	rs3989408		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8709999_8710004delACACAT	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9012624	9012624	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9012624delA								PPP1R3B (3540 upstream) : TNKS (400821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9287304	9287304	+	IGR	DEL	T	-	-	rs34173385		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9287304delT								PPP1R3B (278220 upstream) : TNKS (126141 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9485051	9485054	+	Intron	DEL	TTGC	-	-	rs36130596		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9485051_9485054delTTGC	uc003wss.2	+						TNKS_uc011kwv.1_Intron|TNKS_uc011kww.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9815758	9815759	+	IGR	INS	-	TCCTGT	TCCTGT	rs145278049	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9815758_9815759insTCCTGT								MIR124-1 (54776 upstream) : MSRA (96071 downstream)																																			---	---	---	---
PRSS55	203074	broad.mit.edu	37	8	10394923	10394923	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10394923delA	uc003wta.2	+						uc010lru.2_Intron|PRSS55_uc003wtb.2_Intron	NM_198464	NP_940866			hypothetical protein LOC203074 precursor						proteolysis	integral to membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
C8orf74	203076	broad.mit.edu	37	8	10529893	10529894	+	5'Flank	DEL	AG	-	-	rs150480702	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10529893_10529894delAG	uc003wtd.1	+						C8orf74_uc003wte.1_5'Flank	NM_001040032	NP_001035121			hypothetical protein LOC203076												0				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10755103	10755103	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10755103delT	uc003wtk.1	-	3						NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11064407	11064407	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11064407delT								XKR6 (5532 upstream) : MTMR9 (77593 downstream)																																			---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11313145	11313146	+	Intron	INS	-	GTGT	GTGT	rs150606798	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11313145_11313146insGTGT	uc003wtw.2	-							NM_053279	NP_444509			hypothetical protein LOC83648												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	11822920	11822921	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11822920_11822921insT								CTSB (97274 upstream) : DEFB136 (8527 downstream)																																			---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12368914	12368914	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12368914delT	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12440147	12440147	+	Intron	DEL	T	-	-	rs141399472		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12440147delT	uc003wvy.3	-											Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
LONRF1	91694	broad.mit.edu	37	8	12592554	12592554	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12592554delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	12694215	12694216	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12694215_12694216insA								LOC340357 (25305 upstream) : C8orf79 (108935 downstream)																																			---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13112475	13112476	+	Intron	INS	-	T	T	rs150255671	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13112475_13112476insT	uc003wwm.2	-						DLC1_uc003wwl.1_Intron|DLC1_uc003wwn.2_Intron	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13207812	13207813	+	Intron	DEL	TT	-	-	rs111766759		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13207812_13207813delTT	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.1_Intron	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13235754	13235754	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13235754delA	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.1_Intron	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						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																		---	---	---	---
C8orf48	157773	broad.mit.edu	37	8	13424642	13424642	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13424642delC	uc003wwp.2	+	1	291	c.142delC	c.(142-144)CCCfs	p.P48fs		NM_001007090	NP_001007091	Q96LL4	CH048_HUMAN	hypothetical protein LOC157773	48							protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	13509632	13509633	+	IGR	DEL	AA	-	-	rs137880520		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13509632_13509633delAA								C8orf48 (83836 upstream) : SGCZ (437741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	13873350	13873350	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13873350delT								C8orf48 (447554 upstream) : SGCZ (74024 downstream)																																			---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14456845	14456845	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14456845delT	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	14855475	14855475	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14855475delA	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	15084340	15084340	+	Intron	DEL	A	-	-	rs112030467		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15084340delA	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)														---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15561764	15561765	+	Intron	INS	-	T	T	rs60146654		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15561764_15561765insT	uc003wwt.2	+						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)														---	---	---	---
EFHA2	286097	broad.mit.edu	37	8	16888491	16888491	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16888491delT	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)														---	---	---	---
CNOT7	29883	broad.mit.edu	37	8	17088040	17088040	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17088040delT	uc003wxf.1	-	7					CNOT7_uc003wxg.1_3'UTR	NM_013354	NP_037486			CCR4-NOT transcription complex, subunit 7						carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18422139	18422141	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18422139_18422141delAAA	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)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18839167	18839168	+	Intron	INS	-	CA	CA	rs147443174	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18839167_18839168insCA	uc003wza.2	-							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	18989741	18989742	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18989741_18989742delTG								PSD3 (118545 upstream) : SH2D4A (181465 downstream)																																			---	---	---	---
SH2D4A	63898	broad.mit.edu	37	8	19228867	19228867	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19228867delT	uc003wzb.2	+						SH2D4A_uc011kym.1_Intron|SH2D4A_uc003wzc.2_Intron	NM_022071	NP_071354			SH2 domain containing 4A							cytoplasm|nucleus	protein binding				0				Colorectal(111;0.0732)														---	---	---	---
INTS10	55174	broad.mit.edu	37	8	19680155	19680155	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
SLC18A1	6570	broad.mit.edu	37	8	20007084	20007087	+	Intron	DEL	TCTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20007084_20007087delTCTC	uc011kyq.1	-						SLC18A1_uc003wzl.2_Intron|SLC18A1_uc003wzm.2_Intron|SLC18A1_uc011kyr.1_Intron|SLC18A1_uc003wzn.2_Intron|SLC18A1_uc010ltf.2_Intron|SLC18A1_uc003wzo.2_Intron	NM_001135691	NP_001129163			solute carrier family 18 (vesicular monoamine),						neurotransmitter transport	clathrin sculpted monoamine transport vesicle membrane|integral to membrane|membrane fraction	drug transmembrane transporter activity|monoamine transmembrane transporter activity			ovary(2)	2				Colorectal(74;0.0747)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20130924	20130924	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20130924delC								LZTS1 (18121 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20367368	20367368	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20367368delT								LZTS1 (254565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20387439	20387439	+	IGR	DEL	A	-	-	rs112201779		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20387439delA								LZTS1 (274636 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21418566	21418566	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21418566delT								None (None upstream) : GFRA2 (130964 downstream)																																			---	---	---	---
DOK2	9046	broad.mit.edu	37	8	21771310	21771310	+	5'Flank	DEL	T	-	-	rs71544840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21771310delT	uc003wzy.1	-						DOK2_uc003wzx.1_5'Flank|DOK2_uc003wzz.1_5'Flank|DOK2_uc010lth.1_5'Flank	NM_003974	NP_003965			docking protein 2						blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22817813	22817817	+	IGR	DEL	CCCTC	-	-	rs71546840		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22817813_22817817delCCCTC								PEBP4 (32392 upstream) : RHOBTB2 (27113 downstream)																																			---	---	---	---
R3HCC1	203069	broad.mit.edu	37	8	23149584	23149584	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23149584delT	uc003xdf.2	+						R3HCC1_uc011kzt.1_Intron|R3HCC1_uc003xdg.1_5'Flank	NM_001136108	NP_001129580			R3H domain and coiled-coil containing 1								nucleic acid binding|nucleotide binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
ENTPD4	9583	broad.mit.edu	37	8	23300195	23300196	+	Intron	DEL	AA	-	-	rs66604810		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23300195_23300196delAA	uc003xdl.2	-						ENTPD4_uc011kzu.1_Intron|ENTPD4_uc003xdm.2_Intron|ENTPD4_uc011kzv.1_Intron	NM_004901	NP_004892			ectonucleoside triphosphate diphosphohydrolase 4						UDP catabolic process	autophagic vacuole membrane|cytoplasmic vesicle|integral to Golgi membrane	uridine-diphosphatase activity			ovary(1)|kidney(1)	2		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)														---	---	---	---
NKX3-1	4824	broad.mit.edu	37	8	23540651	23540668	+	5'Flank	DEL	CCTCTCCTTCCCCAATTT	-	-	rs66844534	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23540651_23540668delCCTCTCCTTCCCCAATTT	uc011kzx.1	-						NKX3-1_uc003xdv.1_5'Flank	NM_006167	NP_006158			NK3 homeobox 1						negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23587675	23587675	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23587675delT								NKX2-6 (23753 upstream) : STC1 (111759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23677897	23677897	+	IGR	DEL	A	-	-	rs146385442		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23677897delA								NKX2-6 (113975 upstream) : STC1 (21537 downstream)																																			---	---	---	---
ADAM7	8756	broad.mit.edu	37	8	24335083	24335084	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24335083_24335084delGT	uc003xeb.2	+						ADAM7_uc003xec.2_Intron	NM_003817	NP_003808			a disintegrin and metalloproteinase domain 7						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	25017478	25017479	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25017478_25017479delTT								NEFL (203347 upstream) : DOCK5 (24808 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25230876	25230876	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25230876delT	uc003xeg.2	+						DOCK5_uc003xeh.1_Intron|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	25391272	25391272	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25391272delA	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25408074	25408074	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25408074delG	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25478749	25478750	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25478749_25478750delTG	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	25883393	25883394	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25883393_25883394delAA	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	25985808	25985809	+	Intron	INS	-	GGAGGGAA	GGAGGGAA	rs149982442	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25985808_25985809insGGAGGGAA	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	26055212	26055212	+	Intron	DEL	T	-	-	rs71551851		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26055212delT	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	26479590	26479593	+	Intron	DEL	TTTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26479590_26479593delTTTC	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)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27228563	27228565	+	Intron	DEL	CCA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27228563_27228565delCCA	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron|PTK2B_uc003xfp.1_Intron|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266			PTK2B protein tyrosine kinase 2 beta isoform a						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)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27258658	27258659	+	Intron	INS	-	AAAC	AAAC	rs148984304	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27258658_27258659insAAAC	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron|PTK2B_uc003xfp.1_Intron|PTK2B_uc003xfq.1_Intron	NM_173174	NP_775266			PTK2B protein tyrosine kinase 2 beta isoform a						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)														---	---	---	---
SCARA5	286133	broad.mit.edu	37	8	27811366	27811366	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27811366delT	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)														---	---	---	---
ELP3	55140	broad.mit.edu	37	8	28028870	28028870	+	Intron	DEL	T	-	-	rs111324213		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28028870delT	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)														---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28322178	28322178	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28322178delT	uc003xgt.2	-						FBXO16_uc003xgu.2_Intron|FBXO16_uc003xgv.2_Intron|FBXO16_uc003xgw.2_Intron	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)														---	---	---	---
INTS9	55756	broad.mit.edu	37	8	28689227	28689227	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28689227delT	uc003xha.2	-						INTS9_uc011lav.1_Intron|INTS9_uc011law.1_Intron|INTS9_uc011lax.1_Intron|INTS9_uc010lvc.2_Intron|INTS9_uc003xhb.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29341123	29341123	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29341123delA								DUSP4 (132938 upstream) : C8orf75 (237655 downstream)																																			---	---	---	---
C8orf75	619351	broad.mit.edu	37	8	29584819	29584819	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29584819delT	uc003xhn.2	-							NR_026765				Homo sapiens chromosome 8 open reading frame 75, mRNA (cDNA clone IMAGE:3607242), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	30121521	30121521	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30121521delA								DCTN6 (80462 upstream) : RBPMS (120423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30134230	30134231	+	IGR	DEL	AA	-	-	rs75027602		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30134230_30134231delAA								DCTN6 (93171 upstream) : RBPMS (107713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30196935	30196935	+	IGR	DEL	A	-	-	rs76326062		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30196935delA								DCTN6 (155876 upstream) : RBPMS (45009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30218919	30218919	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30218919delT								DCTN6 (177860 upstream) : RBPMS (23025 downstream)																																			---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30482722	30482722	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30482722delT	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	30544359	30544359	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30544359delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	30684414	30684415	+	IGR	INS	-	T	T	rs147175953		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30684414_30684415insT								PPP2CB (14062 upstream) : TEX15 (4647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30818302	30818304	+	IGR	DEL	AAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30818302_30818304delAAG								TEX15 (72080 upstream) : PURG (35017 downstream)																																			---	---	---	---
WRN	7486	broad.mit.edu	37	8	30927960	30927961	+	Intron	INS	-	T	T	rs147451940	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30927960_30927961insT	uc003xio.3	+							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				---	---	---	---
WRN	7486	broad.mit.edu	37	8	30942985	30942985	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30942985delT	uc003xio.3	+						WRN_uc011lbe.1_Intron|WRN_uc010lvk.2_5'Flank	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	31414044	31414044	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31414044delA								WRN (382768 upstream) : NRG1 (83224 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32328318	32328318	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32328318delT	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)														---	---	---	---
MAK16	84549	broad.mit.edu	37	8	33355008	33355008	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33355008delA	uc003xjj.2	+						C8orf41_uc010lvu.1_Intron	NM_032509	NP_115898			MAK16 homolog							nucleolus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	34059561	34059561	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34059561delT								DUSP26 (602122 upstream) : None (None downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35392956	35392956	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35392956delT	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)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35437900	35437900	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35437900delT	uc003xjr.1	+						UNC5D_uc003xjs.1_Intron	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	36105564	36105564	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36105564delA								UNC5D (453384 upstream) : KCNU1 (536278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36339209	36339209	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36339209delA								UNC5D (687029 upstream) : KCNU1 (302633 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36646881	36646881	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36646881delA	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	36701909	36701909	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36701909delA	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	36873539	36873539	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36873539delA								KCNU1 (79898 upstream) : ZNF703 (679762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36987410	36987411	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36987410_36987411delTT								KCNU1 (193769 upstream) : ZNF703 (565890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37429685	37429685	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37429685delA								KCNU1 (636044 upstream) : ZNF703 (123616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37522199	37522199	+	IGR	DEL	T	-	-	rs111925177		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37522199delT								KCNU1 (728558 upstream) : ZNF703 (31102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37532144	37532144	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37532144delT								KCNU1 (738503 upstream) : ZNF703 (21157 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37725231	37725231	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37725231delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Intron|RAB11FIP1_uc003xko.1_3'UTR|RAB11FIP1_uc003xkp.1_3'UTR	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	38075008	38075008	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38075008delT								BAG4 (6471 upstream) : DDHD2 (14001 downstream)																																			---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38147731	38147732	+	Intron	DEL	AA	-	-	rs33956434		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38147731_38147732delAA	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								---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38685355	38685355	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38685355delG	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcc.1_3'UTR|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_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	38688292	38688292	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38688292delA	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	38714937	38714937	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38714937delT								TACC1 (4392 upstream) : PLEKHA2 (43816 downstream)																																			---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38777499	38777499	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38777499delT	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	38926767	38926769	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38926767_38926769delAAA	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xms.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)															---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39181625	39181626	+	Intron	DEL	AG	-	-	rs13263225	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39181625_39181626delAG	uc003xmx.1	+						ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron|ADAM5P_uc010lws.1_Intron	NR_001448				Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	39588358	39588359	+	IGR	DEL	GT	-	-	rs72272179		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39588358_39588359delGT								ADAM18 (873 upstream) : ADAM2 (12897 downstream)																																			---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39810603	39810603	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39810603delA	uc010lwy.1	+						IDO2_uc003xno.1_Intron	NM_194294	NP_919270			indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2																		---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39843358	39843358	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39843358delT	uc010lwy.1	+						IDO2_uc003xno.1_RNA|IDO2_uc010lwz.1_Intron|IDO2_uc003xnp.1_5'Flank	NM_194294	NP_919270			indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	40327585	40327585	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40327585delT								C8orf4 (314764 upstream) : ZMAT4 (60531 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40621784	40621784	+	Intron	DEL	A	-	-	rs72058650		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40621784delA	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	41238904	41238907	+	IGR	DEL	ACAA	-	-	rs148482803		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41238904_41238907delACAA								SFRP1 (71924 upstream) : GOLGA7 (109174 downstream)																																			---	---	---	---
GINS4	84296	broad.mit.edu	37	8	41392258	41392259	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41392258_41392259delTT	uc003xnx.2	+						GINS4_uc003xny.2_Intron	NM_032336	NP_115712			GINS complex subunit 4						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				skin(1)	1	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)															---	---	---	---
PLAT	5327	broad.mit.edu	37	8	42054354	42054355	+	Intron	DEL	AA	-	-	rs3216302		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42054354_42054355delAA	uc003xos.2	-						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	42136515	42136515	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)													---	---	---	---
POLB	5423	broad.mit.edu	37	8	42203903	42203905	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42203903_42203905delTTT	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
POLB	5423	broad.mit.edu	37	8	42228944	42228944	+	Intron	DEL	T	-	-	rs79893094		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42228944delT	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
Unknown	0	broad.mit.edu	37	8	42639823	42639823	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42639823delA								CHRNA6 (16204 upstream) : THAP1 (51995 downstream)																																			---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42826256	42826257	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42826256_42826257insT	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42859822	42859823	+	Intron	INS	-	A	A	rs71550437		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42859822_42859823insA	uc003xpr.2	+							NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
Unknown	0	broad.mit.edu	37	8	43322423	43322423	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43322423delA								POTEA (104095 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43691778	43691778	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43691778delG								POTEA (473450 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46959192	46959192	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46959192delT								None (None upstream) : BEYLA (793316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47166633	47166633	+	IGR	DEL	C	-	-	rs147623975		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47166633delC								None (None upstream) : BEYLA (585875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47305939	47305939	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47305939delA								None (None upstream) : BEYLA (446569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47620360	47620360	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47620360delG								None (None upstream) : BEYLA (132148 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48586214	48586215	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48586214_48586215delTC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	50199900	50199900	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50199900delT								C8orf22 (211259 upstream) : SNTG1 (622449 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51200465	51200465	+	Intron	DEL	G	-	-	rs5891359		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51200465delG	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	51268594	51268594	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51268594delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	52064758	52064758	+	IGR	DEL	A	-	-	rs111242598		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52064758delA								SNTG1 (359331 upstream) : PXDNL (167386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52072743	52072744	+	IGR	DEL	AA	-	-	rs11285195		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52072743_52072744delAA								SNTG1 (367316 upstream) : PXDNL (159400 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52252040	52252040	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52252040delA	uc003xqu.3	-						PXDNL_uc003xqt.3_Intron	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)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52438898	52438898	+	Intron	DEL	T	-	-	rs67732002		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52438898delT	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)														OREG0018765	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52536731	52536731	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52536731delC	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)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52628469	52628469	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52628469delA	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)																---	---	---	---
PCMTD1	115294	broad.mit.edu	37	8	52737622	52737623	+	Intron	INS	-	AA	AA			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52737622_52737623insAA	uc003xqx.3	-						PCMTD1_uc011ldm.1_Intron|PCMTD1_uc003xqw.3_Intron|PCMTD1_uc011ldn.1_Intron|PCMTD1_uc010lya.2_Intron	NM_052937	NP_443169			protein-L-isoaspartate (D-aspartate)							cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	52881585	52881585	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52881585delA								PCMTD1 (69850 upstream) : ST18 (141807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53354288	53354289	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53354288_53354289delAG								ST18 (31849 upstream) : FAM150A (92309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54070288	54070288	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54070288delT								NPBWR1 (216835 upstream) : OPRK1 (67988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54408044	54408045	+	IGR	INS	-	A	A	rs148729134	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54408044_54408045insA								OPRK1 (243850 upstream) : ATP6V1H (220071 downstream)																																			---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54884170	54884170	+	Intron	DEL	A	-	-	rs78187536		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54884170delA	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	55273994	55274005	+	IGR	DEL	CCTTCCTTCTTT	-	-	rs66756943	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55273994_55274005delCCTTCCTTCTTT								MRPL15 (212920 upstream) : SOX17 (96490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55355188	55355188	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55355188delA								MRPL15 (294114 upstream) : SOX17 (15307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55941524	55941525	+	IGR	DEL	AT	-	-	rs67980207		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55941524_55941525delAT								RP1 (258993 upstream) : XKR4 (73492 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56222612	56222613	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56222612_56222613delTG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56958247	56958247	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56958247delT								LYN (34311 upstream) : RPS20 (22492 downstream)																																			---	---	---	---
SDR16C5	195814	broad.mit.edu	37	8	57234636	57234639	+	5'Flank	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57234636_57234639delTTTT	uc003xsy.1	-						SDR16C5_uc010lyk.1_5'Flank|SDR16C5_uc010lyl.1_5'Flank	NM_138969	NP_620419			epidermal retinal dehydrogenase 2						detection of light stimulus involved in visual perception|keratinocyte proliferation|retinal metabolic process|retinol metabolic process	endoplasmic reticulum membrane|integral to membrane|integral to membrane of membrane fraction	binding|retinol dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	57455655	57455655	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57455655delT	uc003xtb.1	+						uc003xtc.1_Intron					Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	57973877	57973878	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57973877_57973878insT								IMPAD1 (67450 upstream) : C8orf71 (218224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58144756	58144757	+	RNA	DEL	AC	-	-	rs72235980		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58144756_58144757delAC	uc003xtf.2	+	8		c.1853_1854delAC								Homo sapiens mRNA; cDNA DKFZp434D1072 (from clone DKFZp434D1072).																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	58440252	58440252	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58440252delT								C8orf71 (242964 upstream) : FAM110B (466861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58765413	58765414	+	IGR	INS	-	CA	CA	rs142434643	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58765413_58765414insCA								C8orf71 (568125 upstream) : FAM110B (141699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58773118	58773118	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58773118delA								C8orf71 (575830 upstream) : FAM110B (133995 downstream)																																			---	---	---	---
CA8	767	broad.mit.edu	37	8	61190685	61190686	+	Intron	INS	-	GTGA	GTGA	rs35851958		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61190685_61190686insGTGA	uc003xtz.1	-						CA8_uc003xua.1_Intron|CA8_uc003xub.2_Intron	NM_004056	NP_004047			carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)																---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61439823	61439823	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61439823delC	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)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61521200	61521200	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61521200delT	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)															---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62326966	62326966	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62326966delT	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790			retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	62651280	62651281	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62651280_62651281insG								ASPH (24081 upstream) : NKAIN3 (510220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	63046313	63046313	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63046313delT								ASPH (419114 upstream) : NKAIN3 (115188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	63071254	63071254	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63071254delA								ASPH (444055 upstream) : NKAIN3 (90247 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63235312	63235312	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63235312delA	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)																---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63495393	63495395	+	Intron	DEL	ATC	-	-	rs66649248		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63495393_63495395delATC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	64445826	64445845	+	IGR	DEL	CTTCCTTCCTTCCTTCCTTT	-	-	rs147214559	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64445826_64445845delCTTCCTTCCTTCCTTCCTTT								YTHDF3 (320481 upstream) : MIR124-2 (845861 downstream)																																			---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528843	65528843	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	66923831	66923831	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66923831delA								PDE7A (170076 upstream) : DNAJC5B (9960 downstream)																																			---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67055492	67055492	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67055492delT	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973			tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67473507	67473507	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67473507delA								C8orf46 (42750 upstream) : MYBL1 (904 downstream)																																			---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67623280	67623280	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67623280delA	uc003xwr.2	+						SGK3_uc003xwp.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)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68930367	68930367	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68930367delT	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	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																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68949176	68949176	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68949176delA	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	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	69501693	69501696	+	Intron	DEL	AGAA	-	-	rs149688722		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69501693_69501696delAGAA	uc010lyz.2	+						C8orf34_uc003xyb.2_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)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69585212	69585213	+	Intron	INS	-	C	C	rs142665209	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69585212_69585213insC	uc010lyz.2	+						C8orf34_uc003xyb.2_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	69943575	69943575	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69943575delA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	70027050	70027051	+	IGR	INS	-	CTAA	CTAA	rs144772166	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70027050_70027051insCTAA								C8orf34 (295794 upstream) : SULF1 (351808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70035064	70035065	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70035064_70035065delTT								C8orf34 (303808 upstream) : SULF1 (343794 downstream)																																			---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70513274	70513274	+	Intron	DEL	T	-	-	rs11284204		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70513274delT	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)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70623248	70623248	+	Intron	DEL	T	-	-	rs10715743		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70623248delT	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron|SLCO5A1_uc010lzc.2_Intron	NM_030958	NP_112220			solute carrier organic anion transporter family,							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	71457306	71457306	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71457306delA								NCOA2 (141286 upstream) : TRAM1 (28367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71879966	71879966	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71879966delT								XKR9 (231790 upstream) : EYA1 (229704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72466304	72466305	+	IGR	DEL	AC	-	-	rs5892288		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72466304_72466305delAC								EYA1 (191837 upstream) : MSC (287472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72807566	72807566	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72807566delA	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73311251	73311251	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73311251delT	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73481156	73481156	+	Intron	DEL	T	-	-	rs73301694	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73481156delT	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73531355	73531356	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73531355_73531356insT	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73731455	73731455	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73731455delA	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74448579	74448579	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74448579delA	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_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	74629883	74629884	+	Intron	INS	-	GTC	GTC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74629883_74629884insGTC	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_Intron|STAU2_uc003xzp.2_Intron|STAU2_uc011lfi.1_Intron|STAU2_uc003xzq.2_Intron|STAU2_uc010lzk.2_Intron|STAU2_uc010lzl.1_Intron|STAU2_uc003xzs.2_Intron|STAU2_uc003xzr.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)															---	---	---	---
JPH1	56704	broad.mit.edu	37	8	75196936	75196936	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75196936delT	uc003yae.2	-						JPH1_uc003yaf.2_Intron|JPH1_uc003yag.1_Intron	NM_020647	NP_065698			junctophilin 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	75394077	75394077	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75394077delT								GDAP1 (114744 upstream) : MIR2052 (223851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75976770	75976770	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75976770delA								CRISPLD1 (29979 upstream) : HNF4G (343413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76212155	76212155	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76212155delA								CRISPLD1 (265364 upstream) : HNF4G (108028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77008151	77008151	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77008151delT								HNF4G (529092 upstream) : LOC100192378 (514964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77202007	77202007	+	IGR	DEL	T	-	-	rs35834120		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77202007delT								HNF4G (722948 upstream) : LOC100192378 (321108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77834022	77834022	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77834022delA								ZFHX4 (54502 upstream) : PEX2 (58474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78771970	78771970	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78771970delT								PEX2 (859446 upstream) : PKIA (656366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78837457	78837458	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78837457_78837458insA								PEX2 (924933 upstream) : PKIA (590878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79076313	79076314	+	IGR	INS	-	A	A	rs146118612	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79076313_79076314insA								None (None upstream) : PKIA (352022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79396509	79396509	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79396509delA								None (None upstream) : PKIA (31827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81308981	81308981	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81308981delA								TPD52 (225145 upstream) : ZBTB10 (88873 downstream)																																			---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81408751	81408751	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81408751delA	uc003ybx.3	+						ZBTB10_uc003ybv.3_Intron|ZBTB10_uc003ybw.3_Intron|ZBTB10_uc010lzt.2_Intron	NM_001105539	NP_001099009			zinc finger and BTB domain containing 10 isoform						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81624955	81624955	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81624955delA	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81728246	81728247	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81728246_81728247insA	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	82249894	82249894	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82249894delT								FABP5 (52886 upstream) : PMP2 (102670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82413917	82413917	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82413917delA								FABP4 (18444 upstream) : FABP12 (23366 downstream)																																			---	---	---	---
IMPA1	3612	broad.mit.edu	37	8	82596022	82596022	+	Intron	DEL	A	-	-	rs34445438		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82596022delA	uc003ych.2	-						IMPA1_uc011lfq.1_Intron|IMPA1_uc011lfr.1_Intron	NM_005536	NP_005527			inositol(myo)-1(or 4)-monophosphatase 1 isoform						inositol phosphate dephosphorylation|phosphatidylinositol biosynthetic process|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(1)	1					Lithium(DB01356)													---	---	---	---
ZFAND1	79752	broad.mit.edu	37	8	82625928	82625928	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82625928delA	uc003ycj.1	-						ZFAND1_uc010lzx.1_Intron|ZFAND1_uc003yck.1_Intron	NM_024699	NP_078975			zinc finger, AN1-type domain 1								zinc ion binding			ovary(1)	1																		---	---	---	---
CHMP4C	92421	broad.mit.edu	37	8	82651709	82651710	+	Intron	INS	-	A	A	rs144207721	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82651709_82651710insA	uc003ycl.2	+							NM_152284	NP_689497			chromatin modifying protein 4C						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	82758711	82758712	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82758711_82758712delAA								SNX16 (4190 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82905226	82905227	+	IGR	DEL	AA	-	-	rs112868434		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82905226_82905227delAA								SNX16 (150705 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83300921	83300921	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83300921delG								SNX16 (546400 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84507727	84507727	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84507727delA								None (None upstream) : RALYL (587726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84673798	84673798	+	IGR	DEL	C	-	-	rs5892883		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84673798delC								None (None upstream) : RALYL (421655 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85212559	85212559	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85212559delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	86510638	86510643	+	IGR	DEL	TGTGTG	-	-	rs72035360		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86510638_86510643delTGTGTG								CA2 (116917 upstream) : REXO1L1 (57921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	86848891	86848893	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86848891_86848893delTTT								REXO1L1 (273623 upstream) : PSKH2 (211800 downstream)																																			---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87142035	87142035	+	Intron	DEL	A	-	-	rs77261248		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87142035delA	uc003ydp.1	+							NM_152565	NP_689778			ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87273698	87273698	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87273698delT								SLC7A13 (31089 upstream) : WWP1 (81296 downstream)																																			---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87407639	87407640	+	Intron	DEL	AT	-	-	rs142310721		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87407639_87407640delAT	uc003ydt.2	+						WWP1_uc010mai.2_Intron	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	87689211	87689212	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87689211_87689212insT	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																		---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88310717	88310720	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88310717_88310720delTTTT	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88800612	88800612	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88800612delT								CNBD1 (405657 upstream) : DCAF4L2 (82361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89374292	89374296	+	IGR	DEL	AAAAG	-	-	rs71278002		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89374292_89374296delAAAAG								MMP16 (34575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90104820	90104821	+	IGR	INS	-	GT	GT	rs149930867	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90104820_90104821insGT								MMP16 (765103 upstream) : RIPK2 (665154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90160120	90160120	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90160120delT								MMP16 (820403 upstream) : RIPK2 (609855 downstream)																																			---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90924972	90924972	+	Intron	DEL	G	-	-	rs2735888	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90924972delG	uc003yeg.2	+						OSGIN2_uc003yeh.2_Intron	NM_004337	NP_004328			oxidative stress induced growth inhibitor family						germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	91065308	91065308	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91065308delT								DECR1 (1081 upstream) : CALB1 (5530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91127266	91127266	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91127266delT								CALB1 (19579 upstream) : TMEM64 (506957 downstream)																																			---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91908832	91908833	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91908832_91908833insA	uc011lgg.1	+							NM_022351	NP_071746			N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94201477	94201480	+	IGR	DEL	GGAG	-	-	rs2449608		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94201477_94201480delGGAG								C8orf83 (171576 upstream) : FAM92A1 (511293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94620865	94620865	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94620865delA								C8orf83 (590964 upstream) : FAM92A1 (91908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94682168	94682169	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94682168_94682169delCA								C8orf83 (652267 upstream) : FAM92A1 (30604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94696445	94696445	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94696445delA								C8orf83 (666544 upstream) : FAM92A1 (16328 downstream)																																			---	---	---	---
PDP1	54704	broad.mit.edu	37	8	94926864	94926864	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94926864delA	uc003yge.2	+						PDP1_uc003ygf.2_5'Flank|PDP1_uc010max.2_5'Flank|PDP1_uc011lgm.1_5'Flank	NM_018444	NP_060914			pyruvate dehyrogenase phosphatase catalytic						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ESRP1	54845	broad.mit.edu	37	8	95667148	95667148	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95667148delA	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																		---	---	---	---
DPY19L4	286148	broad.mit.edu	37	8	95768113	95768113	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95768113delA	uc003ygx.2	+							NM_181787	NP_861452			dpy-19-like 4							integral to membrane				ovary(2)	2	Breast(36;3.85e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96530689	96530690	+	IGR	INS	-	TG	TG	rs139478222	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96530689_96530690insTG								C8orf37 (249252 upstream) : GDF6 (623870 downstream)																																			---	---	---	---
SDC2	6383	broad.mit.edu	37	8	97556411	97556411	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97556411delA	uc003yhv.1	+							NM_002998	NP_002989			syndecan 2 precursor							integral to plasma membrane	cytoskeletal protein binding|PDZ domain binding			ovary(2)	2	Breast(36;3.41e-05)				Sargramostim(DB00020)													---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97938093	97938094	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97938093_97938094insT	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)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97971911	97971911	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97971911delT	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	98252660	98252664	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98252660_98252664delTTTTT								PGCP (96939 upstream) : TSPYL5 (33051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98550997	98550998	+	IGR	INS	-	G	G	rs146346551	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98550997_98550998insG								TSPYL5 (260821 upstream) : MTDH (105409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98582135	98582135	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98582135delT								TSPYL5 (291959 upstream) : MTDH (74272 downstream)																																			---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98886634	98886635	+	Intron	INS	-	TTCT	TTCT	rs112444936	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98886634_98886635insTTCT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	99358650	99358651	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99358650_99358651insT								NIPAL2 (52029 upstream) : KCNS2 (80599 downstream)																																			---	---	---	---
STK3	6788	broad.mit.edu	37	8	99719643	99719643	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99719643delT	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)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99771585	99771586	+	Intron	INS	-	C	C	rs144459622	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99771585_99771586insC	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	100407893	100407893	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100407893delG	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.1_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)															---	---	---	---
POLR2K	5440	broad.mit.edu	37	8	101164033	101164033	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101164033delT	uc003yjf.2	+							NM_005034	NP_005025			DNA directed RNA polymerase II polypeptide K						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|regulation of transcription from RNA polymerase I promoter|termination of RNA polymerase I transcription|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription elongation from RNA polymerase III promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|zinc ion binding				0	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.59e-09)|all cancers(13;1.74e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)															---	---	---	---
RNF19A	25897	broad.mit.edu	37	8	101274109	101274109	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101274109delT	uc003yjj.1	-						RNF19A_uc003yjk.1_Intron	NM_015435	NP_056250			ring finger protein 19						microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)															---	---	---	---
RNF19A	25897	broad.mit.edu	37	8	101288204	101288204	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101288204delT	uc003yjj.1	-						RNF19A_uc003yjk.1_Intron	NM_015435	NP_056250			ring finger protein 19						microtubule cytoskeleton organization|protein modification process	centrosome|integral to membrane	ligase activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(1)|skin(1)	4	all_cancers(14;3.5e-05)|all_epithelial(15;8.91e-08)|Lung NSC(17;0.000615)|all_lung(17;0.00166)		Epithelial(11;3.06e-11)|all cancers(13;5.78e-09)|OV - Ovarian serous cystadenocarcinoma(57;2.24e-05)|STAD - Stomach adenocarcinoma(118;0.0525)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	101759843	101759843	+	IGR	DEL	C	-	-	rs60600127		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101759843delC								PABPC1 (25528 upstream) : YWHAZ (170961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101922575	101922575	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101922575delT								PABPC1 (188260 upstream) : YWHAZ (8229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101978947	101978950	+	IGR	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101978947_101978950delTTTT								YWHAZ (13324 upstream) : ZNF706 (230318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102008274	102008275	+	IGR	DEL	TA	-	-	rs56010813		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102008274_102008275delTA								YWHAZ (42651 upstream) : ZNF706 (200993 downstream)																																			---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102778766	102778766	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102778766delA	uc003yke.2	-						NCALD_uc003ykf.2_Intron|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_032041	NP_114430			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)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102781852	102781852	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102781852delT	uc003yke.2	-						NCALD_uc003ykf.2_Intron|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_032041	NP_114430			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)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	103073003	103073003	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103073003delA	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	103701612	103701612	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103701612delT								KLF10 (33629 upstream) : AZIN1 (136925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103738835	103738835	+	IGR	DEL	T	-	-	rs113661111		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103738835delT								KLF10 (70852 upstream) : AZIN1 (99702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103834936	103834937	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103834936_103834937delAA								KLF10 (166953 upstream) : AZIN1 (3600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103952538	103952538	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103952538delT								AZIN1 (76141 upstream) : ATP6V1C1 (80710 downstream)																																			---	---	---	---
FZD6	8323	broad.mit.edu	37	8	104314830	104314830	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104314830delT	uc003ylh.2	+						FZD6_uc003yli.2_Intron|FZD6_uc003ylj.2_Intron|FZD6_uc011lhn.1_Intron|FZD6_uc011lho.1_Intron|FZD6_uc011lhp.1_Intron	NM_003506	NP_003497			frizzled 6 isoform a precursor						angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)															---	---	---	---
DCAF13	25879	broad.mit.edu	37	8	104435227	104435227	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104435227delA	uc003yln.2	+						DCAF13_uc003ylm.1_Intron|DCAF13_uc003ylo.2_Intron	NM_015420	NP_056235			WD repeats and SOF1 domain containing						rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1																		---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104846814	104846814	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104846814delT	uc003ylp.2	+						RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_001100117	NP_001093587			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-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	105384320	105384321	+	IGR	DEL	CT	-	-	rs147064189		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105384320_105384321delCT								TM7SF4 (15404 upstream) : DPYS (7332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105993486	105993486	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105993486delT								LRP12 (392266 upstream) : ZFPM2 (337661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106052287	106052287	+	IGR	DEL	A	-	-	rs67990945		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106052287delA								LRP12 (451067 upstream) : ZFPM2 (278860 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106640798	106640799	+	Intron	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106640798_106640799insC	uc003ymd.2	+							NM_012082	NP_036214			zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	106827254	106827256	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106827254_106827256delTTT								ZFPM2 (10489 upstream) : OXR1 (455217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107064229	107064234	+	IGR	DEL	CACACG	-	-	rs66805605		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107064229_107064234delCACACG								ZFPM2 (247464 upstream) : OXR1 (218239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107191940	107191940	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107191940delT								ZFPM2 (375175 upstream) : OXR1 (90533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108069329	108069329	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108069329delT								ABRA (286857 upstream) : ANGPT1 (192382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108248781	108248781	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108248781delA								ABRA (466309 upstream) : ANGPT1 (12930 downstream)																																			---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108476661	108476661	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108476661delA	uc003ymn.2	-						ANGPT1_uc003ymo.2_Intron	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	108803248	108803249	+	IGR	INS	-	CA	CA	rs139962499	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108803248_108803249insCA								ANGPT1 (292994 upstream) : RSPO2 (108296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109155822	109155824	+	IGR	DEL	AAT	-	-	rs72367570	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109155822_109155824delAAT								RSPO2 (59909 upstream) : EIF3E (58149 downstream)																																			---	---	---	---
TTC35	9694	broad.mit.edu	37	8	109479585	109479586	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109479585_109479586delTT	uc003ymw.1	+							NM_014673	NP_055488			tetratricopeptide repeat domain 35							endoplasmic reticulum|nucleus	binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.34e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109806726	109806727	+	IGR	INS	-	G	G	rs139161710	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109806726_109806727insG								TMEM74 (6956 upstream) : TRHR (293012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110548200	110548201	+	IGR	INS	-	T	T	rs144561782	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110548200_110548201insT								PKHD1L1 (4701 upstream) : EBAG9 (3728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111259422	111259422	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111259422delT								KCNV1 (271346 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111289377	111289378	+	IGR	DEL	GT	-	-	rs34714932		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111289377_111289378delGT								KCNV1 (301301 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112261479	112261479	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112261479delG								None (None upstream) : CSMD3 (973682 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113353593	113353593	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113353593delT	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	113808194	113808194	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113808194delA	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	114462060	114462060	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114462060delA								CSMD3 (12818 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	114889121	114889121	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114889121delT								CSMD3 (439879 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115171390	115171390	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115171390delA								CSMD3 (722148 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115920719	115920719	+	IGR	DEL	G	-	-	rs75106036	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115920719delG								None (None upstream) : TRPS1 (500006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116072471	116072471	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116072471delA								None (None upstream) : TRPS1 (348254 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117748040	117748041	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117748040_117748041delAA	uc003yoa.2	-						EIF3H_uc003yob.2_Intron|EIF3H_uc011lhz.1_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	117802378	117802378	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117802378delT								UTP23 (15459 upstream) : RAD21 (55796 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	118077795	118077795	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118077795delG	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250			solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118826474	118826475	+	Intron	DEL	GT	-	-	rs111314468		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118826474_118826475delGT	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	119534405	119534418	+	Intron	DEL	ACACACACACACAT	-	-	rs147236593	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119534405_119534418delACACACACACACAT	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	120186289	120186289	+	IGR	DEL	A	-	-	rs138279662		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120186289delA								COLEC10 (67094 upstream) : MAL2 (34321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120271263	120271264	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120271263_120271264delGA								MAL2 (13352 upstream) : NOV (157288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120304389	120304390	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120304389_120304390insA								MAL2 (46478 upstream) : NOV (124162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120699935	120699936	+	IGR	DEL	TT	-	-	rs11362677		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120699935_120699936delTT								ENPP2 (48829 upstream) : TAF2 (43079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120713710	120713711	+	IGR	INS	-	CT	CT	rs138325298	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120713710_120713711insCT								ENPP2 (62604 upstream) : TAF2 (29304 downstream)																																			---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120770136	120770136	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120770136delA	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)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121334968	121334969	+	Intron	INS	-	T	T	rs144446665	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121334968_121334969insT	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	121403034	121403034	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121403034delT								COL14A1 (18768 upstream) : MRPL13 (5050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121837076	121837076	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121837076delT								SNTB1 (12767 upstream) : HAS2 (788195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121889005	121889005	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121889005delT								SNTB1 (64696 upstream) : HAS2 (736266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121935983	121935984	+	IGR	DEL	GT	-	-	rs10545556		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121935983_121935984delGT								SNTB1 (111674 upstream) : HAS2 (689287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	121965668	121965668	+	IGR	DEL	C	-	-	rs71874976		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121965668delC								SNTB1 (141359 upstream) : HAS2 (659603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123222766	123222767	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123222766_123222767delAC								HAS2AS (565833 upstream) : ZHX2 (571134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123237856	123237856	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123237856delT								HAS2AS (580923 upstream) : ZHX2 (556045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123674966	123674970	+	IGR	DEL	CCCAG	-	-	rs141374196		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123674966_123674970delCCCAG								None (None upstream) : ZHX2 (118931 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123891431	123891431	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123891431delT	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)															---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123951076	123951076	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123951076delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124068773	124068774	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124068773_124068774delAA								DERL1 (14125 upstream) : WDR67 (16146 downstream)																																			---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124354725	124354726	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124354725_124354726delAA	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124424838	124424838	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124424838delA	uc003yqi.3	-											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	124563728	124563729	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124563728_124563729insT								FBXO32 (10282 upstream) : KLHL38 (94186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125293864	125293864	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125293864delA								FER1L6 (161563 upstream) : TMEM65 (29297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125441563	125441572	+	IGR	DEL	AGAAAGAAAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125441563_125441572delAGAAAGAAAG								TMEM65 (56623 upstream) : TRMT12 (21476 downstream)																																			---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126280483	126280483	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126280483delA	uc003yrw.2	+							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)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126309910	126309911	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126309910_126309911delAA	uc003yrw.2	+							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	126395456	126395456	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126395456delA								NSMCE2 (16089 upstream) : TRIB1 (47107 downstream)																																			---	---	---	---
TRIB1	10221	broad.mit.edu	37	8	126444364	126444364	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126444364delC	uc003yrx.2	+						TRIB1_uc011lis.1_5'Flank|TRIB1_uc010mdn.2_5'Flank	NM_025195	NP_079471			G-protein-coupled receptor induced protein						JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide	cytoplasm|nucleus	ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			lung(1)	1	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)													OREG0018971	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	127801810	127801810	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127801810delT								FAM84B (231344 upstream) : LOC727677 (500252 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129038198	129038200	+	Intron	DEL	TTT	-	-	rs72027467		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129038198_129038200delTTT	uc010mdq.2	+						PVT1_uc003ysl.2_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	130268845	130268845	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130268845delA								None (None upstream) : GSDMC (491598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	131052247	131052247	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131052247delG								FAM49B (23350 upstream) : ASAP1 (12106 downstream)																																			---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131121896	131121897	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131121896_131121897insA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131387631	131387631	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131387631delA	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	131768775	131768776	+	IGR	INS	-	TCCT	TCCT	rs142776061	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131768775_131768776insTCCT								ASAP1 (354559 upstream) : ADCY8 (23772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132120525	132120525	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132120525delC								ADCY8 (67690 upstream) : EFR3A (795834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132230810	132230811	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132230810_132230811insA								ADCY8 (177975 upstream) : EFR3A (685548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132394061	132394061	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132394061delA								ADCY8 (341226 upstream) : EFR3A (522298 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133291464	133291464	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133291464delA	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	134060473	134060473	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134060473delT	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_uc010mdy.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)														---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134213590	134213590	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134213590delA	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	134616986	134616987	+	IGR	INS	-	CACT	CACT	rs140697400	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134616986_134616987insCACT								ST3GAL1 (32803 upstream) : ZFAT (873046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134646731	134646731	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134646731delA								ST3GAL1 (62548 upstream) : ZFAT (843302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135097137	135097138	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135097137_135097138delTT								ST3GAL1 (512954 upstream) : ZFAT (392895 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135692336	135692336	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135692336delA	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|ZFAT_uc003yur.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	136197306	136197306	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136197306delT								MIR30D (380118 upstream) : LOC286094 (49068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136697884	136697884	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136697884delG								KHDRBS3 (38038 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136763104	136763107	+	IGR	DEL	CAAA	-	-	rs111292337		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136763104_136763107delCAAA								KHDRBS3 (103258 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138435542	138435542	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138435542delT								None (None upstream) : FAM135B (706726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138703513	138703514	+	IGR	INS	-	GT	GT	rs145319972	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138703513_138703514insGT								None (None upstream) : FAM135B (438754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138886946	138886946	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138886946delA								None (None upstream) : FAM135B (255322 downstream)																																			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139675260	139675261	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139675260_139675261delCA	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	139705494	139705495	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139705494_139705495delTG	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	139727812	139727820	+	Intron	DEL	TAAAAAAAA	-	-	rs143920292		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139727812_139727820delTAAAAAAAA	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	139775630	139775631	+	Intron	INS	-	A	A	rs147461525	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139775630_139775631insA	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)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139902700	139902700	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139902700delT	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	140155884	140155884	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140155884delT								COL22A1 (229648 upstream) : KCNK9 (457198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140227688	140227688	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140227688delA								COL22A1 (301452 upstream) : KCNK9 (385394 downstream)																																			---	---	---	---
KCNK9	51305	broad.mit.edu	37	8	140631560	140631560	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140631560delG	uc003yvf.1	-						KCNK9_uc003yvg.1_Intron|KCNK9_uc003yve.1_5'Flank	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	141307403	141307404	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141307403_141307404delAC	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																		---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141983601	141983601	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141983601delA	uc003yvu.2	-						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)															---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143312129	143312132	+	Intron	DEL	CCAT	-	-	rs36014631		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143312129_143312132delCCAT	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	144306338	144306339	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144306338_144306339insA								GPIHBP1 (7295 upstream) : ZFP41 (22652 downstream)																																			---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144940081	144940081	+	Intron	DEL	C	-	-	rs60421625		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	145068490	145068490	+	IGR	DEL	G	-	-	rs11334650		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145068490delG								GRINA (907 upstream) : SPATC1 (18092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	145069127	145069128	+	IGR	INS	-	G	G	rs137887586	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145069127_145069128insG								GRINA (1544 upstream) : SPATC1 (17454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	145180611	145180612	+	IGR	INS	-	A	A	rs139386608		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145180611_145180612insA								KIAA1875 (7393 upstream) : C8orf30A (12060 downstream)																																			---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145826693	145826694	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145826693_145826694delTG	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	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																		---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145881848	145881849	+	Intron	INS	-	A	A	rs9772455	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145881848_145881849insA	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																		---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145913072	145913073	+	5'Flank	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145913072_145913073insC	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																		---	---	---	---
ZNF517	340385	broad.mit.edu	37	8	146023324	146023324	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146023324delA	uc003zed.1	+						ZNF517_uc010mgd.1_5'Flank|ZNF517_uc003zee.1_5'Flank	NM_213605	NP_998770			zinc finger protein 517						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	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)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)															---	---	---	---
ZNF16	7564	broad.mit.edu	37	8	146167053	146167054	+	Intron	INS	-	T	T	rs113061574		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146167053_146167054insT	uc003zet.2	-						ZNF16_uc003zeu.2_Intron	NM_001029976	NP_001025147			zinc finger protein 16						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	146252585	146252585	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146252585delC								C8orf77 (21154 upstream) : C8orf33 (25239 downstream)																																			---	---	---	---
KANK1	23189	broad.mit.edu	37	9	661087	661088	+	Intron	INS	-	T	T	rs141256402	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:661087_661088insT	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron|KANK1_uc003zgp.1_Intron	NM_015158	NP_055973			KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	710630	710630	+	Intron	DEL	C	-	-	rs68161748		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:710630delC	uc003zgl.1	+						KANK1_uc003zgm.2_Intron|KANK1_uc003zgn.1_Intron|KANK1_uc003zgo.1_Intron|KANK1_uc003zgp.1_Intron|KANK1_uc003zgq.2_Intron|KANK1_uc003zgr.1_Intron|KANK1_uc003zgs.1_Intron	NM_015158	NP_055973			KN motif and ankyrin repeat domains 1 isoform a						negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	2734282	2734312	+	IGR	DEL	CCAAAGATTCCAGGTTCAAGAAAATAGTTTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2734282_2734312delCCAAAGATTCCAGGTTCAAGAAAATAGTTTG								KCNV2 (4525 upstream) : KIAA0020 (69843 downstream)																																			---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	3988706	3988706	+	Intron	DEL	A	-	-	rs79009534		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3988706delA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zhy.1_Intron|GLIS3_uc003zhz.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
GLIS3	169792	broad.mit.edu	37	9	4124192	4124192	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4124192delA	uc003zhw.1	-						GLIS3_uc003zhx.1_Intron|GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron|GLIS3_uc003zib.1_Intron|GLIS3_uc010mhg.1_Intron	NM_152629	NP_689842			GLIS family zinc finger 3 isoform b						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4338389	4338390	+	IGR	INS	-	AC	AC	rs149503916		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4338389_4338390insAC								GLIS3 (38354 upstream) : SLC1A1 (152054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	4750842	4750843	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4750842_4750843delGA								AK3 (8799 upstream) : RCL1 (41991 downstream)																																			---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5450003	5450004	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5450003_5450004delAC	uc003zjd.2	-						CD274_uc011lmb.1_5'Flank|CD274_uc003zje.2_5'Flank	NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	6275223	6275223	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6275223delA								IL33 (17241 upstream) : TPD52L3 (53152 downstream)																																			---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6991841	6991841	+	Intron	DEL	G	-	-	rs77891244		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6991841delG	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	9097403	9097406	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9097403_9097406delTTTT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	9593142	9593143	+	Intron	INS	-	AAAGA	AAAGA	rs149446036	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9593142_9593143insAAAGA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	10002793	10002793	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10002793delA	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	10008589	10008590	+	Intron	INS	-	AT	AT	rs144240855	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10008589_10008590insAT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	10880839	10880839	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10880839delA								PTPRD (268116 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11014860	11014860	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11014860delT								PTPRD (402137 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11278564	11278565	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11278564_11278565delAC								PTPRD (665841 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12532388	12532388	+	IGR	DEL	A	-	-	rs5896513		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12532388delA								None (None upstream) : TYRP1 (160998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12680541	12680541	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12680541delA								None (None upstream) : TYRP1 (12845 downstream)																																			---	---	---	---
C9orf150	286343	broad.mit.edu	37	9	12775861	12775862	+	In_Frame_Ins	INS	-	GGCGGCGGC	GGCGGCGGC	rs139315731	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12775861_12775862insGGCGGCGGC	uc003zkw.2	+	1	850_851	c.147_148insGGCGGCGGC	c.(145-150)insGGCGGCGGC	p.55_56insGGG		NM_203403	NP_981948	Q8IV03	CI150_HUMAN	hypothetical protein LOC286343	58_59	Gly-rich.										0				GBM - Glioblastoma multiforme(1;1.64e-13)														---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13206554	13206557	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13206554_13206557delTTTT	uc010mia.1	-						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	13243363	13243365	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13243363_13243365delTTT	uc010mia.1	-						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)														---	---	---	---
ZDHHC21	340481	broad.mit.edu	37	9	14638672	14638673	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14638672_14638673delAA	uc003zli.2	-						ZDHHC21_uc003zlg.1_Intron	NM_178566	NP_848661			zinc finger, DHHC-type containing 21						nitric oxide metabolic process|regulation of nitric-oxide synthase activity	Golgi membrane|integral to membrane	palmitoyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(50;4.31e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14824710	14824711	+	Intron	DEL	TA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14824710_14824711delTA	uc003zlm.2	-						FREM1_uc010mic.2_Intron	NM_144966	NP_659403			FRAS1 related extracellular matrix 1 precursor						cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15728849	15728849	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15728849delA	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18493667	18493667	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18493667delT	uc003zne.3	+						ADAMTSL1_uc003znb.2_Intron|ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18794644	18794644	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18794644delT	uc003zne.3	+							NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	18925519	18925519	+	IGR	DEL	T	-	-	rs10121293	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18925519delT								ADAMTSL1 (14574 upstream) : FAM154A (2374 downstream)																																			---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	19017188	19017188	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19017188delA	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918			hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	19152717	19152717	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19152717delT								PLIN2 (25144 upstream) : DENND4C (137985 downstream)																																			---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20805169	20805169	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20805169delT	uc003zog.1	+							NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
LOC554202	554202	broad.mit.edu	37	9	21482746	21482747	+	Intron	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21482746_21482747insTG	uc003zpe.2	-						LOC554202_uc003zpf.2_Intron|IFNE_uc003zpg.2_5'Flank	NR_027054				Homo sapiens cDNA FLJ42400 fis, clone ASTRO2003581.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	21779320	21779320	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21779320delA								LOC554202 (219488 upstream) : MTAP (23315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22754172	22754173	+	Intron	DEL	AC	-	-	rs148644095		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22754172_22754173delAC	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	22793984	22793984	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22793984delA	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23461482	23461482	+	IGR	DEL	A	-	-	rs150103841		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23461482delA								None (None upstream) : ELAVL2 (228623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24533486	24533487	+	IGR	INS	-	AGGG	AGGG	rs139450637	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24533486_24533487insAGGG								ELAVL2 (707423 upstream) : None (None downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28039504	28039505	+	Intron	INS	-	GT	GT	rs144564189	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28039504_28039505insGT	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28243647	28243647	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28243647delA	uc003zqu.1	-						LINGO2_uc010mjf.1_Intron|LINGO2_uc003zqv.1_Intron	NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28644200	28644200	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28644200delA	uc003zqv.1	-							NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	29275844	29275845	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29275844_29275845insA								MIR873 (386891 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29907515	29907518	+	IGR	DEL	TGTT	-	-	rs78392881		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29907515_29907518delTGTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31094610	31094611	+	IGR	INS	-	AC	AC	rs144664748	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31094610_31094611insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31303886	31303887	+	IGR	INS	-	TTGT	TTGT	rs141811258	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31303886_31303887insTTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32965416	32965416	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32965416delT								TMEM215 (176219 upstream) : APTX (7193 downstream)																																			---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33156120	33156120	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33156120delT	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33345485	33345485	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33345485delG	uc003zsq.2	+						SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Intron|NFX1_uc003zso.2_Intron|NFX1_uc003zsp.1_Intron|NFX1_uc010mjr.1_Intron|NFX1_uc003zsr.2_Intron	NM_002504	NP_002495			nuclear transcription factor, X-box binding 1						inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
PTENP1	11191	broad.mit.edu	37	9	33675365	33675365	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33675365delA	uc003zth.3	-	1						NR_023917				SubName: Full=Phosphatase and tensin homolog 2; Flags: Fragment;												0																		---	---	---	---
DCTN3	11258	broad.mit.edu	37	9	34616673	34616674	+	Intron	INS	-	AG	AG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34616673_34616674insAG	uc003zux.1	-						DCTN3_uc003zuw.1_Intron	NM_007234	NP_009165			dynactin 3 isoform 1						cytokinesis|G2/M transition of mitotic cell cycle|mitosis	centrosome|cleavage furrow|condensed chromosome kinetochore|cytosol|dynactin complex|midbody|perinuclear region of cytoplasm|spindle	protein binding|structural molecule activity				0	all_epithelial(49;0.0863)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.0388)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34935992	34935992	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34935992delA								C9orf144 (97409 upstream) : KIAA1045 (21529 downstream)																																			---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34988285	34988286	+	5'Flank	DEL	CC	-	-	rs67134260		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34988285_34988286delCC	uc003zvt.2	+						DNAJB5_uc003zvs.2_5'Flank|DNAJB5_uc011los.1_5'Flank	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	35132714	35132714	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35132714delA								KIAA1539 (16821 upstream) : UNC13B (29275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	35939407	35939408	+	IGR	INS	-	TTAG	TTAG	rs111278029		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35939407_35939408insTTAG								LOC158376 (27790 upstream) : OR2S2 (17698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	36032088	36032088	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36032088delA								OR2S2 (73937 upstream) : RECK (4822 downstream)																																			---	---	---	---
RECK	8434	broad.mit.edu	37	9	36123173	36123173	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36123173delT	uc003zyv.2	+	21					RECK_uc003zyw.2_3'UTR|RECK_uc003zyx.2_RNA	NM_021111	NP_066934			RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
MELK	9833	broad.mit.edu	37	9	36582511	36582512	+	Intron	INS	-	AC	AC	rs146640360	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36582511_36582512insAC	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606			maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	37073420	37073420	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37073420delT								PAX5 (38944 upstream) : ZCCHC7 (47049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	37392729	37392729	+	IGR	DEL	G	-	-	rs11308544		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37392729delG								ZCCHC7 (34586 upstream) : GRHPR (29952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	37478481	37478481	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37478481delT								ZBTB5 (13074 upstream) : POLR1E (7464 downstream)																																			---	---	---	---
POLR1E	64425	broad.mit.edu	37	9	37503417	37503417	+	3'UTR	DEL	A	-	-	rs112575562		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37503417delA	uc003zzz.1	+	11					POLR1E_uc003zzy.1_3'UTR|POLR1E_uc011lqk.1_3'UTR|uc004aaa.2_5'Flank	NM_022490	NP_071935			RNA polymerase I associated factor 53						rRNA transcription	cell junction|cytoplasm|nucleolus	DNA binding|DNA-directed RNA polymerase activity|protein binding				0				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38111133	38111134	+	IGR	INS	-	T	T	rs113614364		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38111133_38111134insT								SHB (41923 upstream) : ALDH1B1 (281568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38331652	38331652	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38331652delA								SHB (262442 upstream) : ALDH1B1 (61050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	38601503	38601503	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38601503delA	uc004abg.3	-						uc010mme.2_Intron					RecName: Full=Ankyrin repeat domain-containing protein 18B;																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	67339358	67339358	+	IGR	DEL	C	-	-	rs112612032		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67339358delC								AQP7P1 (49866 upstream) : FAM27B (453572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68995848	68995848	+	IGR	DEL	T	-	-	rs72538827		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68995848delT								None (None upstream) : MIR1299 (6391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69816799	69816804	+	IGR	DEL	TGATGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69816799_69816804delTGATGG								LOC100133920 (151850 upstream) : FOXD4L5 (358905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70837214	70837214	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70837214delA								CBWD3 (337151 upstream) : FOXD4L3 (80569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71196719	71196719	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71196719delA								C9orf71 (40936 upstream) : PIP5K1B (123897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71196827	71196827	+	IGR	DEL	C	-	-	rs71980371		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71196827delC								C9orf71 (41044 upstream) : PIP5K1B (123789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	71315940	71315940	+	IGR	DEL	G	-	-	rs7871897	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71315940delG								C9orf71 (160157 upstream) : PIP5K1B (4676 downstream)																																			---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71414871	71414872	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71414871_71414872delGA	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	71733254	71733255	+	5'Flank	INS	-	GTTTTT	GTTTTT	rs142131657	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71733254_71733255insGTTTTT	uc011lrs.1	+							NM_201629	NP_963923			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																		---	---	---	---
APBA1	320	broad.mit.edu	37	9	72238275	72238275	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72238275delT	uc004ahh.2	-							NM_001163	NP_001154			amyloid beta A4 precursor protein-binding,						axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1																		---	---	---	---
PTAR1	375743	broad.mit.edu	37	9	72365095	72365095	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72365095delA	uc004ahj.3	-						PTAR1_uc004ahi.2_Intron	NM_001099666	NP_001093136			protein prenyltransferase alpha subunit repeat						protein prenylation		protein prenyltransferase activity			central_nervous_system(1)	1																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72698615	72698616	+	Intron	DEL	TT	-	-	rs66470918		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72698615_72698616delTT	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999			MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72730214	72730214	+	Intron	DEL	A	-	-	rs75913461		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72730214delA	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999			MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
KLF9	687	broad.mit.edu	37	9	73020672	73020672	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73020672delA	uc004aht.2	-							NM_001206	NP_001197			Kruppel-like factor 9						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GDA	9615	broad.mit.edu	37	9	74737550	74737551	+	Intron	INS	-	ACAC	ACAC	rs150896947	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74737550_74737551insACAC	uc011lse.1	+							NM_004293	NP_004284			guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	75494485	75494485	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75494485delT								TMC1 (43218 upstream) : ALDH1A1 (21103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	75812863	75812864	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75812863_75812864delTT								ANXA1 (27556 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76468019	76468019	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76468019delA								ANXA1 (682712 upstream) : RORB (644233 downstream)																																			---	---	---	---
RORB	6096	broad.mit.edu	37	9	77150065	77150066	+	Intron	DEL	GT	-	-	rs148187290		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77150065_77150066delGT	uc004ajh.2	+							NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
RORB	6096	broad.mit.edu	37	9	77241666	77241666	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77241666delA	uc004aji.2	+						RORB_uc004ajh.2_Intron	NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
RORB	6096	broad.mit.edu	37	9	77271224	77271224	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77271224delC	uc004aji.2	+						RORB_uc004ajh.2_Intron	NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
OSTF1	26578	broad.mit.edu	37	9	77707967	77707970	+	Intron	DEL	TCTT	-	-	rs5898393		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77707967_77707970delTCTT	uc004ajv.3	+						OSTF1_uc004ajw.3_Intron|OSTF1_uc004ajx.3_Intron	NM_012383	NP_036515			osteoclast stimulating factor 1						ossification|signal transduction	cytoplasm	identical protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	78829210	78829211	+	IGR	INS	-	CA	CA	rs142352274	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78829210_78829211insCA								PCSK5 (20872 upstream) : RFK (171222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	79209699	79209700	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79209699_79209700insA								GCNT1 (87369 upstream) : PRUNE2 (16593 downstream)																																			---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79421936	79421937	+	Intron	INS	-	TG	TG	rs113050758		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79421936_79421937insTG	uc010mpk.2	-							NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79522805	79522805	+	5'Flank	DEL	T	-	-	rs139512048		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79522805delT	uc010mpk.2	-						PRUNE2_uc004akn.2_5'Flank	NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79830069	79830069	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79830069delA	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79838636	79838637	+	Intron	INS	-	AT	AT	rs35488520		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79838636_79838637insAT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	80964688	80964688	+	IGR	DEL	G	-	-	rs1819448	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80964688delG								PSAT1 (19681 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81099499	81099500	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81099499_81099500delTG								PSAT1 (154492 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81485932	81485932	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81485932delT								PSAT1 (540925 upstream) : TLE4 (700946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81841450	81841451	+	IGR	DEL	CA	-	-	rs10867356	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81841450_81841451delCA								PSAT1 (896443 upstream) : TLE4 (345427 downstream)																																			---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82225462	82225462	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82225462delC	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936			transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	82353501	82353501	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82353501delT								TLE4 (11844 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82667614	82667614	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82667614delA								TLE4 (325957 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83677359	83677360	+	IGR	INS	-	TTAA	TTAA	rs150585923	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83677359_83677360insTTAA								None (None upstream) : TLE1 (521240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85456665	85456666	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85456665_85456666delCA								FLJ46321 (846495 upstream) : RASEF (140651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85541309	85541309	+	IGR	DEL	A	-	-	rs72309553		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85541309delA								FLJ46321 (931139 upstream) : RASEF (56008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85783967	85783968	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85783967_85783968delTT								RASEF (105924 upstream) : FRMD3 (73937 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	86094274	86094279	+	Intron	DEL	GAGGAA	-	-	rs58938099		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86094274_86094279delGAGGAA	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598			FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
HNRNPK	3190	broad.mit.edu	37	9	86584096	86584096	+	3'UTR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86584096delC	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																		---	---	---	---
SLC28A3	64078	broad.mit.edu	37	9	86976664	86976664	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86976664delA	uc004anu.1	-							NM_022127	NP_071410			concentrative Na+-nucleoside cotransporter						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	87218271	87218271	+	IGR	DEL	T	-	-	rs71506655	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87218271delT								SLC28A3 (234858 upstream) : NTRK2 (65195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87266777	87266777	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87266777delA								SLC28A3 (283364 upstream) : NTRK2 (16689 downstream)																																			---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88646131	88646131	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88646131delA	uc004aol.2	-						GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89444123	89444123	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89444123delT								ZCCHC6 (474745 upstream) : GAS1 (115156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89976364	89976364	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89976364delA								C9orf170 (201723 upstream) : DAPK1 (136294 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	90664360	90664361	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90664360_90664361delTT	uc004apv.1	-											full-length cDNA clone CS0DI004YC05 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	91131649	91131650	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs62580715		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91131649_91131650insTTCCTTCC								SPIN1 (38029 upstream) : NXNL2 (18366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91272714	91272715	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91272714_91272715delAC								LOC286238 (5639 upstream) : C9orf47 (333063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91368651	91368651	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91368651delA								LOC286238 (101576 upstream) : C9orf47 (237127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91869252	91869260	+	IGR	DEL	GTGTGGTGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91869252_91869260delGTGTGGTGT								SHC3 (75570 upstream) : CKS2 (56853 downstream)																																			---	---	---	---
SECISBP2	79048	broad.mit.edu	37	9	91934385	91934385	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91934385delA	uc004aqj.1	+						SECISBP2_uc010mqn.1_Intron|SECISBP2_uc004aqi.1_Intron|SECISBP2_uc011ltk.1_Intron|SECISBP2_uc004aqk.1_Intron|SECISBP2_uc010mqo.1_Intron|SECISBP2_uc011ltl.1_Intron	NM_024077	NP_076982			SECIS binding protein 2						translation	nucleus	mRNA 3'-UTR binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	92495698	92495698	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92495698delT								LOC100129066 (161024 upstream) : DIRAS2 (876416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93337111	93337111	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93337111delG	uc004aqt.1	-											Homo sapiens cDNA FLJ46333 fis, clone TESTI4045701.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	93783085	93783086	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93783085_93783086delAC								SYK (122252 upstream) : AUH (193013 downstream)																																			---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94397333	94397334	+	Intron	INS	-	GAG	GAG	rs140128560	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94397333_94397334insGAG	uc004ari.1	-							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	95008219	95008220	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95008219_95008220delTG	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)													---	---	---	---
ASPN	54829	broad.mit.edu	37	9	95233200	95233200	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95233200delA	uc004ase.1	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ASPN_uc010mqy.1_Intron	NM_017680	NP_060150			asporin precursor						bone mineralization|negative regulation of tooth mineralization|negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95326069	95326071	+	Intron	DEL	TCC	-	-	rs35894635		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95326069_95326071delTCC	uc004arz.2	+						CENPP_uc010mqx.2_Intron	NM_001012267	NP_001012267			centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96021068	96021069	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96021068_96021069insA	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron|WNK2_uc010mrc.1_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																		---	---	---	---
C9orf129	445577	broad.mit.edu	37	9	96085388	96085389	+	Intron	INS	-	C	C	rs72546539		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96085388_96085389insC	uc010mre.2	-							NM_001098808	NP_001092278			hypothetical protein LOC445577											ovary(1)	1																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96264848	96264851	+	Intron	DEL	ACAC	-	-	rs139110277		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96264848_96264851delACAC	uc004atw.2	+						FAM120A_uc004atv.2_Intron|FAM120A_uc004atx.2_Intron|FAM120A_uc004aty.2_Intron	NM_014612	NP_055427			oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
ZNF169	169841	broad.mit.edu	37	9	97054922	97054923	+	Intron	INS	-	GC	GC	rs74578608	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97054922_97054923insGC	uc004aum.1	+						ZNF169_uc004aun.2_Intron|ZNF169_uc004auo.2_Intron	NM_194320	NP_919301			zinc finger protein 169							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98278766	98278767	+	5'UTR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98278766_98278767insC	uc010mrr.2	-	1					PTCH1_uc004avm.3_Intron|PTCH1_uc004avo.2_5'UTR|PTCH1_uc010mrv.1_Intron|PTCH1_uc010mrw.1_RNA	NM_001083602	NP_001077071			patched isoform M						embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	9	98424640	98424640	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98424640delT								PTCH1 (145393 upstream) : C9orf130 (143732 downstream)																																			---	---	---	---
C9orf130	100128782	broad.mit.edu	37	9	98614843	98614843	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98614843delT	uc004avp.3	-						C9orf130_uc004avr.2_Intron	NR_023390				Homo sapiens cDNA FLJ34818 fis, clone NT2NE2008077.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	99401322	99401324	+	IGR	DEL	AGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99401322_99401324delAGG								CDC14B (19210 upstream) : C9orf21 (2210 downstream)																																			---	---	---	---
KIAA1529	57653	broad.mit.edu	37	9	100133233	100133242	+	Intron	DEL	TTTTTTTTTT	-	-	rs67153822		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100133233_100133242delTTTTTTTTTT	uc011lut.1	+						KIAA1529_uc004axe.1_Intron|KIAA1529_uc004axg.1_Intron|KIAA1529_uc004axh.1_Intron|KIAA1529_uc011luw.1_Intron	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	100496287	100496288	+	IGR	INS	-	TC	TC	rs113300066		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100496287_100496288insTC								XPA (36596 upstream) : FOXE1 (119249 downstream)																																			---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100767636	100767636	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100767636delA	uc004aya.2	+							NM_006401	NP_006392			acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasm|nucleus					0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
TRIM14	9830	broad.mit.edu	37	9	100869956	100869956	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100869956delT	uc004ayd.2	-						TRIM14_uc004ayf.1_Intron|TRIM14_uc004ayg.1_Intron|TRIM14_uc004ayh.1_Intron|TRIM14_uc004ayi.1_Intron|TRIM14_uc004ayj.1_Intron	NM_033220	NP_150089			tripartite motif protein TRIM14 isoform alpha							cytoplasm|intracellular	zinc ion binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101081173	101081174	+	Intron	INS	-	TGTG	TGTG	rs111952099		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101081173_101081174insTGTG	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)													---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101776257	101776257	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101776257delT	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
ERP44	23071	broad.mit.edu	37	9	102769018	102769018	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102769018delA	uc004bam.2	-						ERP44_uc010msy.2_Intron|ERP44_uc010msz.2_Intron	NM_015051	NP_055866			thioredoxin domain containing 4 (endoplasmic						cell redox homeostasis|glycoprotein metabolic process|protein folding|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|ER-Golgi intermediate compartment	protein binding|protein disulfide isomerase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	103523436	103523436	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103523436delT								MURC (173265 upstream) : LPPR1 (267595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105584837	105584838	+	IGR	INS	-	T	T	rs140570982	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105584837_105584838insT								None (None upstream) : CYLC2 (172755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105998666	105998667	+	Intron	INS	-	GT	GT	rs141662874	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105998666_105998667insGT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	106906356	106906357	+	IGR	INS	-	TA	TA	rs138413530	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106906356_106906357insTA								SMC2 (2663 upstream) : OR13F1 (360187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107376670	107376673	+	IGR	DEL	ACAC	-	-	rs113774252		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107376670_107376673delACAC								OR13C2 (8762 upstream) : OR13C9 (2857 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107678478	107678479	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107678478_107678479insA	uc004bcl.2	-						ABCA1_uc004bcm.2_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	107792925	107792925	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107792925delT								ABCA1 (102489 upstream) : SLC44A1 (214004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107912047	107912047	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107912047delT								ABCA1 (221611 upstream) : SLC44A1 (94882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107967244	107967244	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107967244delC								ABCA1 (276808 upstream) : SLC44A1 (39685 downstream)																																			---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108239555	108239556	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108239555_108239556insA	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108562214	108562214	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108562214delC								TMEM38B (24770 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108877283	108877284	+	Intron	DEL	TG	-	-	rs140685531		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108877283_108877284delTG	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109422226	109422226	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109422226delT	uc004bcy.1	+											Homo sapiens cDNA FLJ36044 fis, clone TESTI2017584.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	110033261	110033261	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110033261delA								ZNF462 (259472 upstream) : RAD23B (12283 downstream)																																			---	---	---	---
CTNNAL1	8727	broad.mit.edu	37	9	111753821	111753822	+	Intron	INS	-	A	A	rs140835089	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111753821_111753822insA	uc004bdo.1	-						CTNNAL1_uc010mtt.1_Intron|CTNNAL1_uc004bdp.1_Intron	NM_003798	NP_003789			catenin, alpha-like 1						cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	112090410	112090412	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112090410_112090412delAAA								EPB41L4B (7389 upstream) : PTPN3 (47562 downstream)																																			---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113130428	113130429	+	Intron	INS	-	AG	AG	rs147346500	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113130428_113130429insAG	uc010mtz.2	-						SVEP1_uc010mty.2_Intron	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
LPAR1	1902	broad.mit.edu	37	9	113711271	113711274	+	Intron	DEL	AAAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113711271_113711274delAAAT	uc004bfa.2	-						LPAR1_uc011lwm.1_Intron|LPAR1_uc004bfb.2_Intron|LPAR1_uc004bfc.2_Intron|LPAR1_uc011lwn.1_Intron|LPAR1_uc011lwo.1_Intron|LPAR1_uc010mub.2_Intron	NM_057159	NP_476500			lysophosphatidic acid receptor 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	cell surface|integral to plasma membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114942085	114942085	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114942085delA								SUSD1 (4529 upstream) : ROD1 (38630 downstream)																																			---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115168447	115168447	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115168447delA	uc004bga.1	+						HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Intron|HSDL2_uc011lww.1_Intron	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
SLC46A2	57864	broad.mit.edu	37	9	115655874	115655875	+	5'Flank	DEL	AA	-	-	rs147564161		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115655874_115655875delAA	uc004bgk.2	-							NM_033051	NP_149040			solute carrier family 46, member 2							integral to membrane|plasma membrane	symporter activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115891625	115891625	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115891625delA								C9orf109 (9501 upstream) : SLC31A2 (21613 downstream)																																			---	---	---	---
PRPF4	9128	broad.mit.edu	37	9	116054494	116054494	+	3'UTR	DEL	A	-	-	rs78376128		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116054494delA	uc004bgx.2	+	14					PRPF4_uc004bgy.2_3'UTR	NM_004697	NP_004688			PRP4 pre-mRNA processing factor 4 homolog							Cajal body|nuclear speck|spliceosomal complex|U4/U6 snRNP	protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116487407	116487408	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116487407_116487408delAT								RGS3 (127390 upstream) : ZNF618 (151154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116524464	116524464	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116524464delT								RGS3 (164447 upstream) : ZNF618 (114098 downstream)																																			---	---	---	---
ZNF618	114991	broad.mit.edu	37	9	116764059	116764059	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116764059delG	uc004bid.2	+						ZNF618_uc004bib.1_Intron|ZNF618_uc004bic.2_Intron|ZNF618_uc011lxi.1_Intron|ZNF618_uc011lxj.1_Intron	NM_133374	NP_588615			zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	117437123	117437126	+	IGR	DEL	TTTT	-	-	rs74341511		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117437123_117437126delTTTT								C9orf91 (28427 upstream) : TNFSF15 (114487 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119909741	119909744	+	Intron	DEL	CACC	-	-	rs58379572		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119909741_119909744delCACC	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																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119912397	119912397	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119912397delT	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	121148875	121148875	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121148875delT								TLR4 (669111 upstream) : DBC1 (780033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122222154	122222157	+	IGR	DEL	ACAT	-	-	rs149891107	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122222154_122222157delACAT								DBC1 (90415 upstream) : MIR147 (785100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122261011	122261011	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122261011delT								DBC1 (129272 upstream) : MIR147 (746246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122577100	122577101	+	IGR	INS	-	A	A	rs146757926	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122577100_122577101insA								DBC1 (445361 upstream) : MIR147 (430156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	123090536	123090536	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123090536delT								MIR147 (83208 upstream) : CDK5RAP2 (60612 downstream)																																			---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123436855	123436855	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123436855delT	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron|MEGF9_uc004bkk.3_Intron	NM_001080497	NP_001073966			multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0																		---	---	---	---
TRAF1	7185	broad.mit.edu	37	9	123672693	123672693	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123672693delT	uc004bku.1	-						TRAF1_uc011lyg.1_Intron|TRAF1_uc010mvl.1_Intron	NM_005658	NP_005649			TNF receptor-associated factor 1						apoptosis|positive regulation of NF-kappaB transcription factor activity|protein complex assembly|regulation of apoptosis|signal transduction	cytoplasm	protein binding|zinc ion binding			skin(2)|ovary(1)	3																		---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123927597	123927597	+	Intron	DEL	A	-	-	rs34558172		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123927597delA	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																		---	---	---	---
GGTA1	2681	broad.mit.edu	37	9	124244275	124244276	+	Intron	DEL	AA	-	-	rs138376545		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124244275_124244276delAA	uc004bll.1	-						GGTA1_uc004blj.1_Intron|GGTA1_uc004blk.1_Intron|GGTA1_uc004blm.1_Intron	NR_003191				RecName: Full=Inactive N-acetyllactosaminide alpha-1,3-galactosyltransferase;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	125191507	125191507	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125191507delT								PTGS1 (33526 upstream) : OR1J2 (39333 downstream)																																			---	---	---	---
RC3H2	54542	broad.mit.edu	37	9	125617396	125617400	+	Intron	DEL	AAAAA	-	-	rs5900548		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125617396_125617400delAAAAA	uc010mwc.1	-						RC3H2_uc004bnc.2_Intron|RC3H2_uc004bnd.1_Intron|RC3H2_uc004bne.3_Intron	NM_001100588	NP_001094058			ring finger and CCCH-type zinc finger domains 2							cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125791597	125791598	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125791597_125791598delTT	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron	NM_012197	NP_036329			RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126472814	126472815	+	Intron	DEL	AC	-	-	rs67898285		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126472814_126472815delAC	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	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																		---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127541095	127541097	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127541095_127541097delAAA	uc004bov.2	+						OLFML2A_uc010mwr.1_Intron	NM_182487	NP_872293			olfactomedin-like 2A precursor												0																		---	---	---	---
ARPC5L	81873	broad.mit.edu	37	9	127634876	127634876	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127634876delA	uc004bpa.3	+						ARPC5L_uc011lzq.1_5'Flank	NM_030978	NP_112240			actin related protein 2/3 complex, subunit						regulation of actin filament polymerization	cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127676783	127676783	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127676783delA	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron|GOLGA1_uc010mwt.1_Intron	NM_002077	NP_002068			golgin 97							Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128015680	128015680	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128015680delA								HSPA5 (12019 upstream) : GAPVD1 (8431 downstream)																																			---	---	---	---
MAPKAP1	79109	broad.mit.edu	37	9	128367062	128367062	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128367062delA	uc004bpv.2	-						MAPKAP1_uc011lzu.1_Intron|MAPKAP1_uc011lzv.1_Intron|MAPKAP1_uc004bpw.2_Intron|MAPKAP1_uc004bpx.2_Intron|MAPKAP1_uc004bpy.2_Intron|MAPKAP1_uc004bpz.2_Intron|MAPKAP1_uc010mxa.2_Intron|MAPKAP1_uc010mxb.1_Intron|MAPKAP1_uc004bqa.2_Intron|MAPKAP1_uc010mxc.1_Intron	NM_001006617	NP_001006618			mitogen-activated protein kinase associated						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|response to stress|T cell costimulation	cytoplasmic membrane-bounded vesicle|cytosol|nucleus|plasma membrane	Ras GTPase binding			ovary(2)|lung(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128786338	128786339	+	IGR	DEL	GC	-	-	rs4838310	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128786338_128786339delGC								PBX3 (56685 upstream) : FAM125B (302789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128853786	128853791	+	IGR	DEL	TGTGTG	-	-	rs67284815		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128853786_128853791delTGTGTG								PBX3 (124133 upstream) : FAM125B (235337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129001942	129001943	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129001942_129001943delGT								PBX3 (272289 upstream) : FAM125B (87185 downstream)																																			---	---	---	---
TTC16	158248	broad.mit.edu	37	9	130483275	130483275	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130483275delG	uc004brq.1	+						PTRH1_uc011mah.1_Intron|TTC16_uc011mai.1_Intron|TTC16_uc004brr.1_Intron|TTC16_uc010mxn.1_Intron	NM_144965	NP_659402			tetratricopeptide repeat domain 16								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130881283	130881284	+	5'Flank	INS	-	A	A	rs143990368		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130881283_130881284insA	uc004btg.1	-											Homo sapiens cDNA FLJ42733 fis, clone BRAWH2013871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	131211829	131211831	+	IGR	DEL	AGG	-	-	rs10542585		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131211829_131211831delAGG								CERCAM (12202 upstream) : ODF2 (5635 downstream)																																			---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131217957	131217958	+	5'Flank	INS	-	GA	GA	rs149078806	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131217957_131217958insGA	uc011mbd.1	+						ODF2_uc011maz.1_Intron|ODF2_uc011mba.1_5'Flank|ODF2_uc010myb.2_5'Flank|ODF2_uc011mbb.1_5'Flank|ODF2_uc011mbc.1_5'Flank|ODF2_uc004bva.2_5'Flank|ODF2_uc004bvb.2_5'Flank|ODF2_uc011mbe.1_5'Flank|ODF2_uc004bvc.2_5'Flank|ODF2_uc010myc.2_5'Flank|ODF2_uc011mbf.1_5'Flank|ODF2_uc004bvd.3_5'Flank|ODF2_uc004bve.2_5'Flank	NM_002540	NP_002531			outer dense fiber of sperm tails 2 isoform 1						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
TBC1D13	54662	broad.mit.edu	37	9	131560530	131560530	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131560530delA	uc010myj.2	+						TBC1D13_uc010myk.2_Intron|TBC1D13_uc010myl.2_Intron	NM_018201	NP_060671			TBC1 domain family, member 13							intracellular	Rab GTPase activator activity				0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131707775	131707777	+	5'Flank	DEL	AAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131707775_131707777delAAT	uc004bws.1	+						NUP188_uc004bwq.1_Intron	NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	132127181	132127182	+	IGR	DEL	AA	-	-	rs111607968		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132127181_132127182delAA								C9orf106 (42299 upstream) : C9orf50 (247324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132203209	132203210	+	IGR	INS	-	G	G	rs138691594	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132203209_132203210insG								C9orf106 (118327 upstream) : C9orf50 (171296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132306925	132306925	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132306925delA								C9orf106 (222043 upstream) : C9orf50 (67581 downstream)																																			---	---	---	---
PTGES	9536	broad.mit.edu	37	9	132504443	132504444	+	Intron	DEL	AA	-	-	rs72174226		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132504443_132504444delAA	uc004byi.2	-						PTGES_uc010myy.2_Intron|PTGES_uc004byj.2_Intron	NM_004878	NP_004869			prostaglandin E synthase						prostaglandin biosynthetic process|signal transduction	integral to membrane|membrane fraction	glutathione binding|prostaglandin-E synthase activity			skin(1)	1		Ovarian(14;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	132548550	132548550	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132548550delA								PTGES (33206 upstream) : TOR1B (16882 downstream)																																			---	---	---	---
GPR107	57720	broad.mit.edu	37	9	132840662	132840662	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132840662delA	uc004bze.2	+						GPR107_uc004bzb.2_Intron|GPR107_uc004bzc.3_Intron|GPR107_uc011mbx.1_Intron|GPR107_uc004bzd.2_Intron	NM_001136557	NP_001130029			G protein-coupled receptor 107 isoform 1							integral to membrane				upper_aerodigestive_tract(1)	1		Ovarian(14;0.000531)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	133020966	133020966	+	IGR	DEL	A	-	-	rs1557126	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133020966delA								NCS1 (21383 upstream) : ASS1 (299128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	134160683	134160684	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134160683_134160684delTT								FAM78A (8777 upstream) : PPAPDC3 (4397 downstream)																																			---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134328491	134328491	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134328491delT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	134676206	134676206	+	IGR	DEL	T	-	-	rs139306519		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134676206delT								RAPGEF1 (60989 upstream) : MED27 (59293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	134687421	134687421	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134687421delT								RAPGEF1 (72204 upstream) : MED27 (48078 downstream)																																			---	---	---	---
DDX31	64794	broad.mit.edu	37	9	135511332	135511332	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135511332delA	uc004cbq.1	-						DDX31_uc010mzu.1_Intron	NM_022779	NP_073616			DEAD (Asp-Glu-Ala-Asp) box polypeptide 31							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)														---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136258781	136258784	+	Intron	DEL	TGGA	-	-	rs72775495		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136258781_136258784delTGGA	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137576972	137576973	+	Intron	INS	-	CATT	CATT	rs141729483		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137576972_137576973insCATT	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137600270	137600270	+	Intron	DEL	T	-	-	rs4841925	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137600270delT	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138924864	138924864	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138924864delA	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254			BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0																		---	---	---	---
C9orf142	286257	broad.mit.edu	37	9	139888334	139888334	+	3'UTR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139888334delC	uc004cki.2	+	7						NM_183241	NP_899064			hypothetical protein LOC286257												0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
MAN1B1	11253	broad.mit.edu	37	9	139989030	139989030	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139989030delA	uc004cld.2	+						MAN1B1_uc004clc.2_Intron|MAN1B1_uc011meo.1_Intron|MAN1B1_uc011mep.1_Intron|MAN1B1_uc010ncc.2_Intron	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)														---	---	---	---
TPRN	286262	broad.mit.edu	37	9	140096385	140096385	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140096385delT	uc004clt.2	-						TPRN_uc004clu.2_5'Flank	NM_173691	NP_775962			hypothetical protein LOC286262 isoform 2						sensory perception of sound	stereocilium					0																		---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140219890	140219891	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140219890_140219891insT	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																		---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140407415	140407415	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140407415delA	uc004cnf.2	-						PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Intron	NM_152286	NP_689499			patatin-like phospholipase domain containing 7						lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	739860	739860	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:739860delT								DIP2C (4252 upstream) : LARP4B (115624 downstream)																																			---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1061538	1061570	+	Intron	DEL	CTGGGGTCCTGAGCGCTGAGCCTGGGAGTGGAC	-	-	rs71731536	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061538_1061570delCTGGGGTCCTGAGCGCTGAGCCTGGGAGTGGAC	uc001ift.2	+						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)														---	---	---	---
WDR37	22884	broad.mit.edu	37	10	1177631	1177632	+	3'UTR	INS	-	GTGC	GTGC	rs147470214	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1177631_1177632insGTGC	uc001igf.1	+	14					WDR37_uc009xhm.1_3'UTR|WDR37_uc009xhn.1_RNA|WDR37_uc001igg.1_RNA	NM_014023	NP_054742			WD repeat domain 37												0		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1441629	1441629	+	Intron	DEL	T	-	-	rs111879722		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1441629delT	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)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1599331	1599331	+	Intron	DEL	C	-	-	rs10706282		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1599331delC	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)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1645154	1645155	+	Intron	DEL	CA	-	-	rs146661194		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1645154_1645155delCA	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	1970332	1970333	+	IGR	INS	-	AAAT	AAAT	rs151301359	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1970332_1970333insAAAT								ADARB2 (190614 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2525602	2525602	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2525602delA								ADARB2 (745884 upstream) : PFKP (584150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2679639	2679639	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2679639delA								ADARB2 (899921 upstream) : PFKP (430113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3700325	3700326	+	Intron	DEL	TT	-	-	rs67692911		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3700325_3700326delTT	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
KLF6	1316	broad.mit.edu	37	10	3823542	3823544	+	Intron	DEL	ACT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3823542_3823544delACT	uc001iha.2	-						KLF6_uc010qaj.1_Intron|KLF6_uc010qak.1_Intron|KLF6_uc010qal.1_Intron|KLF6_uc001ihb.2_3'UTR	NM_001300	NP_001291			Kruppel-like factor 6 isoform A						B cell differentiation	nucleus	zinc ion binding			central_nervous_system(3)|lung(1)	4				Colorectal(1;0.238)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	3844820	3844823	+	IGR	DEL	ACAT	-	-	rs113712485		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3844820_3844823delACAT								KLF6 (17347 upstream) : LOC100216001 (776621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4159923	4159924	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4159923_4159924delGA								KLF6 (332450 upstream) : LOC100216001 (461520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4216061	4216062	+	IGR	INS	-	T	T	rs144736450	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4216061_4216062insT								KLF6 (388588 upstream) : LOC100216001 (405382 downstream)																																			---	---	---	---
AKR1C3	8644	broad.mit.edu	37	10	5065286	5065286	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5065286delT	uc001ihr.2	+						AKR1E2_uc001ihl.1_Intron	NM_003739	NP_003730			aldo-keto reductase family 1, member C3						prostaglandin metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (A-specific) activity|indanol dehydrogenase activity|prostaglandin-F synthase activity|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity			skin(1)	1					Dimethyl sulfoxide(DB01093)|NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	5320969	5320971	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5320969_5320971delAAA								AKR1C4 (60059 upstream) : UCN3 (86005 downstream)																																			---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6483432	6483433	+	Intron	DEL	TC	-	-	rs142789353	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6483432_6483433delTC	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248			protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6968812	6968812	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6968812delC								PRKCQ (346574 upstream) : SFMBT2 (235437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7188232	7188232	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7188232delT								PRKCQ (565994 upstream) : SFMBT2 (16017 downstream)																																			---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7249383	7249386	+	Intron	DEL	GAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7249383_7249386delGAAA	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7546324	7546324	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7546324delT								SFMBT2 (92874 upstream) : ITIH5 (55312 downstream)																																			---	---	---	---
GATA3	2625	broad.mit.edu	37	10	8103052	8103052	+	Intron	DEL	C	-	-	rs489160	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8103052delC	uc001ika.2	+						GATA3_uc001ijz.2_Intron	NM_002051	NP_002042			GATA binding protein 3 isoform 2						aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding			breast(17)|ovary(3)|central_nervous_system(2)	22								F|N|S		breast		HDR syndrome (HYPOPARATHYROIDISM|SENSORINEURAL DEAFNESS|AND RENAL DISEASE)						---	---	---	---
Unknown	0	broad.mit.edu	37	10	8762028	8762028	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8762028delG								GATA3 (644866 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10576178	10576179	+	IGR	DEL	AA	-	-	rs148241138		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10576178_10576179delAA								None (None upstream) : SFTA1P (250223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	11699506	11699506	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11699506delA								USP6NL (45827 upstream) : ECHDC3 (84850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	11756815	11756815	+	IGR	DEL	A	-	-	rs72000399		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11756815delA								USP6NL (103136 upstream) : ECHDC3 (27541 downstream)																																			---	---	---	---
C10orf47	254427	broad.mit.edu	37	10	11905543	11905544	+	Intron	DEL	AA	-	-	rs74358513	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11905543_11905544delAA	uc001ikx.2	+						uc001iky.1_Intron	NM_153256	NP_694988			hypothetical protein LOC254427											central_nervous_system(1)	1																		---	---	---	---
UPF2	26019	broad.mit.edu	37	10	11970335	11970336	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11970335_11970336insA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12033629	12033629	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12033629delA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12035989	12035989	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12035989delA	uc001ila.2	-						UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron|UPF2_uc009xiz.1_Intron	NM_080599	NP_542166			UPF2 regulator of nonsense transcripts homolog						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12759590	12759590	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12759590delA	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)														---	---	---	---
CCDC3	83643	broad.mit.edu	37	10	13031930	13031930	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13031930delA	uc001ilq.1	-						CCDC3_uc009xjb.1_Intron|CCDC3_uc001ilr.2_Intron|CCDC3_uc009xjc.1_Intron	NM_031455	NP_113643			coiled-coil domain containing 3 precursor							endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	13287726	13287726	+	IGR	DEL	A	-	-	rs143007429		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13287726delA								UCMA (11398 upstream) : PHYH (32071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	13312079	13312087	+	IGR	DEL	AACAACAAC	-	-	rs113230095		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13312079_13312087delAACAACAAC								UCMA (35751 upstream) : PHYH (7710 downstream)																																			---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13961167	13961167	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13961167delA	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14600193	14600196	+	Intron	DEL	CACT	-	-	rs80227155		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14600193_14600196delCACT	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14627153	14627153	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14627153delC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14799462	14799463	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14799462_14799463delTC	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	14839376	14839376	+	IGR	DEL	A	-	-	rs10906759	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14839376delA								FAM107B (22480 upstream) : CDNF (21875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	15783538	15783538	+	IGR	DEL	T	-	-	rs68082514		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15783538delT								ITGA8 (21768 upstream) : FAM188A (36637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	15986176	15986180	+	IGR	DEL	GCACA	-	-	rs147422818		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15986176_15986180delGCACA								FAM188A (83657 upstream) : PTER (492787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16399236	16399237	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16399236_16399237delCT								FAM188A (496717 upstream) : PTER (79730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16582123	16582124	+	IGR	INS	-	GTGC	GTGC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16582123_16582124insGTGC								C1QL3 (18119 upstream) : RSU1 (50495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	17183529	17183530	+	IGR	INS	-	T	T	rs150904905	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17183529_17183530insT								CUBN (11713 upstream) : TRDMT1 (1453 downstream)																																			---	---	---	---
STAM	8027	broad.mit.edu	37	10	17752443	17752444	+	Intron	DEL	AT	-	-	rs57735619		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17752443_17752444delAT	uc001ipj.1	+						STAM_uc009xjw.1_Intron	NM_003473	NP_003464			signal transducing adaptor molecule 1						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																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18451312	18451312	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18451312delA	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	19277209	19277209	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19277209delC								ARL5B (310269 upstream) : PLXDC2 (828163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19750609	19750610	+	IGR	INS	-	A	A	rs140795443	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19750609_19750610insA								ARL5B (783669 upstream) : PLXDC2 (354762 downstream)																																			---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20483355	20483355	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20483355delT	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	20954567	20954568	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20954567_20954568insA								PLXDC2 (385452 upstream) : NEBL (114337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21537167	21537167	+	IGR	DEL	T	-	-	rs76998587		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21537167delT								NEBL (74051 upstream) : C10orf114 (246255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21627153	21627153	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21627153delT								NEBL (164037 upstream) : C10orf114 (156269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22041331	22041331	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22041331delG								MLLT10 (8776 upstream) : DNAJC1 (4147 downstream)																																			---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22291409	22291409	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22291409delA	uc001irc.2	-						DNAJC1_uc001ird.2_Intron	NM_022365	NP_071760			DnaJ (Hsp40) homolog, subfamily C, member 1						negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
ARMC3	219681	broad.mit.edu	37	10	23236255	23236255	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23236255delA	uc001irm.3	+						ARMC3_uc010qcv.1_Intron|ARMC3_uc010qcw.1_Intron	NM_173081	NP_775104			armadillo repeat containing 3								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	23978045	23978046	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23978045_23978046delTT								OTUD1 (246737 upstream) : KIAA1217 (5629 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24119595	24119596	+	Intron	INS	-	TAGG	TAGG	rs143607296	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24119595_24119596insTAGG	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24890792	24890792	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	26103861	26103862	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26103861_26103862delAA								GPR158 (212706 upstream) : MYO3A (119140 downstream)																																			---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26246228	26246228	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26246228delG	uc001isn.2	+						MYO3A_uc009xko.1_Intron|MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron|MYO3A_uc001ism.2_Intron	NM_017433	NP_059129			myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
MKX	283078	broad.mit.edu	37	10	27997218	27997218	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27997218delT	uc001ity.3	-						MKX_uc001itx.3_Intron	NM_173576	NP_775847			mohawk homeobox						muscle organ development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
MKX	283078	broad.mit.edu	37	10	28008752	28008752	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28008752delA	uc001ity.3	-						MKX_uc001itx.3_Intron	NM_173576	NP_775847			mohawk homeobox						muscle organ development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28152748	28152748	+	Intron	DEL	T	-	-	rs112482791		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28152748delT	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28808697	28808698	+	IGR	INS	-	AA	AA	rs149999936		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28808697_28808698insAA								MPP7 (216702 upstream) : WAC (12729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28939527	28939528	+	IGR	DEL	AA	-	-	rs148885642		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28939527_28939528delAA								WAC (29606 upstream) : BAMBI (26896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29241744	29241744	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29241744delA								BAMBI (269876 upstream) : LYZL1 (336246 downstream)																																			---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29780846	29780846	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29780846delT	uc001iut.1	-						SVIL_uc010qdw.1_Intron|SVIL_uc001iuu.1_Intron|SVIL_uc009xlc.2_Intron	NM_021738	NP_068506			supervillin isoform 2						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	30069842	30069843	+	IGR	DEL	CT	-	-	rs145747927	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30069842_30069843delCT								SVIL (43978 upstream) : KIAA1462 (231886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30086952	30086954	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30086952_30086954delTTT								SVIL (61088 upstream) : KIAA1462 (214775 downstream)																																			---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30308919	30308919	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30308919delA	uc001iux.2	-						KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Intron	NM_020848	NP_065899			hypothetical protein LOC57608											ovary(4)	4																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30362610	30362611	+	Intron	INS	-	CTTC	CTTC	rs145825538	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30362610_30362611insCTTC	uc001iuz.2	-											RecName: Full=Uncharacterized protein KIAA1462;											ovary(4)	4																		---	---	---	---
MTPAP	55149	broad.mit.edu	37	10	30617803	30617804	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30617803_30617804delAG	uc001iva.3	-						MTPAP_uc001ivb.3_Intron	NM_018109	NP_060579			PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	31996717	31996717	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31996717delT								ZEB1 (178590 upstream) : ARHGAP12 (98508 downstream)																																			---	---	---	---
ARHGAP12	94134	broad.mit.edu	37	10	32106658	32106658	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32106658delA	uc001ivz.1	-						ARHGAP12_uc001ivy.1_Intron|ARHGAP12_uc009xls.2_Intron|ARHGAP12_uc001iwb.1_Intron|ARHGAP12_uc001iwc.1_Intron|ARHGAP12_uc009xlq.1_Intron|ARHGAP12_uc001iwd.1_Intron|ARHGAP12_uc009xlr.1_Intron	NM_018287	NP_060757			Rho GTPase activating protein 12						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		Prostate(175;0.0199)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	32239229	32239229	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32239229delT								ARHGAP12 (21459 upstream) : KIF5B (58711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32266289	32266289	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32266289delA								ARHGAP12 (48519 upstream) : KIF5B (31651 downstream)																																			---	---	---	---
C10orf68	79741	broad.mit.edu	37	10	32916898	32916898	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32916898delT	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron	NM_024688	NP_078964			chromosome 10 open reading frame 68											skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	33321982	33321983	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33321982_33321983insA								ITGB1 (74689 upstream) : NRP1 (144437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34002944	34002945	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34002944_34002945delAA								NRP1 (378938 upstream) : PARD3 (397153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34153682	34153682	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34153682delA								NRP1 (529676 upstream) : PARD3 (246416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34275841	34275841	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34275841delT								NRP1 (651835 upstream) : PARD3 (124257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34328475	34328475	+	IGR	DEL	T	-	-	rs113585168		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34328475delT								NRP1 (704469 upstream) : PARD3 (71623 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34733989	34733989	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34733989delT	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|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.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)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	35058794	35058795	+	Intron	INS	-	AC	AC	rs148152538	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35058794_35058795insAC	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|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.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)																---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35673140	35673140	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35673140delA	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449			cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0																		---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35707764	35707764	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35707764delT	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449			cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0																		---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35754890	35754891	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35754890_35754891delTG	uc001iyw.3	+						CCNY_uc001iyu.3_Intron|CCNY_uc001iyv.3_Intron|CCNY_uc001iyx.3_Intron|CCNY_uc009xmb.2_Intron|CCNY_uc010qet.1_Intron	NM_145012	NP_659449			cyclin Y isoform 1						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	36721517	36721518	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36721517_36721518delGT								FZD8 (791155 upstream) : ANKRD30A (693267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36999628	36999628	+	IGR	DEL	C	-	-	rs34399208		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36999628delC								None (None upstream) : ANKRD30A (415157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37691031	37691031	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37691031delC								ANKRD30A (169536 upstream) : ZNF248 (399416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39009437	39009438	+	IGR	INS	-	AGTGACCTCA	AGTGACCTCA			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39009437_39009438insAGTGACCTCA								LOC399744 (268357 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42371004	42371005	+	IGR	INS	-	TGATG	TGATG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42371004_42371005insTGATG								None (None upstream) : LOC441666 (456310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42379610	42379614	+	IGR	DEL	TGTCA	-	-	rs139640914		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42379610_42379614delTGTCA								None (None upstream) : LOC441666 (447701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42614788	42614792	+	IGR	DEL	TAAGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42614788_42614792delTAAGT								None (None upstream) : LOC441666 (212523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42660250	42660250	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42660250delA								None (None upstream) : LOC441666 (167065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42799746	42799750	+	IGR	DEL	TTCCT	-	-	rs59133388		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42799746_42799750delTTCCT								None (None upstream) : LOC441666 (27565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42923457	42923457	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42923457delA	uc001izx.2	-											Homo sapiens cyclin Y-like 2, mRNA (cDNA clone IMAGE:4704933), with apparent retained intron.																														---	---	---	---
ZNF33B	7582	broad.mit.edu	37	10	43136447	43136448	+	5'Flank	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43136447_43136448insG	uc001jaf.1	-						ZNF33B_uc009xmg.1_5'Flank|ZNF33B_uc001jae.1_5'Flank|ZNF33B_uc001jag.1_5'Flank	NM_006955	NP_008886			zinc finger protein 33B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43321685	43321686	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43321685_43321686delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43347250	43347267	+	IGR	DEL	TGTTGTTGTTGTTGTTGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43347250_43347267delTGTTGTTGTTGTTGTTGT								BMS1 (16867 upstream) : RET (225250 downstream)																																			---	---	---	---
RASGEF1A	221002	broad.mit.edu	37	10	43699949	43699949	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43699949delG	uc001jap.1	-						RASGEF1A_uc001jao.1_Intron	NM_145313	NP_660356			RasGEF domain family, member 1A						cell migration|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																OREG0020137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	10	43777443	43777444	+	IGR	INS	-	T	T	rs150205539	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43777443_43777444insT								RASGEF1A (15076 upstream) : FXYD4 (89648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43803649	43803649	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43803649delA								RASGEF1A (41282 upstream) : FXYD4 (63443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44504411	44504411	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44504411delC								HNRNPA3P1 (218546 upstream) : CXCL12 (361196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44920220	44920220	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44920220delT								CXCL12 (39678 upstream) : TMEM72 (486544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44993385	44993390	+	IGR	DEL	TGTGTT	-	-	rs66638126		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44993385_44993390delTGTGTT								CXCL12 (112843 upstream) : TMEM72 (413374 downstream)																																			---	---	---	---
LOC100133308	100133308	broad.mit.edu	37	10	45607043	45607044	+	Intron	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45607043_45607044insTG	uc001jbz.2	-						LOC100133308_uc009xmq.1_Intron					Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0																		---	---	---	---
LOC100133308	100133308	broad.mit.edu	37	10	45641409	45641409	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45641409delC	uc001jbz.2	-						LOC100133308_uc009xmq.1_Intron|uc001jca.3_5'Flank					Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	45775752	45775752	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45775752delG								LOC100133308 (125708 upstream) : OR13A1 (22350 downstream)																																			---	---	---	---
FAM21C	253725	broad.mit.edu	37	10	46224179	46224179	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46224179delA	uc001jcu.2	+						FAM21C_uc001jcs.1_Intron|FAM21C_uc001jct.2_Intron|FAM21C_uc010qfi.1_Intron	NM_015262	NP_056077			hypothetical protein LOC253725											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	46989395	46989411	+	IGR	DEL	AACAGGGGGACTACAGA	-	-	rs72031633		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46989395_46989411delAACAGGGGGACTACAGA								SYT15 (18794 upstream) : GPRIN2 (4135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	47638032	47638032	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47638032delG								FAM35B2 (216796 upstream) : ANTXRL (20202 downstream)																																			---	---	---	---
ANTXRL	195977	broad.mit.edu	37	10	47664757	47664758	+	Intron	DEL	GC	-	-	rs10546434		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47664757_47664758delGC	uc001jel.2	+							NR_003601				Homo sapiens cDNA FLJ32754 fis, clone TESTI2001671.												0																		---	---	---	---
ZNF488	118738	broad.mit.edu	37	10	48359275	48359275	+	Intron	DEL	T	-	-	rs34211862		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48359275delT	uc001jex.2	+						ZNF488_uc001jey.2_Intron	NM_153034	NP_694579			zinc finger protein 488						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	48980053	48980053	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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).																														---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	49945403	49945403	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49945403delA	uc001jha.3	+							NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
CHAT	1103	broad.mit.edu	37	10	50877076	50877077	+	Intron	DEL	GA	-	-	rs72126547		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50877076_50877077delGA	uc010qgs.1	+							NM_020986	NP_066266			choline acetyltransferase isoform 1						neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	50934762	50934763	+	IGR	INS	-	A	A	rs74131126		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50934762_50934763insA								C10orf53 (17806 upstream) : OGDHL (7925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	52446702	52446703	+	IGR	INS	-	T	T	rs138711130		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52446702_52446703insT								SGMS1 (61779 upstream) : ASAH2B (52993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	52467358	52467359	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52467358_52467359delTC								SGMS1 (82435 upstream) : ASAH2B (32337 downstream)																																			---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53276190	53276190	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53276190delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53305817	53305817	+	Intron	DEL	T	-	-	rs34133066		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53305817delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53570166	53570166	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53570166delG	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	55420168	55420182	+	IGR	DEL	AGGTCAGAGAACACG	-	-	rs72281622		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55420168_55420182delAGGTCAGAGAACACG								MBL2 (888708 upstream) : PCDH15 (142353 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55962084	55962085	+	Intron	DEL	AA	-	-	rs80057503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55962084_55962085delAA	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	57152740	57152741	+	Intron	DEL	TG	-	-	rs34723306		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57152740_57152741delTG	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 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)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58256694	58256694	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58256694delT								ZWINT (135660 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59431867	59431867	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59431867delA								None (None upstream) : IPMK (523751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59652313	59652313	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59652313delA								None (None upstream) : IPMK (303305 downstream)																																			---	---	---	---
TFAM	7019	broad.mit.edu	37	10	60152445	60152447	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60152445_60152447delTTT	uc001jkf.2	+						TFAM_uc001jkg.2_Intron|TFAM_uc001jkh.2_Intron	NM_003201	NP_003192			transcription factor A, mitochondrial precursor						DNA-dependent DNA replication|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase I promoter|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	mitochondrial light strand promoter sense binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	61742104	61742104	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61742104delT								C10orf40 (21433 upstream) : ANK3 (46056 downstream)																																			---	---	---	---
ANK3	288	broad.mit.edu	37	10	62053918	62053918	+	Intron	DEL	T	-	-	rs34213470		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62053918delT	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	62249784	62249785	+	Intron	INS	-	A	A	rs140949387	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62249784_62249785insA	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																		---	---	---	---
TMEM26	219623	broad.mit.edu	37	10	63196084	63196084	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63196084delA	uc001jlo.2	-						TMEM26_uc010qij.1_Intron|TMEM26_uc001jlq.2_Intron	NM_178505	NP_848600			transmembrane protein 26							integral to membrane					0	Prostate(12;0.0112)																	---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63849288	63849288	+	Intron	DEL	T	-	-	rs111270606		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63849288delT	uc001jlt.1	+							NM_032199	NP_115575			AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	64665654	64665657	+	IGR	DEL	GAAA	-	-	rs10569806		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64665654_64665657delGAAA								EGR2 (86727 upstream) : NRBF2 (227350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65444059	65444059	+	IGR	DEL	A	-	-	rs148934022		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65444059delA								REEP3 (62088 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65470437	65470437	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65470437delT								REEP3 (88466 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67346870	67346870	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67346870delT								ANXA2P3 (760236 upstream) : CTNNA3 (332855 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67924844	67924845	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67924844_67924845insA	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																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68047284	68047284	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68047284delA	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																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68398962	68398962	+	Intron	DEL	G	-	-	rs5785773		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68398962delG	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_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																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69394951	69394951	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69394951delA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.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	69699479	69699480	+	Intron	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69699479_69699480delAT	uc001jng.3	-						HERC4_uc009xpq.2_Intron|HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_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																		---	---	---	---
HERC4	26091	broad.mit.edu	37	10	69768985	69768986	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69768985_69768986delAA	uc001jng.3	-						HERC4_uc001jnf.3_Intron|HERC4_uc001jnh.3_Intron|HERC4_uc009xpr.2_Intron|HERC4_uc001jni.3_Intron|HERC4_uc001jnj.2_Intron	NM_022079	NP_071362			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																		---	---	---	---
DNA2	1763	broad.mit.edu	37	10	70227176	70227176	+	Intron	DEL	T	-	-	rs71856177		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70227176delT	uc001jof.2	-						DNA2_uc001jog.1_Intron|DNA2_uc001joh.1_Intron	NM_001080449	NP_001073918			DNA replication helicase 2 homolog						base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70301787	70301787	+	IGR	DEL	A	-	-	rs79228353		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70301787delA								SLC25A16 (14203 upstream) : TET1 (18330 downstream)																																			---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70675471	70675473	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70675471_70675473delAAA	uc001jou.2	+						DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70676891	70676891	+	Intron	DEL	T	-	-	rs112172919		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70676891delT	uc001jou.2	+						DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
H2AFY2	55506	broad.mit.edu	37	10	71839428	71839434	+	Intron	DEL	TCAGTTG	-	-	rs72043868		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71839428_71839434delTCAGTTG	uc001jqm.2	+						H2AFY2_uc001jqn.2_Intron	NM_018649	NP_061119			H2A histone family, member Y2						chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72147014	72147016	+	IGR	DEL	AAA	-	-	rs4746033		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72147014_72147016delAAA								LRRC20 (4632 upstream) : EIF4EBP2 (16845 downstream)																																			---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72258343	72258343	+	Intron	DEL	T	-	-	rs142510728		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72258343delT	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72720552	72720555	+	IGR	DEL	GTGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72720552_72720555delGTGT								PCBD1 (72011 upstream) : UNC5B (251743 downstream)																																			---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73173465	73173465	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73173465delT	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73180243	73180245	+	Intron	DEL	TGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73180243_73180245delTGG	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73200563	73200563	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73200563delC	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CHST3	9469	broad.mit.edu	37	10	73721932	73721947	+	5'Flank	DEL	CGGGGGTGGTGGGAGA	-	-	rs111699730		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73721932_73721947delCGGGGGTGGTGGGAGA	uc001jsn.2	+							NM_004273	NP_004264			chondroitin 6-sulfotransferase 3						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	75724456	75724457	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75724456_75724457delTT								C10orf55 (41921 upstream) : VCL (30494 downstream)																																			---	---	---	---
VCL	7414	broad.mit.edu	37	10	75770407	75770407	+	Intron	DEL	A	-	-	rs76251874	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75770407delA	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706			vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)																	---	---	---	---
ADK	132	broad.mit.edu	37	10	75931569	75931574	+	Intron	DEL	TGTGTG	-	-	rs59896288		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75931569_75931574delTGTGTG	uc001jwi.2	+						ADK_uc010qlb.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76883335	76883335	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76883335delG	uc001jwx.1	+						SAMD8_uc001jwy.1_Intron	NM_144660	NP_653261			sterile alpha motif domain containing 8						sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76886426	76886427	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76886426_76886427delTT	uc001jwx.1	+						SAMD8_uc001jwy.1_Intron	NM_144660	NP_653261			sterile alpha motif domain containing 8						sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	77089189	77089196	+	Intron	DEL	CTTCCTTT	-	-	rs4746286		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77089189_77089196delCTTCCTTT	uc001jxd.1	+											Homo sapiens cDNA FLJ13383 fis, clone PLACE1001024.																														---	---	---	---
MIR606	693191	broad.mit.edu	37	10	77312184	77312184	+	5'Flank	DEL	C	-	-	rs1367290		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77312184delC	hsa-mir-606|MI0003619	+																							0																		---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77851035	77851036	+	Intron	DEL	GT	-	-	rs111971480		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77851035_77851036delGT	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78742087	78742089	+	Intron	DEL	AAA	-	-	rs35078324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78742087_78742089delAAA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	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	78954834	78954834	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78954834delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	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	79098997	79098997	+	Intron	DEL	T	-	-	rs144360936	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79098997delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	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	79332514	79332514	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79332514delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	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)													---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79603069	79603069	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79603069delA	uc001jzk.2	-						DLG5_uc001jzj.2_Intron|DLG5_uc009xru.1_Intron|DLG5_uc001jzl.3_5'Flank	NM_004747	NP_004738			discs large homolog 5						cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	80481147	80481147	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80481147delT								RPS24 (664577 upstream) : LOC283050 (221937 downstream)																																			---	---	---	---
LOC283050	283050	broad.mit.edu	37	10	80717594	80717595	+	Intron	INS	-	GATGGATA	GATGGATA	rs145429499	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80717594_80717595insGATGGATA	uc001jzz.2	-						LOC283050_uc001jzx.2_Intron|LOC283050_uc001jzy.2_Intron	NR_024431				Homo sapiens cDNA FLJ40604 fis, clone THYMU2011806.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	81121662	81121663	+	IGR	DEL	CA	-	-	rs112035034		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81121662_81121663delCA								PPIF (6578 upstream) : ZCCHC24 (20422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82057637	82057637	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82057637delT								MAT1A (8203 upstream) : DYDC1 (38227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83246106	83246106	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83246106delA								SH2D4B (839790 upstream) : NRG3 (388964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85393690	85393690	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85393690delG								NRG3 (646755 upstream) : GHITM (505495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85564778	85564779	+	IGR	INS	-	TG	TG	rs137884582	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85564778_85564779insTG								NRG3 (817843 upstream) : GHITM (334406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85926013	85926015	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85926013_85926015delAAA								GHITM (12702 upstream) : C10orf99 (7539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	86612075	86612078	+	IGR	DEL	TTTT	-	-	rs142322790	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86612075_86612078delTTTT								FAM190B (333799 upstream) : GRID1 (747234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87025484	87025484	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87025484delC								FAM190B (747208 upstream) : GRID1 (333828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87174783	87174784	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87174783_87174784delAG								FAM190B (896507 upstream) : GRID1 (184528 downstream)																																			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87579686	87579687	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87579686_87579687delGA	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)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87848655	87848655	+	Intron	DEL	A	-	-	rs77483927		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87848655delA	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)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87861391	87861391	+	Intron	DEL	T	-	-	rs113005177		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87861391delT	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)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87887935	87887936	+	Intron	INS	-	A	A	rs140603972	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87887935_87887936insA	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)			---	---	---	---
MMRN2	79812	broad.mit.edu	37	10	88709287	88709288	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88709287_88709288delAA	uc001kea.2	-						MMRN2_uc010qmn.1_Intron|MMRN2_uc009xtb.2_Intron	NM_024756	NP_079032			multimerin 2 precursor							extracellular space				large_intestine(1)	1																		---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88736678	88736679	+	Intron	INS	-	TG	TG	rs149037275	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88736678_88736679insTG	uc001kee.2	+							NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88756928	88756929	+	Intron	DEL	TA	-	-	rs10599921		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88756928_88756929delTA	uc001kee.2	+						AGAP11_uc001kef.2_Intron	NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
RNLS	55328	broad.mit.edu	37	10	89894308	89894309	+	Intron	INS	-	T	T	rs74916537	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89894308_89894309insT	uc010qms.1	-											SubName: Full=cDNA FLJ55083, highly similar to Renalase (EC 1.4.-.-);							extracellular region	oxidoreductase activity			ovary(1)	1																		---	---	---	---
PANK1	53354	broad.mit.edu	37	10	91347952	91347952	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91347952delA	uc001kgp.1	-						PANK1_uc001kgn.1_Intron|PANK1_uc001kgo.1_Intron|PANK1_uc009xtu.1_Intron	NM_148977	NP_683878			pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	92188709	92188710	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92188709_92188710delTG								KIF20B (654009 upstream) : HTR7 (311868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	92343284	92343285	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92343284_92343285delAA								KIF20B (808584 upstream) : HTR7 (157293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	93397688	93397688	+	IGR	DEL	T	-	-	rs148353588		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93397688delT								PPP1R3C (4830 upstream) : TNKS2 (160463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	93517969	93517969	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93517969delA								PPP1R3C (125111 upstream) : TNKS2 (40182 downstream)																																			---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	93941755	93941756	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93941755_93941756delAA	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	93998384	93998384	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93998384delA	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	94153752	94153753	+	IGR	INS	-	T	T	rs146356738		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94153752_94153753insT								MARCH5 (40031 upstream) : IDE (59847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	94854193	94854194	+	IGR	INS	-	TGTT	TGTT	rs139301980	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94854193_94854194insTGTT								CYP26A1 (16552 upstream) : MYOF (211993 downstream)																																			---	---	---	---
TMEM20	159371	broad.mit.edu	37	10	95699605	95699605	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95699605delT	uc001kji.2	+											Homo sapiens cDNA FLJ33990 fis, clone DFNES2007299.							integral to membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;3.46e-05)|Renal(717;0.018)|Ovarian(717;0.0228)|all_hematologic(284;0.189)		STAD - Stomach adenocarcinoma(243;0.00345)														---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96094287	96094287	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96094287delA	uc001kjq.1	-							NM_022451	NP_071896			nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313731	96313731	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96313731delT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96331305	96331305	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96331305delA	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97098471	97098473	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97098471_97098473delTTT	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron	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)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97106050	97106050	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97106050delT	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			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)														---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97400108	97400108	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97400108delT	uc001kkz.2	-						ALDH18A1_uc001kky.2_Intron|ALDH18A1_uc010qog.1_Intron|ALDH18A1_uc010qoh.1_Intron	NM_002860	NP_002851			pyrroline-5-carboxylate synthetase isoform 1						proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)													---	---	---	---
TLL2	7093	broad.mit.edu	37	10	98142196	98142197	+	Intron	DEL	AA	-	-	rs142863098		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98142196_98142197delAA	uc001kml.1	-							NM_012465	NP_036597			tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99084018	99084018	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99084018delT								FRAT1 (2346 upstream) : FRAT2 (8236 downstream)																																			---	---	---	---
RRP12	23223	broad.mit.edu	37	10	99134529	99134532	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99134529_99134532delAAAA	uc001knf.2	-						RRP12_uc009xvl.2_5'Flank|RRP12_uc009xvm.2_Intron|RRP12_uc010qou.1_Intron|RRP12_uc009xvn.2_Intron	NM_015179	NP_055994			ribosomal RNA processing 12 homolog isoform 1							integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102352511	102352511	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102352511delA								HIF1AN (38831 upstream) : PAX2 (152957 downstream)																																			---	---	---	---
PAX2	5076	broad.mit.edu	37	10	102504069	102504069	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102504069delG	uc001krk.3	+						PAX2_uc001krl.3_5'Flank|PAX2_uc001krm.3_5'Flank|PAX2_uc001kro.3_5'Flank|PAX2_uc001krn.3_5'Flank|PAX2_uc010qps.1_5'Flank	NM_003990	NP_003981			paired box protein 2 isoform e						anti-apoptosis|axonogenesis|brain morphogenesis|branching involved in ureteric bud morphogenesis|cell fate determination|cellular response to glucose stimulus|cellular response to hydrogen peroxide|cellular response to retinoic acid|cochlea development|glial cell differentiation|inner ear morphogenesis|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesodermal cell fate specification|mesonephros development|metanephric collecting duct development|metanephric distal convoluted tubule development|metanephric mesenchymal cell differentiation|metanephric nephron tubule formation|negative regulation of caspase activity|negative regulation of cytolysis|negative regulation of mesenchymal stem cell apoptosis involved in metanephric nephron morphogenesis|negative regulation of reactive oxygen species metabolic process|negative regulation of transcription, DNA-dependent|nephric duct formation|neural tube closure|optic chiasma development|optic cup morphogenesis involved in camera-type eye development|optic nerve structural organization|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of epithelial cell proliferation|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of metanephric DCT cell differentiation|positive regulation of metanephric glomerulus development|positive regulation of optic nerve formation|positive regulation of transcription from RNA polymerase II promoter|pronephric field specification|protein kinase B signaling cascade|reactive oxygen species metabolic process|regulation of metanephric nephron tubule epithelial cell differentiation|regulation of metanephros size|retinal pigment epithelium development|stem cell differentiation|transcription from RNA polymerase II promoter|ureter maturation|vestibulocochlear nerve formation|visual perception	centriolar satellite|nucleus|protein complex|protein-DNA complex	core promoter proximal region sequence-specific DNA binding|superoxide-generating NADPH oxidase activity				0		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)														---	---	---	---
PDZD7	79955	broad.mit.edu	37	10	102788360	102788360	+	Intron	DEL	A	-	-	rs71975380		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102788360delA	uc001kso.1	-						PDZD7_uc001ksn.2_Intron|SFXN3_uc001ksp.2_5'Flank	NM_024895	NP_079171			PDZ domain containing 7							cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	103501060	103501064	+	IGR	DEL	AAAAA	-	-	rs112507967		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103501060_103501064delAAAAA								FBXW4 (46317 upstream) : FGF8 (28823 downstream)																																			---	---	---	---
C10orf76	79591	broad.mit.edu	37	10	103789677	103789677	+	Intron	DEL	G	-	-	rs10786660	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103789677delG	uc009xwy.1	-						C10orf76_uc001kui.2_Intron	NM_024541	NP_078817			hypothetical protein LOC79591							integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)														---	---	---	---
PSD	5662	broad.mit.edu	37	10	104177926	104177927	+	Intron	INS	-	AC	AC	rs140673906	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104177926_104177927insAC	uc001kvg.1	-						PSD_uc001kvh.1_Intron|PSD_uc009xxd.1_Intron|PSD_uc001kvi.1_Intron|FBXL15_uc001kvj.1_5'Flank|FBXL15_uc001kvk.2_5'Flank|FBXL15_uc001kvl.1_5'Flank	NM_002779	NP_002770			pleckstrin and Sec7 domain containing						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)														---	---	---	---
TMEM180	79847	broad.mit.edu	37	10	104237194	104237194	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104237194delA	uc010qqm.1	+											SubName: Full=cDNA FLJ61437;							integral to membrane				ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104646089	104646090	+	Intron	INS	-	T	T	rs147355245		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104646089_104646090insT	uc001kwk.2	+						AS3MT_uc001kwj.2_Intron|AS3MT_uc009xxh.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104755490	104755490	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104755490delT	uc001kwm.2	+						CNNM2_uc001kwn.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)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104814054	104814054	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104814054delT	uc001kwm.2	+						CNNM2_uc001kwn.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)												OREG0020489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105208932	105208933	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105208932_105208933delAA	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_3'UTR	NM_015916	NP_057000			calcium homeostasis modulator 2							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	105686743	105686743	+	IGR	DEL	T	-	-	rs72027121		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105686743delT								OBFC1 (8698 upstream) : SLK (40727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	106104904	106104905	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106104904_106104905insA								ITPRIP (6742 upstream) : CCDC147 (8617 downstream)																																			---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106837280	106837287	+	Intron	DEL	ACACACAC	-	-	rs34110774		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106837280_106837287delACACACAC	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107241658	107241658	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107241658delA								SORCS3 (216665 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107722744	107722744	+	IGR	DEL	T	-	-	rs5787622		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107722744delT								SORCS3 (697751 upstream) : SORCS1 (610678 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108376209	108376209	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108376209delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108684954	108684954	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108684954delT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	109365762	109365763	+	IGR	INS	-	TG	TG	rs139620789	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109365762_109365763insTG								SORCS1 (441470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110286025	110286026	+	IGR	DEL	AC	-	-	rs66623215		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110286025_110286026delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110800564	110800564	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110800564delT								None (None upstream) : XPNPEP1 (823960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110890269	110890269	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110890269delT								None (None upstream) : XPNPEP1 (734255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111130749	111130750	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111130749_111130750delAA								None (None upstream) : XPNPEP1 (493774 downstream)																																			---	---	---	---
MXI1	4601	broad.mit.edu	37	10	112043719	112043720	+	Intron	DEL	TG	-	-	rs145540678	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112043719_112043720delTG	uc001kza.2	+						MXI1_uc001kyy.2_Intron|MXI1_uc001kyz.2_Intron|MXI1_uc010qrc.1_Intron|MXI1_uc009xxu.2_Intron|MXI1_uc009xxv.2_Intron	NM_005962	NP_005953			MAX interactor 1 isoform a						cytoplasmic sequestering of transcription factor|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription corepressor activity				0		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114319621	114319621	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114319621delT	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115373014	115373014	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115373014delA	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326			nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115376611	115376611	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115376611delT	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326			nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117550280	117550280	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117550280delA	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	117733876	117733877	+	IGR	INS	-	TCCAA	TCCAA	rs146312646	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117733876_117733877insTCCAA								ATRNL1 (25382 upstream) : GFRA1 (82567 downstream)																																			---	---	---	---
C10orf96	374355	broad.mit.edu	37	10	118118330	118118330	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118118330delT	uc001lck.2	+							NM_198515	NP_940917			hypothetical protein LOC374355											ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)														---	---	---	---
PNLIP	5406	broad.mit.edu	37	10	118313457	118313457	+	Intron	DEL	A	-	-	rs72574709		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118313457delA	uc001lcm.2	+							NM_000936	NP_000927			pancreatic lipase precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|skin(1)	3				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)													---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118719425	118719426	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118719425_118719426delCA	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)														---	---	---	---
EMX2OS	196047	broad.mit.edu	37	10	119253460	119253461	+	Intron	INS	-	AAAC	AAAC	rs145277525	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119253460_119253461insAAAC	uc001ldf.2	-						EMX2OS_uc001ldg.2_Intron					Homo sapiens cDNA FLJ41539 fis, clone BRTHA2018165.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	119417516	119417517	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119417516_119417517insT								EMX2 (108460 upstream) : RAB11FIP2 (346912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119656054	119656057	+	IGR	DEL	GAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119656054_119656057delGAAA								EMX2 (346998 upstream) : RAB11FIP2 (108372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119997563	119997564	+	IGR	DEL	TG	-	-	rs111595711		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119997563_119997564delTG								CASC2 (27904 upstream) : C10orf84 (71008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120007915	120007922	+	IGR	DEL	AAGGAAGG	-	-	rs111918187		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120007915_120007922delAAGGAAGG								CASC2 (38256 upstream) : C10orf84 (60650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	121440936	121440936	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121440936delG								BAG3 (3609 upstream) : INPP5F (44673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	121930678	121930678	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121930678delA								SEC23IP (229433 upstream) : PPAPDC1A (285788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	122496301	122496302	+	IGR	INS	-	TTCT	TTCT	rs139546701	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122496301_122496302insTTCT								PPAPDC1A (146934 upstream) : WDR11 (114393 downstream)																																			---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123750316	123750316	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123750316delT	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744			transforming, acidic coiled-coil containing							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)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123807909	123807912	+	Intron	DEL	TTCC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123807909_123807912delTTCC	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744			transforming, acidic coiled-coil containing							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)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123834867	123834868	+	Intron	INS	-	C	C	rs148366839	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123834867_123834868insC	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron	NM_206862	NP_996744			transforming, acidic coiled-coil containing							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)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123885617	123885617	+	Intron	DEL	A	-	-	rs66639825		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123885617delA	uc001lfv.2	+						TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Intron|TACC2_uc010qtv.1_Intron|TACC2_uc001lfx.2_Intron|TACC2_uc001lfy.2_5'Flank	NM_206862	NP_996744			transforming, acidic coiled-coil containing							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)																---	---	---	---
IKZF5	64376	broad.mit.edu	37	10	124764662	124764662	+	Intron	DEL	T	-	-	rs7899321	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124764662delT	uc001lha.2	-							NM_022466	NP_071911			zinc finger protein, subfamily 1A, 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222)		Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	125138363	125138363	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125138363delT	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	125704577	125704577	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125704577delT								CPXM2 (4798 upstream) : CHST15 (62609 downstream)																																			---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126252525	126252525	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126252525delT	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron	NM_022126	NP_071409			phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126999469	126999469	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126999469delA								CTBP2 (149845 upstream) : LOC100169752 (263471 downstream)																																			---	---	---	---
UROS	7390	broad.mit.edu	37	10	127486342	127486342	+	Intron	DEL	A	-	-	rs34128376		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127486342delA	uc001liw.3	-						UROS_uc001liv.3_Intron|UROS_uc010quh.1_Intron|UROS_uc001lix.3_Intron|UROS_uc001liy.3_Intron	NM_000375	NP_000366			uroporphyrinogen III synthase						heme biosynthetic process|uroporphyrinogen III biosynthetic process	cytosol|mitochondrion	uroporphyrinogen-III synthase activity				0		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)																---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127769667	127769668	+	Intron	INS	-	G	G	rs140647421	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127769667_127769668insG	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465			ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128891920	128891920	+	Intron	DEL	T	-	-	rs76604512		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128891920delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	129285467	129285467	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129285467delA								DOCK1 (34686 upstream) : NPS (62146 downstream)																																			---	---	---	---
CLRN3	119467	broad.mit.edu	37	10	129682756	129682756	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129682756delG	uc001lka.1	-						CLRN3_uc001ljz.1_5'UTR	NM_152311	NP_689524			clarin 3							integral to membrane				skin(1)	1		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	130500785	130500785	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130500785delA								MKI67 (576317 upstream) : MGMT (764669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130645157	130645158	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130645157_130645158delTG								MKI67 (720689 upstream) : MGMT (620296 downstream)																																			---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131321657	131321657	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131321657delG	uc001lkh.2	+							NM_002412	NP_002403			O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131403843	131403843	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131403843delA	uc001lkh.2	+							NM_002412	NP_002403			O-6-methylguanine-DNA methyltransferase											ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
Unknown	0	broad.mit.edu	37	10	131783657	131783657	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131783657delA								EBF3 (21566 upstream) : GLRX3 (151006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131874255	131874255	+	Intron	DEL	G	-	-	rs112456635		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131874255delG	uc010qus.1	-											Homo sapiens cDNA FLJ36799 fis, clone ADRGL2007357.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	132006034	132006037	+	IGR	DEL	CACT	-	-	rs10536047		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132006034_132006037delCACT								GLRX3 (23250 upstream) : TCERG1L (884619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132021781	132021781	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132021781delT								GLRX3 (38997 upstream) : TCERG1L (868875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132136871	132136871	+	IGR	DEL	G	-	-	rs113099776		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132136871delG								GLRX3 (154087 upstream) : TCERG1L (753785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132457183	132457183	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132457183delC								GLRX3 (474399 upstream) : TCERG1L (433473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132692593	132692604	+	IGR	DEL	ACACACACACAT	-	-	rs5789062		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132692593_132692604delACACACACACAT								GLRX3 (709809 upstream) : TCERG1L (198052 downstream)																																			---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132968205	132968205	+	Intron	DEL	A	-	-	rs10717121		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132968205delA	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132990500	132990502	+	Intron	DEL	AAG	-	-	rs145749305		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132990500_132990502delAAG	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	133184726	133184737	+	IGR	DEL	CAGAGGGAGGAG	-	-	rs3125558	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133184726_133184737delCAGAGGGAGGAG								TCERG1L (74742 upstream) : PPP2R2D (563223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133616559	133616560	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133616559_133616560delGA								TCERG1L (506575 upstream) : PPP2R2D (131400 downstream)																																			---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134109387	134109387	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134109387delA	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.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	134634375	134634377	+	Intron	DEL	TGC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134634375_134634377delTGC	uc010qux.1	-							NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																														---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135202325	135202359	+	Intron	DEL	GTCATCCCGGGGCTCTCTTTCTCCATGCAGGTCTG	-	-	rs144417516	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	11	1662939	1662940	+	IGR	INS	-	CACCCCAGACCACCT	CACCCCAGACCACCT	rs145390398	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1662939_1662940insCACCCCAGACCACCT								KRTAP5-5 (10782 upstream) : FAM99A (23889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1789835	1789836	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1789835_1789836delTT								CTSD (4613 upstream) : SYT8 (58873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1935710	1935711	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1935710_1935711delTG								LSP1 (22218 upstream) : TNNT3 (5088 downstream)																																			---	---	---	---
ASCL2	430	broad.mit.edu	37	11	2294253	2294254	+	5'Flank	INS	-	C	C	rs143443792	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2294253_2294254insC	uc001lvu.2	-							NM_005170	NP_005161			achaete-scute complex homolog-like 2						central nervous system development|negative regulation of transcription from RNA polymerase II promoter|peripheral nervous system development|response to hypoxia	cytoplasm|nucleus	E-box binding|sequence-specific DNA binding transcription factor activity				0		all_epithelial(84;5.75e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.191)|all_lung(207;0.24)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	2455419	2455420	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2455419_2455420delTG								TRPM5 (11144 upstream) : KCNQ1 (10801 downstream)																																			---	---	---	---
NAP1L4	4676	broad.mit.edu	37	11	2976593	2976593	+	Intron	DEL	T	-	-	rs113278184		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2976593delT	uc001lxc.2	-						NAP1L4_uc001lxb.2_5'Flank|NAP1L4_uc009ydt.2_Intron|NAP1L4_uc010qxm.1_Intron|NAP1L4_uc010qxn.1_Intron	NM_005969	NP_005960			nucleosome assembly protein 1-like 4						nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)														---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3781343	3781346	+	Intron	DEL	AAAA	-	-	rs77150654		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3781343_3781346delAAAA	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.1_Intron	NM_016320	NP_057404			nucleoporin 98kD isoform 1						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								---	---	---	---
Unknown	0	broad.mit.edu	37	11	6366592	6366593	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6366592_6366593delTC								PRKCDBP (24852 upstream) : SMPD1 (45062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	6719282	6719283	+	IGR	INS	-	G	G	rs139971238	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6719282_6719283insG								MRPL17 (14650 upstream) : GVIN1 (15100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7770736	7770736	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7770736delA								OVCH2 (42795 upstream) : OR5P2 (46785 downstream)																																			---	---	---	---
C11orf16	56673	broad.mit.edu	37	11	8949098	8949098	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8949098delC	uc001mhb.3	-						C11orf16_uc001mhc.3_Intron	NM_020643	NP_065694			hypothetical protein LOC56673											upper_aerodigestive_tract(1)|pancreas(1)	2				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9234180	9234180	+	Intron	DEL	A	-	-	rs112190160		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9234180delA	uc001mhl.2	-						DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9262256	9262257	+	Intron	INS	-	A	A	rs139278051	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9262256_9262257insA	uc001mhl.2	-						DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9688779	9688780	+	Intron	INS	-	TG	TG	rs139870073	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9688779_9688780insTG	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	10035432	10035433	+	Intron	INS	-	TCAT	TCAT	rs145187504	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10035432_10035433insTCAT	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)														---	---	---	---
AMPD3	272	broad.mit.edu	37	11	10473731	10473732	+	5'Flank	INS	-	T	T	rs151276764	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10473731_10473732insT	uc001mio.1	+						AMPD3_uc010rbz.1_Intron|AMPD3_uc001min.1_Intron|AMPD3_uc009yfw.1_Intron|AMPD3_uc009yfx.1_Intron	NM_001025389	NP_001020560			adenosine monophosphate deaminase 3 isoform 1B						AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11042071	11042071	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11042071delC								ZBED5 (162451 upstream) : GALNTL4 (250350 downstream)																																			---	---	---	---
GALNTL4	374378	broad.mit.edu	37	11	11495216	11495216	+	Intron	DEL	C	-	-	rs111588307		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11495216delC	uc001mjo.2	-							NM_198516	NP_940918			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)														---	---	---	---
GALNTL4	374378	broad.mit.edu	37	11	11587339	11587339	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11587339delG	uc001mjo.2	-							NM_198516	NP_940918			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0				all cancers(16;3.67e-05)|Epithelial(150;0.000184)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13608502	13608502	+	IGR	DEL	C	-	-	rs139836634		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13608502delC								PTH (90935 upstream) : FAR1 (81704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15522171	15522172	+	IGR	INS	-	A	A	rs139323451	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15522171_15522172insA								INSC (253419 upstream) : SOX6 (465824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	17047744	17047745	+	IGR	INS	-	TT	TT	rs141019229	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17047744_17047745insTT								PLEKHA7 (11781 upstream) : RPS13 (48195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	17047776	17047778	+	IGR	DEL	CTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17047776_17047778delCTT								PLEKHA7 (11813 upstream) : RPS13 (48162 downstream)																																			---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18308458	18308458	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18308458delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
LDHAL6A	160287	broad.mit.edu	37	11	18500558	18500558	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18500558delT	uc001mop.1	+	8					LDHAL6A_uc001moq.2_3'UTR	NM_001144071	NP_001137543			lactate dehydrogenase A-like 6A						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	20328189	20328190	+	IGR	INS	-	T	T	rs35167188		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20328189_20328190insT								DBX1 (146319 upstream) : HTATIP2 (57041 downstream)																																			---	---	---	---
PRMT3	10196	broad.mit.edu	37	11	20473569	20473569	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20473569delA	uc001mqb.2	+						PRMT3_uc001mqc.2_Intron|PRMT3_uc010rdn.1_Intron	NM_005788	NP_005779			protein arginine methyltransferase 3 isoform 1								zinc ion binding				0																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20730030	20730030	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20730030delT	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																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20887103	20887104	+	Intron	INS	-	T	T	rs148874686	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20887103_20887104insT	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																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21390442	21390442	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21390442delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_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																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21443642	21443645	+	Intron	DEL	TGTG	-	-	rs143659965		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21443642_21443645delTGTG	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron|NELL1_uc001mqg.2_Intron|NELL1_uc001mqh.2_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	21759090	21759090	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21759090delT								NELL1 (161863 upstream) : ANO5 (455632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23836079	23836079	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23836079delC								SVIP (984697 upstream) : LUZP2 (682477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24108384	24108384	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24108384delT								None (None upstream) : LUZP2 (410172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24303838	24303838	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24303838delA								None (None upstream) : LUZP2 (214718 downstream)																																			---	---	---	---
BBOX1	8424	broad.mit.edu	37	11	27147009	27147009	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27147009delA	uc001mre.1	+						BBOX1_uc009yih.1_Intron|BBOX1_uc001mrg.1_Intron	NM_003986	NP_003977			gamma-butyrobetaine dioxygenase						carnitine biosynthetic process	actin cytoskeleton|cytosol|intracellular membrane-bounded organelle	gamma-butyrobetaine dioxygenase activity|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1					Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	29931880	29931880	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29931880delA								None (None upstream) : KCNA4 (99886 downstream)																																			---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31920396	31920396	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31920396delT	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
HIPK3	10114	broad.mit.edu	37	11	33307887	33307887	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33307887delA	uc001mul.1	+						HIPK3_uc001mum.1_Intron|HIPK3_uc009yjv.1_Intron	NM_005734	NP_005725			homeodomain interacting protein kinase 3 isoform						anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33678703	33678704	+	Intron	INS	-	G	G	rs146189632	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33678703_33678704insG	uc001mup.3	+							NM_012194	NP_036326			hypothetical protein LOC25758							integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33824832	33824832	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33824832delA								FBXO3 (28761 upstream) : LMO2 (55293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33966809	33966810	+	IGR	INS	-	TTCG	TTCG	rs150389032	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33966809_33966810insTTCG								LMO2 (52973 upstream) : CAPRIN1 (106420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33996214	33996215	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33996214_33996215delAC								LMO2 (82378 upstream) : CAPRIN1 (77015 downstream)																																			---	---	---	---
EHF	26298	broad.mit.edu	37	11	34664616	34664617	+	Intron	DEL	TG	-	-	rs59989036		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34664616_34664617delTG	uc001mvr.1	+						EHF_uc009yke.1_Intron|EHF_uc009ykf.1_Intron	NM_012153	NP_036285			ets homologous factor						cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)															---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35483159	35483159	+	Intron	DEL	A	-	-	rs11033133		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35483159delA	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
TRIM44	54765	broad.mit.edu	37	11	35757476	35757476	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35757476delA	uc001mwi.2	+							NM_017583	NP_060053			DIPB protein							intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	37210689	37210690	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37210689_37210690delCT								C11orf74 (514299 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38039730	38039730	+	IGR	DEL	A	-	-	rs150413308		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38039730delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38650412	38650412	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38650412delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39877969	39877969	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39877969delA								None (None upstream) : LRRC4C (257784 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40781512	40781513	+	Intron	INS	-	A	A	rs147406865		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40781512_40781513insA	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	41715727	41715727	+	IGR	DEL	T	-	-	rs139742960		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41715727delT								LRRC4C (234404 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	41921495	41921495	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41921495delA								LRRC4C (440172 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43160714	43160714	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43160714delA								None (None upstream) : API5 (172791 downstream)																																			---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43511286	43511286	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43511286delA	uc001mxi.2	+						TTC17_uc010rfj.1_Intron|TTC17_uc001mxl.2_Intron|TTC17_uc001mxm.2_5'Flank	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	44784166	44784167	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44784166_44784167delTG								CD82 (142853 upstream) : TSPAN18 (97712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44804392	44804392	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44804392delT								CD82 (163079 upstream) : TSPAN18 (77487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45510319	45510320	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45510319_45510320delAA								SYT13 (202435 upstream) : CHST1 (160107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45766255	45766255	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45766255delA								CHST1 (79083 upstream) : DKFZp779M0652 (26728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45821088	45821100	+	IGR	DEL	GAAAAAAAAAAAA	-	-	rs10572268		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45821088_45821100delGAAAAAAAAAAAA								DKFZp779M0652 (27180 upstream) : SLC35C1 (4523 downstream)																																			---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46439215	46439215	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46439215delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46474812	46474812	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46474812delT	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron|hsa-mir-3160-1|MI0014189_5'Flank	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46517765	46517765	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46517765delA	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46666126	46666126	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46666126delA	uc009yld.2	+						KIAA0652_uc001nda.2_Intron|KIAA0652_uc001ndb.2_Intron|KIAA0652_uc001ncz.2_Intron|KIAA0652_uc001ndc.2_Intron|KIAA0652_uc010rgv.1_Intron	NM_001142673	NP_001136145			autophagy-related protein 13 isoform 1						autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
ARHGAP1	392	broad.mit.edu	37	11	46720892	46720892	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46720892delG	uc001ndd.2	-						ARHGAP1_uc009yle.1_Intron|ARHGAP1_uc009ylf.1_Intron|ZNF408_uc001nde.1_5'Flank|ZNF408_uc010rgw.1_5'Flank	NM_004308	NP_004299			Rho GTPase activating protein 1						Rho protein signal transduction	cytosol|intracellular membrane-bounded organelle	SH3 domain binding|SH3/SH2 adaptor activity			skin(1)	1		Lung NSC(402;1.76e-12)|all_lung(304;1.3e-11)		GBM - Glioblastoma multiforme(35;5.17e-06)|BRCA - Breast invasive adenocarcinoma(625;0.00112)|Lung(87;0.153)														---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46832848	46832848	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46832848delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47184724	47184725	+	Intron	INS	-	A	A	rs35809127		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47184724_47184725insA	uc001nds.2	+							NM_001003678	NP_001003678			hypothetical protein LOC79096 isoform 4												0																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47324581	47324581	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47324581delT	uc001ner.1	+						MADD_uc001neq.2_Intron|MADD_uc001nev.1_Intron|MADD_uc001nes.1_Intron|MADD_uc001net.1_Intron|MADD_uc009yln.1_Intron|MADD_uc001neu.1_Intron|MADD_uc001nex.2_Intron|MADD_uc001nez.2_Intron|MADD_uc001new.2_Intron|MADD_uc009ylo.2_Intron	NM_003682	NP_003673			MAP-kinase activating death domain-containing						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)														---	---	---	---
RAPSN	5913	broad.mit.edu	37	11	47467776	47467776	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47467776delA	uc001nfi.1	-						RAPSN_uc001nfj.1_Intron|RAPSN_uc009yls.1_Intron	NM_005055	NP_005046			43 kD receptor-associated protein of the synapse						synaptic transmission, cholinergic	cell junction|cytoskeleton|postsynaptic membrane	acetylcholine receptor binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47629708	47629709	+	IGR	INS	-	G	G	rs141340200	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47629708_47629709insG								C1QTNF4 (13747 upstream) : MTCH2 (9150 downstream)																																			---	---	---	---
MTCH2	23788	broad.mit.edu	37	11	47657242	47657242	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47657242delT	uc010rho.1	-						MTCH2_uc001nge.2_Intron|MTCH2_uc010rhp.1_Intron	NM_014342	NP_055157			mitochondrial carrier 2						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48359344	48359345	+	IGR	INS	-	C	C	rs151275604	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48359344_48359345insC								OR4C3 (11864 upstream) : OR4C45 (7557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48363727	48363728	+	IGR	INS	-	CAT	CAT	rs137940535	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48363727_48363728insCAT								OR4C3 (16247 upstream) : OR4C45 (3174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48694593	48694593	+	IGR	DEL	A	-	-	rs75637845		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48694593delA								OR4A47 (183321 upstream) : FOLH1 (473595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49144970	49144970	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49144970delT								OR4A47 (633698 upstream) : FOLH1 (23218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49424288	49424288	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49424288delT								FOLH1 (194066 upstream) : LOC440040 (155792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49436886	49436886	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49436886delT								FOLH1 (206664 upstream) : LOC440040 (143194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49569015	49569015	+	IGR	DEL	A	-	-	rs144513255		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49569015delA								FOLH1 (338793 upstream) : LOC440040 (11065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50755489	50755490	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50755489_50755490insT								LOC646813 (375686 upstream) : OR4A5 (655958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55189539	55189542	+	IGR	DEL	TTCC	-	-	rs71752565	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55189539_55189542delTTCC								OR4A15 (53146 upstream) : OR4C15 (132241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55549582	55549582	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55549582delA								OR5D13 (7725 upstream) : OR5D14 (13450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55716346	55716347	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55716346_55716347insA								OR5I1 (12470 upstream) : OR10AG1 (18688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58100994	58100994	+	IGR	DEL	T	-	-	rs2186408	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58100994delT								OR10W1 (65262 upstream) : OR5B17 (24606 downstream)																																			---	---	---	---
LPXN	9404	broad.mit.edu	37	11	58324856	58324856	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58324856delA	uc001nmw.2	-						LPXN_uc009ymp.2_Intron|LPXN_uc010rkj.1_Intron|LPXN_uc010rkk.1_Intron	NM_004811	NP_004802			leupaxin isoform 2						cell adhesion|protein complex assembly|signal transduction	cytoplasm	zinc ion binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	59066135	59066136	+	IGR	INS	-	GGAAGGAA	GGAAGGAA	rs36130299		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59066135_59066136insGGAAGGAA								MPEG1 (85641 upstream) : OR5AN1 (65796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59244318	59244319	+	IGR	INS	-	A	A	rs73482815	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59244318_59244319insA								OR4D6 (18941 upstream) : OR4D10 (584 downstream)																																			---	---	---	---
PATL1	219988	broad.mit.edu	37	11	59410732	59410732	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59410732delA	uc001noe.3	-						PATL1_uc009yms.1_Intron	NM_152716	NP_689929			protein associated with topoisomerase II homolog						cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
MS4A13	503497	broad.mit.edu	37	11	60287641	60287641	+	Intron	DEL	G	-	-	rs77005265	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60287641delG	uc001nps.2	+						MS4A13_uc009ync.2_Intron|MS4A13_uc009ynd.2_Intron	NM_001012417	NP_001012417			membrane-spanning 4-domains, subfamily A, member							integral to membrane					0																		---	---	---	---
PRPF19	27339	broad.mit.edu	37	11	60666410	60666410	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)	---	---	---	---
CD6	923	broad.mit.edu	37	11	60783054	60783054	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60783054delA	uc001nqq.2	+						CD6_uc001nqp.2_Intron|CD6_uc001nqr.2_Intron|CD6_uc001nqs.2_Intron|CD6_uc001nqt.2_Intron	NM_006725	NP_006716			CD6 molecule precursor						cell adhesion	cell surface|integral to plasma membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
CD5	921	broad.mit.edu	37	11	60866961	60866961	+	5'Flank	DEL	T	-	-	rs111448448		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60866961delT	uc009ynk.2	+							NM_014207	NP_055022			CD5 molecule precursor						cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)														---	---	---	---
CD5	921	broad.mit.edu	37	11	60880115	60880116	+	Intron	INS	-	A	A	rs147569895	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60880115_60880116insA	uc009ynk.2	+							NM_014207	NP_055022			CD5 molecule precursor						cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	61377858	61377859	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61377858_61377859delAC								SYT7 (29560 upstream) : RPLP0P2 (4649 downstream)																																			---	---	---	---
FTH1	2495	broad.mit.edu	37	11	61737261	61737261	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61737261delA	uc001nsu.2	-							NM_002032	NP_002023			ferritin, heavy polypeptide 1						cell proliferation|cellular membrane organization|immune response|intracellular sequestering of iron ion|iron ion transport|negative regulation of cell proliferation|post-Golgi vesicle-mediated transport	cytosol|intracellular ferritin complex	ferric iron binding|ferroxidase activity|protein binding			ovary(1)	1					Iron Dextran(DB00893)													---	---	---	---
ASRGL1	80150	broad.mit.edu	37	11	62152652	62152652	+	Intron	DEL	T	-	-	rs141380541		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62152652delT	uc001nte.3	+						ASRGL1_uc001ntf.3_Intron|ASRGL1_uc001ntg.3_Intron	NM_025080	NP_079356			asparaginase-like 1						asparagine catabolic process via L-aspartate|protein maturation	cytoplasm|microtubule cytoskeleton|nucleus	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)													---	---	---	---
TMEM223	79064	broad.mit.edu	37	11	62557913	62557913	+	3'UTR	DEL	G	-	-	rs76936705		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62557913delG	uc001nve.2	-	2						NM_001080501	NP_001073970			transmembrane protein 223							integral to membrane					0																		---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63251632	63251634	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63251632_63251634delAAA	uc001nwy.2	-						HRASLS5_uc001nwz.2_Intron|HRASLS5_uc010rmq.1_Intron|HRASLS5_uc009yos.2_Intron	NM_054108	NP_473449			HRAS-like suppressor family, member 5 isoform 1											ovary(1)	1																		---	---	---	---
PLA2G16	11145	broad.mit.edu	37	11	63372233	63372233	+	Intron	DEL	A	-	-	rs2732327		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63372233delA	uc001nxh.2	-						PLA2G16_uc001nxi.2_Intron|PLA2G16_uc009you.1_Intron	NM_007069	NP_009000			HRAS-like suppressor 3						lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1																		---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63463874	63463875	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63463874_63463875insA	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
EHD1	10938	broad.mit.edu	37	11	64648928	64648930	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64648928_64648930delAAA	uc001obu.1	-						EHD1_uc001obv.1_5'Flank|EHD1_uc010rnq.1_5'Flank	NM_006795	NP_006786			EH-domain containing 1						blood coagulation|cholesterol homeostasis|endocytic recycling|intracellular protein transport|low-density lipoprotein particle clearance|positive regulation of cholesterol storage|protein homooligomerization	early endosome membrane|lipid particle|plasma membrane|platelet dense tubular network membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|protein binding				0																		---	---	---	---
CTSW	1521	broad.mit.edu	37	11	65647105	65647105	+	5'Flank	DEL	A	-	-	rs12225345	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65647105delA	uc001ogc.1	+						CTSW_uc001ogb.1_5'Flank	NM_001335	NP_001326			cathepsin W preproprotein						immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)	1				READ - Rectum adenocarcinoma(159;0.168)														---	---	---	---
PACS1	55690	broad.mit.edu	37	11	65997429	65997430	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65997429_65997430delAA	uc001oha.1	+						PACS1_uc010rou.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66118649	66118650	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66118649_66118650insT								B3GNT1 (3488 upstream) : SLC29A2 (11343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66376740	66376740	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66376740delA								CCS (3251 upstream) : RBM14 (7313 downstream)																																			---	---	---	---
RBM14	10432	broad.mit.edu	37	11	66388690	66388690	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
C11orf80	79703	broad.mit.edu	37	11	66595437	66595438	+	Intron	INS	-	A	A	rs75673191		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66595437_66595438insA	uc001ojf.2	+						C11orf80_uc001ojg.2_Intron|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_Intron|C11orf80_uc010rpl.1_Intron|C11orf80_uc001ojj.2_Intron	NM_024650	NP_078926			hypothetical protein LOC79703												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66818736	66818736	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66818736delA								SYT12 (407 upstream) : RHOD (5553 downstream)																																			---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	66901185	66901185	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66901185delT	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron	NM_012308	NP_036440			F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	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|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
RPS6KB2	6199	broad.mit.edu	37	11	67199056	67199056	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67199056delG	uc001old.2	+						RPS6KB2_uc001olf.2_Intron|RPS6KB2_uc001olg.2_Intron|RPS6KB2_uc009yrq.2_Intron|RPS6KB2_uc001ole.2_Intron|RPS6KB2_uc001olh.2_Intron|RPS6KB2_uc009yrr.2_Intron	NM_003952	NP_003943			ribosomal protein S6 kinase, 70kDa, polypeptide						nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68145315	68145331	+	Intron	DEL	GGATCTCAGCTTTCCCC	-	-	rs143128134		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68145315_68145331delGGATCTCAGCTTTCCCC	uc001ont.2	+						LRP5_uc009ysg.2_Intron	NM_002335	NP_002326			low density lipoprotein receptor-related protein						adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
GAL	51083	broad.mit.edu	37	11	68449323	68449324	+	5'Flank	DEL	TC	-	-	rs111597537		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68449323_68449324delTC	uc001oob.2	+							NM_015973	NP_057057			galanin preproprotein						growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)														---	---	---	---
FGF3	2248	broad.mit.edu	37	11	69626219	69626220	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69626219_69626220delAA	uc001oph.2	-							NM_005247	NP_005238			fibroblast growth factor 3 precursor						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of cardiac muscle tissue development|positive regulation of cell division|positive regulation of cell proliferation	extracellular region	growth factor activity			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)															---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70150442	70150442	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70150442delA	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron	NM_003626	NP_003617			PTPRF interacting protein alpha 1 isoform b						cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	70309410	70309410	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70309410delC								CTTN (26721 upstream) : SHANK2 (4552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	71281749	71281750	+	IGR	INS	-	TG	TG	rs146397927	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71281749_71281750insTG								KRTAP5-10 (4083 upstream) : KRTAP5-11 (11153 downstream)																																			---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71721086	71721086	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71721086delC	uc001orl.1	-						NUMA1_uc001orj.2_5'Flank|NUMA1_uc009ysw.1_Intron|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001orn.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								---	---	---	---
Unknown	0	broad.mit.edu	37	11	71990333	71990333	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71990333delT								PHOX2A (35113 upstream) : CLPB (13139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	72256896	72256896	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72256896delT								CLPB (111212 upstream) : PDE2A (30290 downstream)																																			---	---	---	---
PDE2A	5138	broad.mit.edu	37	11	72314333	72314333	+	Intron	DEL	T	-	-	rs33965768		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72314333delT	uc010rrc.1	-						PDE2A_uc001oso.2_Intron|PDE2A_uc010rra.1_Intron|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron	NM_002599	NP_002590			phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)													---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72420091	72420093	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72420091_72420093delAAA	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_Intron|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73204224	73204224	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73204224delA	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
MRPL48	51642	broad.mit.edu	37	11	73497968	73497968	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73497968delG	uc001ouh.3	+						MRPL48_uc009ytt.2_5'Flank|MRPL48_uc010rri.1_5'Flank|MRPL48_uc009ytu.2_5'Flank	NM_016055	NP_057139			mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
MRPL48	51642	broad.mit.edu	37	11	73561486	73561486	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73561486delA	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139			mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
PAAF1	80227	broad.mit.edu	37	11	73610869	73610869	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73610869delT	uc001ouk.1	+						PAAF1_uc001oul.1_Intron|PAAF1_uc009ytx.1_Intron|PAAF1_uc001oum.1_Intron	NM_025155	NP_079431			proteasomal ATPase-associated factor 1						interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)																	---	---	---	---
PAAF1	80227	broad.mit.edu	37	11	73618087	73618087	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73618087delT	uc001ouk.1	+						PAAF1_uc001oul.1_Intron|PAAF1_uc009ytx.1_Intron|PAAF1_uc001oum.1_Intron	NM_025155	NP_079431			proteasomal ATPase-associated factor 1						interspecies interaction between organisms	proteasome complex	protein binding			ovary(1)|skin(1)	2	Breast(11;7.42e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	74768150	74768154	+	IGR	DEL	TTCCG	-	-	rs75060683	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74768150_74768154delTTCCG								NEU3 (49409 upstream) : OR2AT4 (31643 downstream)																																			---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76228257	76228257	+	Intron	DEL	G	-	-	rs2513519	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76228257delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	76550796	76550796	+	IGR	DEL	A	-	-	rs72008747		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76550796delA								TSKU (41599 upstream) : ACER3 (21121 downstream)																																			---	---	---	---
PAK1	5058	broad.mit.edu	37	11	77157943	77157944	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77157943_77157944delAA	uc001oyh.3	-						PAK1_uc001oyg.3_Intron	NM_002576	NP_002567			p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)																	---	---	---	---
C11orf67	28971	broad.mit.edu	37	11	77589553	77589553	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77589553delA	uc001oyr.1	+						C11orf67_uc001oyp.2_Intron	NM_024684	NP_078960			hypothetical protein LOC28971												0	all_cancers(14;5.69e-19)|all_epithelial(13;2.15e-21)|Breast(9;1.16e-15)|Ovarian(111;0.152)		Epithelial(5;1.37e-49)|all cancers(3;5.58e-46)|BRCA - Breast invasive adenocarcinoma(5;7.26e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	77738414	77738415	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77738414_77738415insT								KCTD14 (4094 upstream) : THRSP (36492 downstream)																																			---	---	---	---
GAB2	9846	broad.mit.edu	37	11	77989772	77989772	+	Intron	DEL	T	-	-	rs113211729		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77989772delT	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)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	78034564	78034564	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78034564delA	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)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	78081772	78081773	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78081772_78081773delTG	uc001ozh.2	-							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	79791747	79791747	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79791747delA								ODZ4 (640052 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79949011	79949018	+	IGR	DEL	TGTGTGTG	-	-	rs12287446		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79949011_79949018delTGTGTGTG								ODZ4 (797316 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81019609	81019609	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81019609delT								None (None upstream) : None (None downstream)																																			---	---	---	---
RAB30	27314	broad.mit.edu	37	11	82713570	82713570	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82713570delA	uc001ozu.2	-						RAB30_uc009yve.2_Intron|RAB30_uc010rst.1_Intron|RAB30_uc001ozv.2_Intron	NM_014488	NP_055303			RAB30, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi stack|plasma membrane	GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	82849043	82849044	+	IGR	DEL	TT	-	-	rs79590681		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82849043_82849044delTT								RAB30 (66159 upstream) : PCF11 (19093 downstream)																																			---	---	---	---
ANKRD42	338699	broad.mit.edu	37	11	82955954	82955954	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82955954delT	uc001ozz.1	+						ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409			ankyrin repeat domain 42											skin(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83841940	83841940	+	Intron	DEL	A	-	-	rs75017708		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83841940delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			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	84315055	84315057	+	Intron	DEL	ATC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84315055_84315057delATC	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)																---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85524734	85524737	+	5'Flank	DEL	CCTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85524734_85524737delCCTC	uc010rti.1	-						SYTL2_uc010rtj.1_5'Flank	NM_032943	NP_116561			synaptotagmin-like 2 isoform a						intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
ME3	10873	broad.mit.edu	37	11	86293952	86293952	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86293952delA	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)													---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86751705	86751707	+	Intron	DEL	AAA	-	-	rs74525986		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86751705_86751707delAAA	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86817152	86817152	+	Intron	DEL	T	-	-	rs112863769		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86817152delT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	87196100	87196101	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87196100_87196101delTG								TMEM135 (161532 upstream) : RAB38 (650330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	88879906	88879915	+	IGR	DEL	ACACACACAT	-	-	rs71046285		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88879906_88879915delACACACACAT								GRM5 (80793 upstream) : TYR (31125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	89769257	89769257	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89769257delA	uc010rua.1	+							NM_020358	NP_065091			ring finger protein 18																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	90105240	90105242	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90105240_90105242delTTT								CHORDC1 (148708 upstream) : MIR1261 (497047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90156655	90156655	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90156655delA								CHORDC1 (200123 upstream) : MIR1261 (445634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90432944	90432944	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90432944delA								CHORDC1 (476412 upstream) : MIR1261 (169345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91821823	91821823	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91821823delA								None (None upstream) : FAT3 (263439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91948819	91948820	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91948819_91948820insA								None (None upstream) : FAT3 (136442 downstream)																																			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92180387	92180388	+	Intron	DEL	GC	-	-	rs148737395	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92180387_92180388delGC	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	92211787	92211788	+	Intron	INS	-	T	T	rs111834951		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92211787_92211788insT	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	92321373	92321374	+	Intron	INS	-	T	T	rs148428718	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92321373_92321374insT	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93026295	93026295	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93026295delT								SLC36A4 (95200 upstream) : CCDC67 (36861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93732169	93732169	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93732169delA								C11orf90 (148501 upstream) : HEPHL1 (22209 downstream)																																			---	---	---	---
MRE11A	4361	broad.mit.edu	37	11	94210968	94210968	+	Intron	DEL	G	-	-	rs5793683		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94210968delG	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582			meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)											Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				---	---	---	---
Unknown	0	broad.mit.edu	37	11	95236364	95236367	+	IGR	DEL	ACAT	-	-	rs71877952		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95236364_95236367delACAT								SESN3 (270659 upstream) : FAM76B (265739 downstream)																																			---	---	---	---
MTMR2	8898	broad.mit.edu	37	11	95602244	95602244	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95602244delA	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240			myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	96517727	96517728	+	IGR	INS	-	T	T	rs35586205		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96517727_96517728insT								JRKL (391000 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97254616	97254616	+	IGR	DEL	G	-	-	rs5793854		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97254616delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98249330	98249331	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98249330_98249331insT								None (None upstream) : CNTN5 (642540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98550114	98550115	+	IGR	INS	-	T	T	rs35250245		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98550114_98550115insT								None (None upstream) : CNTN5 (341756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98797598	98797598	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98797598delA								None (None upstream) : CNTN5 (94273 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99727187	99727187	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99727187delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	100517131	100517134	+	IGR	DEL	GGAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100517131_100517134delGGAA								CNTN5 (289659 upstream) : ARHGAP42 (41273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101976227	101976227	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101976227delA	uc001pgr.2	+											Homo sapiens cDNA clone IMAGE:4793073.																														---	---	---	---
MMP27	64066	broad.mit.edu	37	11	102575615	102575615	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102575615delG	uc001phd.1	-							NM_022122	NP_071405			matrix metalloproteinase 27 precursor						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103168943	103168944	+	Intron	INS	-	T	T	rs150520776	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103168943_103168944insT	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	103251606	103251606	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103251606delA	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	103777548	103777551	+	IGR	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103777548_103777551delTTTT								DYNC2H1 (426957 upstream) : PDGFD (364 downstream)																																			---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103920254	103920254	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103920254delT	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)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	104006647	104006647	+	Intron	DEL	C	-	-	rs111526160		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104006647delC	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)														---	---	---	---
CASP4	837	broad.mit.edu	37	11	104820121	104820121	+	Intron	DEL	C	-	-	rs149184787	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104820121delC	uc001pid.1	-						CASP4_uc001pib.1_Intron|CASP4_uc009yxg.1_Intron|CASP4_uc010rux.1_3'UTR	NM_001225	NP_001216			caspase 4 isoform alpha precursor						apoptosis|induction of apoptosis|proteolysis	intracellular	cysteine-type endopeptidase activity|protein binding			lung(2)|ovary(1)|skin(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	106192737	106192737	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106192737delT								AASDHPPT (223318 upstream) : GUCY1A2 (365173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106392600	106392600	+	IGR	DEL	T	-	-	rs138192986		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106392600delT								AASDHPPT (423181 upstream) : GUCY1A2 (165310 downstream)																																			---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106879137	106879137	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106879137delA	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)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107281222	107281222	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107281222delA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107299328	107299330	+	Intron	DEL	AAA	-	-	rs35070417		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107299328_107299330delAAA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107706160	107706160	+	Intron	DEL	T	-	-	rs144961466		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107706160delT	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)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108170043	108170043	+	Intron	DEL	T	-	-	rs34021496		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108170043delT	uc001pkb.1	+						ATM_uc009yxr.1_Intron|ATM_uc001pke.1_Intron|ATM_uc001pkg.1_Intron	NM_000051	NP_000042			ataxia telangiectasia mutated isoform 1						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			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)			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109375772	109375772	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109375772delA								C11orf87 (75934 upstream) : ZC3H12C (588154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109833451	109833451	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109833451delT								C11orf87 (533613 upstream) : ZC3H12C (130475 downstream)																																			---	---	---	---
RDX	5962	broad.mit.edu	37	11	110129593	110129598	+	Intron	DEL	TTTTTT	-	-	rs72064962		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110129593_110129598delTTTTTT	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897			radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)														---	---	---	---
SIK2	23235	broad.mit.edu	37	11	111536581	111536581	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111536581delA	uc001plt.2	+							NM_015191	NP_056006			SNF1-like kinase 2						intracellular protein kinase cascade|regulation of insulin receptor signaling pathway	Golgi apparatus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|skin(1)	3																		---	---	---	---
ALG9	79796	broad.mit.edu	37	11	111688225	111688226	+	Intron	INS	-	A	A	rs582515		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111688225_111688226insA	uc001pmb.2	-						ALG9_uc001ply.2_Intron|ALG9_uc001plz.2_Intron|ALG9_uc010rwm.1_Intron|ALG9_uc010rwn.1_Intron|ALG9_uc010rwo.1_Intron	NM_001077690	NP_001071158			asparagine-linked glycosylation 9 protein						dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-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)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112785923	112785924	+	IGR	INS	-	A	A	rs111888303		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112785923_112785924insA								PTS (645246 upstream) : NCAM1 (46071 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112946138	112946138	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112946138delT	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114010436	114010436	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114010436delT	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)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114061453	114061454	+	Intron	DEL	AC	-	-	rs10558106	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114061453_114061454delAC	uc001pop.2	+						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)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114061477	114061482	+	Intron	DEL	ACACAT	-	-	rs4084235		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114061477_114061482delACACAT	uc001pop.2	+						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	114233373	114233373	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114233373delT								NNMT (50135 upstream) : C11orf71 (28797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114260020	114260020	+	IGR	DEL	T	-	-	rs111609198		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114260020delT								NNMT (76782 upstream) : C11orf71 (2150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114324217	114324217	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114324217delT								REXO2 (3219 upstream) : FAM55A (68221 downstream)																																			---	---	---	---
FAM55B	120406	broad.mit.edu	37	11	114553571	114553571	+	Intron	DEL	A	-	-	rs35146922		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114553571delA	uc009yyy.2	+							NM_182495	NP_872301			hypothetical protein LOC120406							integral to membrane				ovary(1)	1																		---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115043977	115043977	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115043977delG	uc001ppf.3	-							NM_001098517	NP_001091987			immunoglobulin superfamily, member 4D isoform 2						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)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115099506	115099506	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115099506delA	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	115510464	115510465	+	IGR	DEL	AA	-	-	rs63326060		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115510464_115510465delAA								CADM1 (135223 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115876608	115876609	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115876608_115876609insC								CADM1 (501367 upstream) : BUD13 (742279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116100118	116100119	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116100118_116100119delTT								CADM1 (724877 upstream) : BUD13 (518769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116110892	116110892	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116110892delG								CADM1 (735651 upstream) : BUD13 (507996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116116083	116116083	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116116083delT								CADM1 (740842 upstream) : BUD13 (502805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116516379	116516379	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116516379delA								None (None upstream) : BUD13 (102509 downstream)																																			---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117154536	117154536	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117154536delT	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion 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;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117307231	117307232	+	Intron	DEL	TG	-	-	rs146622587		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117307231_117307232delTG	uc001prh.1	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117829908	117829911	+	IGR	DEL	TAGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117829908_117829911delTAGT								TMPRSS13 (29793 upstream) : IL10RA (27195 downstream)																																			---	---	---	---
CD3E	916	broad.mit.edu	37	11	118176898	118176899	+	Intron	INS	-	A	A	rs144180852	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118176898_118176899insA	uc001psq.3	+						CD3E_uc009yzz.1_Intron|CD3E_uc010rya.1_Intron	NM_000733	NP_000724			CD3E antigen, epsilon polypeptide precursor						G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	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;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)													---	---	---	---
CD3G	917	broad.mit.edu	37	11	118223798	118223798	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118223798delT	uc001psu.2	+						CD3G_uc009zaa.1_3'UTR	NM_000073	NP_000064			CD3G antigen, gamma polypeptide precursor						establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	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)														---	---	---	---
VPS11	55823	broad.mit.edu	37	11	118950771	118950771	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118950771delT	uc010ryx.1	+						VPS11_uc010ryy.1_Intron	NM_021729	NP_068375			vacuolar protein sorting 11						protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119344155	119344155	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119344155delA	uc001pwo.2	+						uc001pwp.1_Intron					Homo sapiens cDNA FLJ40501 fis, clone TESTI2045171.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119685893	119685893	+	IGR	DEL	T	-	-	rs35847629		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119685893delT								PVRL1 (86458 upstream) : TRIM29 (296102 downstream)																																			---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120122054	120122054	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120122054delC	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron|uc001pxd.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120156765	120156765	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120156765delT	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120511417	120511419	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120511417_120511419delTTT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120756096	120756099	+	Intron	DEL	TTTT	-	-	rs66495767		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120756096_120756099delTTTT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TBCEL	219899	broad.mit.edu	37	11	120940499	120940499	+	Intron	DEL	A	-	-	rs74380809		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120940499delA	uc009zay.2	+						TBCEL_uc001pxo.2_Intron|TBCEL_uc001pxp.2_Intron|TBCEL_uc001pxq.2_Intron	NM_001130047	NP_001123519			tubulin folding cofactor E-like							cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120989717	120989718	+	Intron	INS	-	AA	AA	rs138566217	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120989717_120989718insAA	uc010rzo.1	+							NM_005422	NP_005413			tectorin alpha precursor						cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121246581	121246582	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121246581_121246582insA								SC5DL (62464 upstream) : SORL1 (76379 downstream)																																			---	---	---	---
C11orf63	79864	broad.mit.edu	37	11	122816009	122816009	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122816009delG	uc001pym.2	+							NM_024806	NP_079082			hypothetical protein LOC79864 isoform 1											ovary(3)	3		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)														---	---	---	---
SCN3B	55800	broad.mit.edu	37	11	123520420	123520421	+	Intron	DEL	TT	-	-	rs77709183		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123520420_123520421delTT	uc001pza.1	-						SCN3B_uc001pzb.1_Intron	NM_001040151	NP_001035241			voltage-gated sodium channel beta-3 subunit						axon guidance	integral to membrane|plasma membrane	voltage-gated sodium channel activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123538146	123538146	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123538146delA								SCN3B (12831 upstream) : ZNF202 (56851 downstream)																																			---	---	---	---
SPA17	53340	broad.mit.edu	37	11	124548413	124548414	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124548413_124548414delTG	uc001qap.2	+							NM_017425	NP_059121			sperm autoantigenic protein 17						binding of sperm to zona pellucida|ciliary or flagellar motility|signal transduction|spermatogenesis	cytoplasm|flagellum|membrane|motile cilium|primary cilium	cAMP-dependent protein kinase regulator activity				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126321230	126321231	+	Intron	INS	-	GTGTGCATGTGTGAGC	GTGTGCATGTGTGAGC	rs4937137		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126321230_126321231insGTGTGCATGTGTGAGC	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126823905	126823906	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126823905_126823906delTG	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127417578	127417578	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127417578delC								KIRREL3 (544223 upstream) : ETS1 (911078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128482343	128482344	+	IGR	DEL	CC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128482343_128482344delCC								ETS1 (24890 upstream) : FLI1 (74086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129450759	129450760	+	IGR	INS	-	GT	GT	rs111785376		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129450759_129450760insGT								BARX2 (128586 upstream) : TMEM45B (234981 downstream)																																			---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132375398	132375400	+	Intron	DEL	GCT	-	-	rs151090931		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132375398_132375400delGCT	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	132414116	132414116	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	132449280	132449281	+	Intron	INS	-	TG	TG	rs147056078	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132449280_132449281insTG	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	132593451	132593451	+	Intron	DEL	T	-	-	rs66867792		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132593451delT	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	133320292	133320293	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133320292_133320293delTT	uc001qgu.2	-							NM_001012393	NP_001012393			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	134398162	134398163	+	IGR	INS	-	TG	TG	rs141608209	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134398162_134398163insTG								B3GAT1 (116350 upstream) : None (None downstream)																																			---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	605436	605437	+	Intron	DEL	AA	-	-	rs7971615	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:605436_605437delAA	uc001qii.1	+							NM_173593	NP_775864			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
NINJ2	4815	broad.mit.edu	37	12	697356	697364	+	Intron	DEL	GGGACGGAG	-	-	rs74475206		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:697356_697364delGGGACGGAG	uc001qil.2	-						NINJ2_uc010sdr.1_Intron|NINJ2_uc010sds.1_Intron	NM_016533	NP_057617			ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1105261	1105261	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1105261delG	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.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)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1271654	1271655	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1271654_1271655delTT	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	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)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1526602	1526604	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1526602_1526604delTTT	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_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)															---	---	---	---
WNT5B	81029	broad.mit.edu	37	12	1724156	1724157	+	Intron	DEL	TC	-	-	rs3840794		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1724156_1724157delTC	uc009zdq.2	+						WNT5B_uc001qjj.2_5'Flank	NM_032642	NP_116031			wingless-type MMTV integration site family,						angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)															---	---	---	---
WNT5B	81029	broad.mit.edu	37	12	1748784	1748784	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1748784delG	uc009zdq.2	+						WNT5B_uc001qjj.2_Intron|WNT5B_uc001qjk.2_Intron|WNT5B_uc001qjl.2_Intron	NM_032642	NP_116031			wingless-type MMTV integration site family,						angiogenesis|anterior/posterior pattern formation|cell migration involved in gastrulation|cellular response to retinoic acid|chondrocyte differentiation|convergent extension involved in axis elongation|convergent extension involved in gastrulation|dorsal/ventral axis specification|endocrine pancreas development|fat cell differentiation|lens fiber cell development|negative regulation of canonical Wnt receptor signaling pathway|neuron differentiation|positive regulation of cell migration|positive regulation of fat cell differentiation|respiratory system development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	2829800	2829801	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2829800_2829801delAC								CACNA1C (22685 upstream) : FKBP4 (74307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	3874559	3874560	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3874559_3874560insA								EFCAB4B (12193 upstream) : PARP11 (43467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4225050	4225050	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4225050delA								PARP11 (242442 upstream) : CCND2 (157852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5140865	5140865	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5140865delA								KCNA1 (113445 upstream) : KCNA5 (12220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	5424964	5424965	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5424964_5424965delAA								KCNA5 (269016 upstream) : NTF3 (116315 downstream)																																			---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5767536	5767538	+	Intron	DEL	ATC	-	-	rs71445664		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5767536_5767538delATC	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
ZNF384	171017	broad.mit.edu	37	12	6788966	6788966	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6788966delA	uc010sfh.1	-						ZNF384_uc001qpz.2_Intron|ZNF384_uc001qqa.2_Intron|ZNF384_uc001qqb.2_Intron|ZNF384_uc001qqc.2_Intron|ZNF384_uc001qqd.2_Intron|ZNF384_uc001qqe.2_Intron|ZNF384_uc009zew.1_5'Flank	NM_001135734	NP_001129206			nuclear matrix transcription factor 4 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/ZNF384(4)	haematopoietic_and_lymphoid_tissue(4)|central_nervous_system(3)|kidney(1)	8								T	EWSR1|TAF15 	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	12	6850113	6850113	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6850113delT								COPS7A (9074 upstream) : MLF2 (7047 downstream)																																			---	---	---	---
CD4	920	broad.mit.edu	37	12	6918662	6918665	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6918662_6918665delAAAA	uc001qqv.1	+						CD4_uc009zez.1_Intron|CD4_uc009zfa.1_Intron|CD4_uc009zfb.1_Intron|CD4_uc010sfj.1_Intron|CD4_uc009zfc.1_Intron|CD4_uc010sfk.1_Intron|CD4_uc010sfl.1_Intron	NM_000616	NP_000607			CD4 antigen precursor						cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)																---	---	---	---
CDCA3	83461	broad.mit.edu	37	12	6959326	6959327	+	Intron	DEL	TG	-	-	rs33958983		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6959326_6959327delTG	uc001qrg.2	-						CDCA3_uc001qre.2_Intron|uc001qrf.1_5'Flank|USP5_uc001qri.3_5'Flank|USP5_uc001qrh.3_5'Flank	NM_031299	NP_112589			cell division cycle associated 3						cell division|mitosis	cytosol					0																		---	---	---	---
FAM66C	440078	broad.mit.edu	37	12	8346255	8346256	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8346255_8346256delTG	uc001que.3	+						FAM66C_uc001quf.3_Intron|FAM66C_uc009zgc.2_Intron|FAM66C_uc001qug.3_Intron	NR_026788				Homo sapiens cDNA FLJ38982 fis, clone NT2RI2005239.												0																		---	---	---	---
MFAP5	8076	broad.mit.edu	37	12	8815716	8815716	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8815716delT	uc001qut.1	-						MFAP5_uc001qus.2_5'Flank|MFAP5_uc009zge.1_5'Flank	NM_003480	NP_003471			microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
A2M	2	broad.mit.edu	37	12	9240156	9240164	+	Intron	DEL	TACATTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9240156_9240164delTACATTTTT	uc001qvk.1	-						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	9483966	9483974	+	5'Flank	DEL	TGGAGCAGG	-	-	rs144105962		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9483966_9483974delTGGAGCAGG	uc001qvr.2	-						uc001qvs.2_5'Flank					DQ601159																												OREG0021666	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	12	10381564	10381564	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10381564delA								GABARAPL1 (5842 upstream) : KLRD1 (75486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10446294	10446294	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10446294delA								GABARAPL1 (70572 upstream) : KLRD1 (10756 downstream)																																			---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10783476	10783476	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11264550	11264551	+	Intron	INS	-	A	A	rs138484507	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11264550_11264551insA	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12130497	12130497	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12130497delA	uc001raa.1	+							NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
GPRC5D	55507	broad.mit.edu	37	12	13104917	13104917	+	5'Flank	DEL	A	-	-	rs75550763		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13104917delA	uc010shp.1	-							NM_018654	NP_061124			G protein-coupled receptor, family C, group 5,							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	14187145	14187145	+	IGR	DEL	G	-	-	rs149120726		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14187145delG								GRIN2B (54123 upstream) : ATF7IP (331466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14412919	14412919	+	IGR	DEL	T	-	-	rs71436801		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14412919delT								GRIN2B (279897 upstream) : ATF7IP (105692 downstream)																																			---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14678617	14678620	+	Intron	DEL	ACAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14678617_14678620delACAC	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15459235	15459236	+	IGR	DEL	AC	-	-	rs147450469		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15459235_15459236delAC								RERG (84931 upstream) : PTPRO (16251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16225910	16225910	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16225910delT								DERA (35596 upstream) : MGST1 (274166 downstream)																																			---	---	---	---
MGST1	4257	broad.mit.edu	37	12	16519556	16519557	+	Intron	DEL	TG	-	-	rs138119758		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16519556_16519557delTG	uc009zih.1	+											Homo sapiens cDNA FLJ76401 complete cds, highly similar to Homo sapiens microsomal glutathione S-transferase 1 (MGST1), transcript variant 1b, mRNA.						protein homotrimerization|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	glutathione transferase activity				0		Hepatocellular(102;0.121)			Glutathione(DB00143)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	16970496	16970496	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16970496delA								LMO3 (207738 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17346488	17346491	+	IGR	DEL	ACAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17346488_17346491delACAC								LMO3 (583730 upstream) : RERGL (887313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17875412	17875413	+	IGR	INS	-	T	T	rs138096015	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17875412_17875413insT								None (None upstream) : RERGL (358391 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18447390	18447390	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18447390delT	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18456270	18456273	+	Intron	DEL	TCTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18456270_18456273delTCTT	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	20062979	20062980	+	IGR	INS	-	TCTA	TCTA	rs139632109	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20062979_20062980insTCTA								AEBP2 (387806 upstream) : PDE3A (459217 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	22193961	22193961	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22193961delA								ABCC9 (99625 upstream) : CMAS (5198 downstream)																																			---	---	---	---
ST8SIA1	6489	broad.mit.edu	37	12	22413100	22413100	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22413100delT	uc001rfo.3	-						ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025			alpha-2,8-sialyltransferase 1						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3																		---	---	---	---
ETNK1	55500	broad.mit.edu	37	12	22775559	22775559	+	5'Flank	DEL	T	-	-	rs35174231		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22775559delT	uc001rft.2	+						ETNK1_uc009ziz.2_5'Flank|ETNK1_uc001rfs.2_5'Flank	NM_018638	NP_061108			ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23746798	23746799	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23746798_23746799delGA	uc001rfw.2	-						SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron	NM_006940	NP_008871			SRY (sex determining region Y)-box 5 isoform a						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
IFLTD1	160492	broad.mit.edu	37	12	25777512	25777512	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25777512delA	uc010sjj.1	-							NM_001145727	NP_001139199			intermediate filament tail domain containing 1							intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26548525	26548526	+	Intron	INS	-	A	A	rs145276837	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26548525_26548526insA	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	27223483	27223484	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27223483_27223484delTG								MED21 (40801 upstream) : C12orf71 (10507 downstream)																																			---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27572952	27572953	+	Intron	INS	-	CA	CA	rs142781412	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27572952_27572953insCA	uc001rht.1	+						ARNTL2_uc001rhw.2_Intron|ARNTL2_uc010sjp.1_Intron|ARNTL2_uc001rhu.1_Intron|ARNTL2_uc009zji.1_Intron|ARNTL2_uc001rhv.1_Intron|uc001rhx.2_Intron	NM_020183	NP_064568			aryl hydrocarbon receptor nuclear						circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27841020	27841020	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27841020delA	uc001ric.1	+						PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron|PPFIBP1_uc001rif.1_Intron	NM_003622	NP_003613			PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)																	---	---	---	---
MRPS35	60488	broad.mit.edu	37	12	27869927	27869927	+	Intron	DEL	A	-	-	rs112665458		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27869927delA	uc001rih.2	+						MRPS35_uc001rii.2_Intron	NM_021821	NP_068593			mitochondrial ribosomal protein S35 precursor						DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)																	---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28523756	28523759	+	Intron	DEL	GAGA	-	-	rs143361204		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28523756_28523759delGAGA	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rip.1_Intron|CCDC91_uc001rir.2_Intron|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788			GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28944160	28944161	+	IGR	INS	-	CA	CA	rs143943331	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28944160_28944161insCA								CCDC91 (241062 upstream) : FAR2 (358071 downstream)																																			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29892649	29892649	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29892649delT	uc001rjb.2	-						TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	29961214	29961214	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29961214delA								TMTC1 (23522 upstream) : IPO8 (820709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30091761	30091761	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30091761delC								TMTC1 (154069 upstream) : IPO8 (690162 downstream)																																			---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31644904	31644904	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31644904delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.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	32018743	32018743	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32018743delA								H3F3C (73568 upstream) : C12orf35 (93610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	32633108	32633108	+	IGR	DEL	G	-	-	rs67939703		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32633108delG								BICD1 (101968 upstream) : FGD4 (5798 downstream)																																			---	---	---	---
FGD4	121512	broad.mit.edu	37	12	32710867	32710867	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32710867delT	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rkx.3_Intron	NM_139241	NP_640334			FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	33444939	33444939	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33444939delA								PKP2 (395159 upstream) : SYT10 (83409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33452396	33452397	+	IGR	INS	-	AAGG	AAGG	rs143444187	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33452396_33452397insAAGG								PKP2 (402616 upstream) : SYT10 (75951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34499733	34499733	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34499733delT								ALG10 (318499 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	40590305	40590310	+	IGR	DEL	ACACAC	-	-	rs71957089		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40590305_40590310delACACAC								SLC2A13 (90644 upstream) : LRRK2 (28503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42197162	42197163	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42197162_42197163insA								PDZRN4 (228778 upstream) : GXYLT1 (278487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42409300	42409301	+	IGR	DEL	TT	-	-	rs143860272		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42409300_42409301delTT								PDZRN4 (440916 upstream) : GXYLT1 (66349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43632012	43632012	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43632012delA								PRICKLE1 (648440 upstream) : ADAMTS20 (116001 downstream)																																			---	---	---	---
TWF1	5756	broad.mit.edu	37	12	44197958	44197959	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44197958_44197959delTT	uc001rob.2	-						TWF1_uc001rnz.2_Intron|TWF1_uc001roa.2_Intron|TWF1_uc001roc.2_Intron	NM_002822	NP_002813			twinfilin 1							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)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44406832	44406834	+	Intron	DEL	TTT	-	-	rs112180367		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44406832_44406834delTTT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44728356	44728356	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44728356delT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	45372298	45372299	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45372298_45372299delAA								NELL2 (64587 upstream) : DBX2 (36240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	45499807	45499807	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45499807delT								RACGAP1P (40613 upstream) : PLEKHA9 (67040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47800832	47800833	+	IGR	INS	-	ACACAC	ACACAC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47800832_47800833insACACAC								FAM113B (170391 upstream) : RPAP3 (254883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48795872	48795873	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48795872_48795873delTT								ZNF641 (50851 upstream) : ANP32D (70575 downstream)																																			---	---	---	---
ADCY6	112	broad.mit.edu	37	12	49163028	49163028	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49163028delA	uc001rsh.3	-						ADCY6_uc001rsj.3_Intron|ADCY6_uc001rsi.3_Intron	NM_015270	NP_056085			adenylate cyclase 6 isoform a						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	ATP binding|metal ion binding				0																		---	---	---	---
CACNB3	784	broad.mit.edu	37	12	49221205	49221206	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49221205_49221206delCA	uc001rsl.1	+						CACNB3_uc010sly.1_Intron|CACNB3_uc010slz.1_Intron|CACNB3_uc001rsk.1_Intron	NM_000725	NP_000716			calcium channel, voltage-dependent, beta 3						axon guidance|membrane depolarization|synaptic transmission	cytosol|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0					Verapamil(DB00661)													---	---	---	---
RND1	27289	broad.mit.edu	37	12	49258168	49258169	+	Intron	DEL	GT	-	-	rs72158960		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49258168_49258169delGT	uc001rsn.2	-							NM_014470	NP_055285			GTP-binding protein RHO6 precursor						actin filament organization|axon guidance|negative regulation of cell adhesion|neuron remodeling|small GTPase mediated signal transduction	adherens junction|cytoskeleton|cytosol	GTP binding|GTPase activity|receptor binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49267768	49267769	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49267768_49267769insA								RND1 (8115 upstream) : CCDC65 (30124 downstream)																																			---	---	---	---
TUBA1B	10376	broad.mit.edu	37	12	49553371	49553372	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49553371_49553372insT	uc001rto.2	-							NM_006082	NP_006073			tubulin, alpha, ubiquitous						'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding				0																		---	---	---	---
TMBIM6	7009	broad.mit.edu	37	12	50145215	50145215	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50145215delA	uc001rux.2	+						TMBIM6_uc010sml.1_Intron|TMBIM6_uc001ruy.2_Intron|TMBIM6_uc001ruz.2_Intron	NM_003217	NP_003208			testis enhanced gene transcript (BAX inhibitor						apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	50170496	50170496	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50170496delT								TMBIM6 (11779 upstream) : NCKAP5L (14433 downstream)																																	OREG0021803	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50727335	50727335	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50727335delA	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50791619	50791619	+	5'Flank	DEL	T	-	-	rs71083563		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50791619delT	uc001rwl.2	-							NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50957669	50957670	+	Intron	INS	-	T	T	rs143947916	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50957669_50957670insT	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	51147656	51147656	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51147656delA								DIP2B (5208 upstream) : ATF1 (10163 downstream)																																			---	---	---	---
SMAGP	57228	broad.mit.edu	37	12	51642184	51642191	+	Intron	DEL	ACACACAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51642184_51642191delACACACAC	uc001ryc.1	-						SMAGP_uc001ryd.1_Intron|SMAGP_uc001rye.1_Intron|SMAGP_uc001ryf.1_Intron	NM_001033873	NP_001029045			small trans-membrane and glycosylated protein							cytoplasmic vesicle membrane|integral to membrane|plasma membrane					0																		---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52001060	52001061	+	Intron	DEL	TG	-	-	rs150114723	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52001060_52001061delTG	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	52204039	52204039	+	Frame_Shift_Del	DEL	A	-	-	rs11833203	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52204039delA	uc001rzb.1	+	1	251	c.81delA	c.(79-81)TTAfs	p.L27fs						SubName: Full=HCG1997999; SubName: Full=cDNA FLJ33996 fis, clone DFNES2008881;																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	52874149	52874149	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52874149delA								KRT6C (6580 upstream) : KRT6A (6810 downstream)																																			---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53309499	53309499	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53309499delA	uc009zmk.1	-						KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_002273	NP_002264			keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
CSAD	51380	broad.mit.edu	37	12	53560118	53560118	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53560118delA	uc001sby.2	-						CSAD_uc001sbw.2_Intron|CSAD_uc009zmt.2_Intron|CSAD_uc010snx.1_Intron|CSAD_uc001sbz.2_Intron|CSAD_uc009zmu.2_Intron|CSAD_uc001sca.3_Intron	NM_015989	NP_057073			cysteine sulfinic acid decarboxylase						carboxylic acid metabolic process		pyridoxal phosphate binding|sulfinoalanine decarboxylase activity			ovary(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)									Hereditary_Prostate_Cancer				---	---	---	---
Unknown	0	broad.mit.edu	37	12	54241721	54241721	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54241721delT								CALCOCO1 (120414 upstream) : HOXC13 (90855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54571441	54571442	+	IGR	DEL	AA	-	-	rs72255092		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54571441_54571442delAA								LOC400043 (44822 upstream) : SMUG1 (2341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54990870	54990870	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54990870delT								PPP1R1A (8427 upstream) : GLYCAM1 (11101 downstream)																																	OREG0021899	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	12	55158641	55158641	+	IGR	DEL	G	-	-	rs61494491		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55158641delG								DCD (116492 upstream) : MUCL1 (89658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	56045262	56045262	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56045262delA								OR10P1 (13646 upstream) : METTL7B (30068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	56068246	56068246	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56068246delA								OR10P1 (36630 upstream) : METTL7B (7084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	56259925	56259926	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56259925_56259926delAA								MMP19 (23190 upstream) : WIBG (35271 downstream)																																			---	---	---	---
SUOX	6821	broad.mit.edu	37	12	56394570	56394570	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56394570delT	uc001six.2	+						SUOX_uc009zoh.2_Intron|SUOX_uc001siy.2_Intron|SUOX_uc001siz.2_Intron|SUOX_uc001sja.2_5'Flank	NM_000456	NP_000447			sulfite oxidase precursor							mitochondrial intermembrane space	electron carrier activity|molybdenum ion binding|sulfite oxidase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)															---	---	---	---
ANKRD52	283373	broad.mit.edu	37	12	56645586	56645586	+	Intron	DEL	T	-	-	rs112384328		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56645586delT	uc001skm.3	-							NM_173595	NP_775866			ankyrin repeat domain 52								protein binding			ovary(2)	2																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	57022157	57022158	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57022157_57022158delAA	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc010sqr.1_Intron	NM_013449	NP_038477			bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57670675	57670675	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57670675delA	uc009zpm.1	-						R3HDM2_uc010srn.1_Intron|R3HDM2_uc001snu.2_Intron|R3HDM2_uc001snr.2_Intron|R3HDM2_uc001sns.2_Intron|R3HDM2_uc001snt.2_Intron|R3HDM2_uc009zpn.1_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
ARHGAP9	64333	broad.mit.edu	37	12	57875042	57875042	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57875042delT	uc001sod.2	-						ARHGAP9_uc001sob.2_5'Flank|ARHGAP9_uc001soc.2_5'Flank|ARHGAP9_uc001soe.1_Intron|ARHGAP9_uc010sro.1_5'Flank	NM_032496	NP_115885			Rho GTPase activating protein 9 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			lung(1)	1			GBM - Glioblastoma multiforme(3;3.37e-34)															---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57942925	57942925	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57942925delT	uc001sor.1	+						DCTN2_uc009zpu.1_5'Flank|DCTN2_uc009zpv.1_5'Flank|DCTN2_uc009zpw.1_5'Flank|DCTN2_uc001som.1_5'Flank|DCTN2_uc001soo.1_5'Flank|DCTN2_uc001son.1_5'Flank|DCTN2_uc001sop.1_5'Flank|DCTN2_uc001soq.1_5'Flank|DCTN2_uc009zpx.1_5'Flank|KIF5A_uc010srr.1_5'Flank	NM_004984	NP_004975			kinesin family member 5A						blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
CDK4	1019	broad.mit.edu	37	12	58145599	58145599	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58145599delA	uc001spv.2	-						CDK4_uc010ssb.1_Intron|CDK4_uc001spw.2_Intron	NM_000075	NP_000066			cyclin-dependent kinase 4						cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|positive regulation of fibroblast proliferation|regulation of gene expression|response to drug|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane	ATP binding|cyclin-dependent protein kinase activity|protein binding			lung(1)|breast(1)|central_nervous_system(1)	3	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)					Mis			melanoma 			Hereditary_Melanoma				---	---	---	---
Unknown	0	broad.mit.edu	37	12	58627298	58627298	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58627298delT								XRCC6BP1 (276247 upstream) : LRIG3 (638640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	58938117	58938117	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58938117delT								XRCC6BP1 (587066 upstream) : LRIG3 (327821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61128501	61128501	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61128501delT								SLC16A7 (953094 upstream) : FAM19A2 (973542 downstream)																																			---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63132145	63132145	+	Intron	DEL	A	-	-	rs115837339	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63132145delA	uc001srk.3	-							NM_020700	NP_065751			protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)														---	---	---	---
AVPR1A	552	broad.mit.edu	37	12	63547192	63547192	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63547192delA	uc001sro.1	-							NM_000706	NP_000697			arginine vasopressin receptor 1A						activation of phospholipase C activity|elevation of cytosolic calcium ion concentration|generation of precursor metabolites and energy	endosome|integral to plasma membrane	protein kinase C binding|vasopressin receptor activity				0			BRCA - Breast invasive adenocarcinoma(9;0.193)	GBM - Glioblastoma multiforme(28;0.0569)	Conivaptan(DB00872)|Desmopressin(DB00035)|Felypressin(DB00093)|Terlipressin(DB02638)|Vasopressin(DB00067)													---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64415937	64415938	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64415937_64415938delGT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron|SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						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)														---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65724427	65724427	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65724427delC	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346			methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67387978	67387978	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67387978delA								GRIP1 (190084 upstream) : CAND1 (275083 downstream)																																			---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67686248	67686248	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67686248delT	uc001stn.2	+							NM_018448	NP_060918			TIP120 protein						cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67735772	67735772	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67735772delG								CAND1 (27384 upstream) : DYRK2 (306740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	67755328	67755329	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67755328_67755329delAG								CAND1 (46940 upstream) : DYRK2 (287183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	67847786	67847786	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67847786delA								CAND1 (139398 upstream) : DYRK2 (194726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	69531136	69531136	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69531136delA								CPM (174116 upstream) : CPSF6 (102181 downstream)																																			---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71834177	71834177	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71834177delG	uc001swl.2	+						TSPAN8_uc001swk.1_Intron|LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658			leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
TMEM19	55266	broad.mit.edu	37	12	72083943	72083943	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72083943delT	uc001sws.2	+						TMEM19_uc001swr.1_Intron|TMEM19_uc009zru.1_Intron	NM_018279	NP_060749			transmembrane protein 19							integral to membrane					0		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	73193697	73193697	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73193697delA								TRHDE (134276 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74669120	74669123	+	Intron	DEL	TTTT	-	-	rs113849001		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74669120_74669123delTTTT	uc009zrx.1	-						uc001sxc.2_Intron					Homo sapiens cDNA clone IMAGE:3926153, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	75375958	75375958	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75375958delA								ATXN7L3B (440735 upstream) : KCNC2 (57939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75979285	75979285	+	IGR	DEL	T	-	-	rs34393682		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75979285delT								KRR1 (73867 upstream) : PHLDA1 (439943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76599766	76599766	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76599766delA								NAP1L1 (121028 upstream) : BBS10 (138500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78079266	78079267	+	IGR	INS	-	ACACACACAA	ACACACACAA	rs144152262	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78079266_78079267insACACACACAA								E2F7 (619906 upstream) : NAV3 (145802 downstream)																																			---	---	---	---
SYT1	6857	broad.mit.edu	37	12	79317504	79317505	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79317504_79317505delTG	uc001sys.2	+						SYT1_uc001syt.2_Intron|SYT1_uc001syu.2_Intron	NM_001135805	NP_001129277			synaptotagmin I						detection of calcium ion|glutamate secretion|neurotransmitter secretion|protein homooligomerization	cell junction|chromaffin granule membrane|clathrin sculpted acetylcholine transport vesicle membrane|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|clathrin sculpted glutamate transport vesicle membrane|clathrin sculpted monoamine transport vesicle membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	1-phosphatidylinositol binding|low-density lipoprotein particle receptor binding|metal ion binding|syntaxin-1 binding|transporter activity			skin(3)|pancreas(2)|ovary(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	79869029	79869030	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79869029_79869030insT								SYT1 (23242 upstream) : PAWR (116717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80648804	80648804	+	IGR	DEL	T	-	-	rs80186622		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80648804delT								PPP1R12A (319569 upstream) : PTPRQ (189322 downstream)																																			---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	80955474	80955474	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80955474delT	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	81453064	81453064	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81453064delT								LIN7A (121370 upstream) : ACSS3 (18745 downstream)																																			---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81618935	81618936	+	Intron	INS	-	TG	TG	rs141396702	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81618935_81618936insTG	uc001szl.1	+						ACSS3_uc001szm.1_Intron|ACSS3_uc001szn.1_Intron	NM_024560	NP_078836			acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81688219	81688226	+	Intron	DEL	AGGAAGGA	-	-	rs72104251		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81688219_81688226delAGGAAGGA	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82268697	82268698	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82268697_82268698insT								PPFIA2 (115588 upstream) : CCDC59 (477392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85070542	85070542	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85070542delT								None (None upstream) : SLC6A15 (182727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85382383	85382383	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85382383delA								SLC6A15 (75777 upstream) : TSPAN19 (25712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85852816	85852816	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85852816delA								ALX1 (157257 upstream) : RASSF9 (345515 downstream)																																			---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	87138082	87138082	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87138082delA	uc001tal.3	-						MGAT4C_uc001taj.3_Intron|MGAT4C_uc001tak.3_Intron	NM_013244	NP_037376			alpha-1,3-mannosyl-glycoprotein						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	87682216	87682217	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87682216_87682217delTG								MGAT4C (449535 upstream) : C12orf50 (691599 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88525006	88525007	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88525006_88525007delAA	uc001tar.2	-						CEP290_uc001tat.2_5'Flank|CEP290_uc009zsl.1_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88683090	88683091	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88683090_88683091delTT								TMTC3 (89427 upstream) : KITLG (203478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89795256	89795257	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89795256_89795257delTT								DUSP6 (48960 upstream) : POC1B (18244 downstream)																																			---	---	---	---
POC1B	282809	broad.mit.edu	37	12	89873919	89873920	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89873919_89873920insT	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440			WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	90197083	90197083	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90197083delA								LOC338758 (91355 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91690816	91690821	+	IGR	DEL	TTCAAC	-	-	rs113247521		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91690816_91690821delTTCAAC								DCN (114010 upstream) : BTG1 (688045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91835853	91835855	+	IGR	DEL	TAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91835853_91835855delTAT								DCN (259047 upstream) : BTG1 (543011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91972933	91972934	+	IGR	INS	-	CA	CA	rs140415888	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91972933_91972934insCA								DCN (396127 upstream) : BTG1 (405932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92370639	92370641	+	IGR	DEL	AAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92370639_92370641delAAC								DCN (793833 upstream) : BTG1 (8225 downstream)																																			---	---	---	---
CLLU1	574028	broad.mit.edu	37	12	92840553	92840553	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92840553delT	uc001tce.1	+											Homo sapiens mRNA for non-coding transcript (CLLU1 gene), splice variant 1.											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	94940800	94940807	+	IGR	DEL	CTCTGGAT	-	-	rs113459448		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94940800_94940807delCTCTGGAT								LOC144486 (84458 upstream) : TMCC3 (20093 downstream)																																			---	---	---	---
USP44	84101	broad.mit.edu	37	12	95917658	95917658	+	Intron	DEL	T	-	-	rs79631841		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95917658delT	uc001teg.2	-						USP44_uc001teh.2_Intron|USP44_uc009zte.2_Intron	NM_001042403	NP_001035862			ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95976371	95976371	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95976371delT								USP44 (31108 upstream) : NTN4 (75213 downstream)																																			---	---	---	---
NTN4	59277	broad.mit.edu	37	12	96183637	96183638	+	Intron	DEL	CG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96183637_96183638delCG	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052			netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	96966217	96966218	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96966217_96966218delTT	uc001ter.1	+											Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	98462223	98462223	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98462223delT								RMST (503430 upstream) : LOC100128191 (444530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98790200	98790200	+	IGR	DEL	T	-	-	rs142359930		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98790200delT								RMST (831407 upstream) : LOC100128191 (116553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98866602	98866602	+	IGR	DEL	A	-	-	rs78715034		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98866602delA								RMST (907809 upstream) : LOC100128191 (40151 downstream)																																			---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99384692	99384693	+	Intron	DEL	TT	-	-	rs139773007		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99384692_99384693delTT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.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	99770004	99770004	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99770004delA	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)														---	---	---	---
FAM71C	196472	broad.mit.edu	37	12	100041822	100041822	+	5'UTR	DEL	A	-	-	rs35601898		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100041822delA	uc001tgn.2	+	1					ANKS1B_uc001tge.1_Intron|ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_153364	NP_699195			hypothetical protein LOC196472												0				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)														---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100461768	100461768	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100461768delA	uc001tgq.2	-						UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100517102	100517103	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100517102_100517103insA	uc001tgq.2	-						UHRF1BP1L_uc001tgr.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	101104940	101104940	+	IGR	DEL	C	-	-	rs7316856	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101104940delC								GAS2L3 (86257 upstream) : ANO4 (6364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	101819503	101819503	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101819503delT								ARL1 (17931 upstream) : SPIC (49696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	101919268	101919271	+	IGR	DEL	TCTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101919268_101919271delTCTC								SPIC (38494 upstream) : MYBPC1 (69476 downstream)																																			---	---	---	---
C12orf48	55010	broad.mit.edu	37	12	102531295	102531295	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102531295delT	uc001tjf.2	+						C12orf48_uc001tjd.2_Intron|C12orf48_uc001tje.2_Intron|C12orf48_uc001tjg.2_Intron|C12orf48_uc010swa.1_Intron|C12orf48_uc001tjh.2_Intron|C12orf48_uc010swb.1_Intron|C12orf48_uc001tji.2_Intron|C12orf48_uc009zuc.2_Intron|C12orf48_uc001tjj.2_Intron|C12orf48_uc001tjk.2_Intron|C12orf48_uc009zud.2_Intron	NM_017915	NP_060385			hypothetical protein LOC55010						response to DNA damage stimulus	cytoplasm|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	102716336	102716336	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102716336delT								PMCH (124722 upstream) : IGF1 (73309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103443723	103443723	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103443723delA								ASCL1 (89436 upstream) : C12orf42 (187647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103506874	103506874	+	IGR	DEL	T	-	-	rs34855011		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103506874delT								ASCL1 (152587 upstream) : C12orf42 (124496 downstream)																																			---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104098559	104098559	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104098559delT	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																		---	---	---	---
LOC253724	253724	broad.mit.edu	37	12	104269383	104269384	+	Intron	INS	-	AAT	AAT	rs142889757	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104269383_104269384insAAT	uc010swf.1	-							NR_027249				Homo sapiens cDNA FLJ56788 complete cds, moderately similar to Mus musculus 5'-nucleotidase domain containing 3 (Nt5dc3), transcript variant 2, mRNA.												0																		---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104728170	104728170	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104728170delT	uc010swk.1	+						TXNRD1_uc010swl.1_Intron|TXNRD1_uc010swm.1_Intron|TXNRD1_uc010swn.1_Intron|TXNRD1_uc010swo.1_Intron|TXNRD1_uc010swp.1_Intron|TXNRD1_uc010swq.1_Intron|TXNRD1_uc001tku.2_Intron|TXNRD1_uc009zun.2_Intron	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	104831621	104831621	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104831621delT								TXNRD1 (87563 upstream) : CHST11 (19128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105864233	105864234	+	IGR	DEL	GT	-	-	rs72006851		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105864233_105864234delGT								C12orf75 (98938 upstream) : NUAK1 (592891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106212359	106212359	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106212359delA								C12orf75 (447064 upstream) : NUAK1 (244766 downstream)																																			---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106897215	106897215	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106897215delT	uc001tlp.2	+						POLR3B_uc001tlq.2_Intron	NM_018082	NP_060552			DNA-directed RNA polymerase III B isoform 1						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107624674	107624674	+	IGR	DEL	T	-	-	rs72343489		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107624674delT								CRY1 (137076 upstream) : BTBD11 (87523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	107645623	107645638	+	IGR	DEL	ACACACACACACACAC	-	-	rs72168417		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107645623_107645638delACACACACACACACAC								CRY1 (158025 upstream) : BTBD11 (66559 downstream)																																			---	---	---	---
TMEM119	338773	broad.mit.edu	37	12	108994005	108994008	+	5'Flank	DEL	CATT	-	-	rs35746085		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108994005_108994008delCATT	uc001tng.2	-						TMEM119_uc001tnf.2_5'Flank	NM_181724	NP_859075			transmembrane protein 119 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	109130067	109130068	+	IGR	DEL	GA	-	-	rs34151365		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109130067_109130068delGA								CORO1C (4772 upstream) : SSH1 (46399 downstream)																																			---	---	---	---
USP30	84749	broad.mit.edu	37	12	109512511	109512512	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109512511_109512512delTG	uc010sxi.1	+						USP30_uc001tnu.3_Intron	NM_032663	NP_116052			ubiquitin specific peptidase 30						ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109628432	109628432	+	Intron	DEL	T	-	-	rs10571468		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109628432delT	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110413910	110413911	+	Intron	INS	-	AC	AC	rs145928011	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110413910_110413911insAC	uc001tps.2	-						GIT2_uc001tpq.2_Intron|GIT2_uc001tpv.2_Intron|GIT2_uc001tpu.2_Intron|GIT2_uc001tpt.2_Intron|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Intron|GIT2_uc010sxv.1_Intron	NM_057169	NP_476510			G protein-coupled receptor kinase interacting						regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ANKRD13A	88455	broad.mit.edu	37	12	110444407	110444408	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110444407_110444408insT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc009zvm.1_Intron|ANKRD13A_uc010sxw.1_Intron	NM_033121	NP_149112			ankyrin repeat domain 13												0																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110566612	110566616	+	Intron	DEL	AAAAG	-	-	rs76566316		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110566612_110566616delAAAAG	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111221808	111221809	+	IGR	DEL	TT	-	-	rs76284834		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111221808_111221809delTT								PPP1CC (41051 upstream) : CCDC63 (63002 downstream)																																			---	---	---	---
CCDC63	160762	broad.mit.edu	37	12	111317311	111317311	+	Intron	DEL	T	-	-	rs75370933		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111317311delT	uc001trv.1	+						CCDC63_uc009zvt.1_Intron|CCDC63_uc010sye.1_Intron|CCDC63_uc001trw.1_Intron	NM_152591	NP_689804			coiled-coil domain containing 63											skin(6)|ovary(1)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	112781582	112781582	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112781582delA								C12orf51 (37544 upstream) : RPL6 (61413 downstream)																																			---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113141898	113141900	+	Intron	DEL	TTT	-	-	rs2384051	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113141898_113141900delTTT	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
RPH3A	22895	broad.mit.edu	37	12	113147789	113147789	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113147789delT	uc010syl.1	+							NM_001143854	NP_001137326			rabphilin 3A homolog isoform 1						intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(2)|skin(2)	7				BRCA - Breast invasive adenocarcinoma(302;0.00453)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	113950895	113950896	+	IGR	INS	-	CAT	CAT	rs141029416	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113950895_113950896insCAT								LHX5 (41018 upstream) : RBM19 (303647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114231068	114231069	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114231068_114231069delCA								LHX5 (321191 upstream) : RBM19 (23474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114499871	114499871	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114499871delG								RBM19 (95695 upstream) : TBX5 (291865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115613156	115613157	+	IGR	INS	-	GT	GT	rs149066230	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115613156_115613157insGT								TBX3 (491187 upstream) : MED13L (783226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115633997	115633998	+	IGR	INS	-	TTCCTTCC	TTCCTTCC	rs139227338	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115633997_115633998insTTCCTTCC								TBX3 (512028 upstream) : MED13L (762385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115760827	115760830	+	IGR	DEL	AAGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115760827_115760830delAAGG								TBX3 (638858 upstream) : MED13L (635553 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116471553	116471554	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116471553_116471554delGT	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)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116621624	116621625	+	Intron	DEL	TA	-	-	rs57716114		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116621624_116621625delTA	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)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116684116	116684116	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116684116delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	116734906	116734906	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116734906delA								MED13L (19915 upstream) : NCRNA00173 (236321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117047206	117047206	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117047206delT								MAP1LC3B2 (32781 upstream) : C12orf49 (106390 downstream)																																			---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117629533	117629533	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117629533delA	uc001twk.2	-						FBXO21_uc001twj.2_5'Flank|FBXO21_uc009zwq.2_5'Flank	NM_033624	NP_296373			F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	117849032	117849032	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117849032delT								NOS1 (49450 upstream) : KSR2 (41785 downstream)																																			---	---	---	---
KSR2	283455	broad.mit.edu	37	12	117996846	117996847	+	Intron	INS	-	GGAT	GGAT	rs71444628		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117996846_117996847insGGAT	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)																	---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118172550	118172551	+	Intron	INS	-	ATGGATGG	ATGGATGG	rs112891284		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118172550_118172551insATGGATGG	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)																	---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118708034	118708034	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118708034delA	uc001twx.2	-						TAOK3_uc001twy.3_Intron	NM_016281	NP_057365			TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119553682	119553682	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119553682delT	uc001txa.1	+							NM_194286	NP_919262			KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
CIT	11113	broad.mit.edu	37	12	120222205	120222205	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120222205delC	uc001txi.1	-						CIT_uc001txh.1_5'UTR|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	120725824	120725825	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120725824_120725825delAA								NME2P1 (5192 upstream) : SIRT4 (14338 downstream)																																			---	---	---	---
GATC	283459	broad.mit.edu	37	12	120893498	120893498	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120893498delT	uc010szi.1	+							NM_176818	NP_789788			glutamyl-tRNA(Gln) amidotransferase, subunit C						regulation of translational fidelity						0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121251474	121251474	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121251474delA	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron	NM_139015	NP_620584			signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
C12orf43	64897	broad.mit.edu	37	12	121444024	121444026	+	Intron	DEL	AAG	-	-	rs144577739		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121444024_121444026delAAG	uc001tzh.1	-						C12orf43_uc009zxa.1_Intron|C12orf43_uc010szo.1_Intron|C12orf43_uc010szp.1_Intron|C12orf43_uc001tzi.1_Intron	NM_022895	NP_075046			hypothetical protein LOC64897												0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121914098	121914099	+	Intron	INS	-	A	A	rs150541167		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121914098_121914099insA	uc001uat.2	-						KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_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																		---	---	---	---
ORAI1	84876	broad.mit.edu	37	12	122077594	122077594	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122077594delT	uc010szz.1	+							NM_032790	NP_116179			calcium release-activated calcium channel						platelet activation|positive regulation of calcium ion transport	integral to plasma membrane	protein binding|store-operated calcium channel activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)														---	---	---	---
BCL7A	605	broad.mit.edu	37	12	122478929	122478930	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122478929_122478930delTT	uc001ubp.2	+						BCL7A_uc001ubo.2_Intron	NM_001024808	NP_001019979			B-cell CLL/lymphoma 7A isoform b						negative regulation of transcription, DNA-dependent					ovary(1)|lung(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)				T	MYC	BNHL								---	---	---	---
MLXIP	22877	broad.mit.edu	37	12	122584608	122584608	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122584608delT	uc001ubq.2	+							NM_014938	NP_055753			MLX interacting protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial outer membrane|nucleus	DNA binding			ovary(2)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)														---	---	---	---
LRRC43	254050	broad.mit.edu	37	12	122675402	122675403	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122675402_122675403delAA	uc009zxm.2	+						LRRC43_uc001ubw.3_Intron|LRRC43_uc009zxn.2_Intron	NM_001098519	NP_001091989			leucine rich repeat containing 43 isoform 1												0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)														---	---	---	---
LRRC43	254050	broad.mit.edu	37	12	122684134	122684134	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122684134delT	uc009zxm.2	+						LRRC43_uc001ubw.3_Intron|LRRC43_uc009zxn.2_Intron	NM_001098519	NP_001091989			leucine rich repeat containing 43 isoform 1												0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122744832	122744832	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122744832delT	uc001ucd.2	-						VPS33A_uc001ucc.2_Intron|VPS33A_uc001uce.2_Intron	NM_022916	NP_075067			vacuolar protein sorting 33A						lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122821509	122821510	+	Intron	INS	-	T	T	rs35632864		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122821509_122821510insT	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122962860	122962860	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122962860delA	uc001ucn.2	-						ZCCHC8_uc001ucl.2_5'UTR|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	123387120	123387120	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123387120delA								VPS37B (6408 upstream) : ABCB9 (26420 downstream)																																			---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	123996487	123996488	+	Intron	INS	-	TG	TG	rs143408241	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123996487_123996488insTG	uc001ufe.2	-						RILPL1_uc001ufd.2_Intron|RILPL1_uc010tas.1_Intron	NM_178314	NP_847884			Rab interacting lysosomal protein-like 1						neuroprotection	cytosol					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
TCTN2	79867	broad.mit.edu	37	12	124171671	124171671	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124171671delT	uc001ufp.2	+						TCTN2_uc009zya.2_Intron	NM_024809	NP_079085			tectonic family member 2 isoform 1						cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)														---	---	---	---
TCTN2	79867	broad.mit.edu	37	12	124172778	124172779	+	Intron	INS	-	A	A	rs58689399		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124172778_124172779insA	uc001ufp.2	+						TCTN2_uc009zya.2_Intron	NM_024809	NP_079085			tectonic family member 2 isoform 1						cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124415758	124415758	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124415758delA	uc001uft.3	+						DNAH10_uc001ufu.3_Intron	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	124578178	124578179	+	IGR	INS	-	TGA	TGA	rs147804483	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124578178_124578179insTGA								ZNF664 (78211 upstream) : FAM101A (195531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	124585613	124585613	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124585613delT								ZNF664 (85646 upstream) : FAM101A (188097 downstream)																																			---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124868080	124868080	+	Intron	DEL	A	-	-	rs148277001		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124868080delA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124977178	124977179	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124977178_124977179insG	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
SCARB1	949	broad.mit.edu	37	12	125283403	125283403	+	Intron	DEL	G	-	-	rs1672907	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125283403delG	uc001ugo.3	-						SCARB1_uc001ugn.3_Intron|SCARB1_uc001ugm.3_Intron|SCARB1_uc010tbd.1_Intron|SCARB1_uc010tbe.1_Intron|SCARB1_uc001ugp.3_Intron	NM_005505	NP_005496			scavenger receptor class B, member 1 isoform 1						adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			kidney(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)													---	---	---	---
DHX37	57647	broad.mit.edu	37	12	125465810	125465810	+	Intron	DEL	A	-	-	rs35864151		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125465810delA	uc001ugy.2	-							NM_032656	NP_116045			DEAH (Asp-Glu-Ala-His) box polypeptide 37								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125806398	125806398	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125806398delA								AACS (178526 upstream) : TMEM132B (4764 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125810215	125810218	+	5'Flank	DEL	CTGT	-	-	rs72371051		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125810215_125810218delCTGT	uc001uhe.1	+							NM_052907	NP_443139			transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127832420	127832421	+	IGR	INS	-	GT	GT	rs141902707	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127832420_127832421insGT								LOC100128554 (875090 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127874197	127874198	+	IGR	INS	-	GT	GT	rs144376282	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127874197_127874198insGT								LOC100128554 (916867 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128585693	128585694	+	IGR	DEL	GA	-	-	rs35542065		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128585693_128585694delGA								None (None upstream) : TMEM132C (313597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128800078	128800078	+	IGR	DEL	A	-	-	rs111235215		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128800078delA								None (None upstream) : TMEM132C (99213 downstream)																																			---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	129123553	129123561	+	Intron	DEL	TGATGGTGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129123553_129123561delTGATGGTGG	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	129170147	129170148	+	Intron	INS	-	T	T	rs143726479	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129170147_129170148insT	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129588029	129588029	+	Intron	DEL	A	-	-	rs35026163		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129588029delA	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	12	130397627	130397627	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130397627delA								TMEM132D (9415 upstream) : LOC100190940 (120372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130427669	130427669	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130427669delG								TMEM132D (39457 upstream) : LOC100190940 (90330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130681933	130681934	+	IGR	INS	-	GT	GT	rs148518451	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130681933_130681934insGT								FZD10 (31649 upstream) : PIWIL1 (140680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130705797	130705798	+	IGR	INS	-	T	T	rs113562269		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130705797_130705798insT								FZD10 (55513 upstream) : PIWIL1 (116816 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131131012	131131023	+	Intron	DEL	CTACCTCCCTCA	-	-	rs7136998	by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131131012_131131023delCTACCTCCCTCA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131510091	131510091	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131510091delT	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122			G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	132137845	132137851	+	IGR	DEL	TTGTGTG	-	-	rs79042307		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132137845_132137851delTTGTGTG								LOC116437 (440370 upstream) : SFRS8 (57784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133040651	133040653	+	IGR	DEL	CAT	-	-	rs143355315	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133040651_133040653delCAT								GALNT9 (134746 upstream) : FBRSL1 (26504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133055289	133055289	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133055289delG								GALNT9 (149384 upstream) : FBRSL1 (11868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133416437	133416438	+	IGR	INS	-	T	T	rs12810751		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133416437_133416438insT								GOLGA3 (10987 upstream) : CHFR (500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	19570996	19570997	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19570996_19570997insA								LOC284232 (124887 upstream) : LOC348021 (11402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	19926653	19926653	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19926653delT								LOC100101938 (7540 upstream) : TPTE2 (70368 downstream)																																			---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20254751	20254751	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20254751delA	uc001umj.1	-						PSPC1_uc001umk.1_Intron	NM_001042414				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)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20603942	20603942	+	Intron	DEL	T	-	-	rs67169743		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20603942delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444			zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20833143	20833143	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20833143delT								GJB6 (26609 upstream) : CRYL1 (144666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	21935625	21935625	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21935625delT								MRP63 (182407 upstream) : ZDHHC20 (14885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22876539	22876539	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22876539delA								FGF9 (597899 upstream) : SGCG (878521 downstream)																																			---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23861544	23861547	+	Intron	DEL	TGAA	-	-	rs145628381		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23861544_23861547delTGAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24135501	24135501	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24135501delT								SACS (127660 upstream) : TNFRSF19 (9222 downstream)																																			---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24307418	24307419	+	Intron	INS	-	T	T	rs150870175	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24307418_24307419insT	uc001uox.3	-							NM_005932	NP_005923			mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	25800506	25800506	+	IGR	DEL	T	-	-	rs11396975		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25800506delT								FAM123A (54201 upstream) : MTMR6 (1801 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26234794	26234794	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26234794delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	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)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26324940	26324940	+	Intron	DEL	A	-	-	rs113645249		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26324940delA	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	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)														---	---	---	---
CDK8	1024	broad.mit.edu	37	13	26887498	26887498	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26887498delT	uc001uqr.1	+						CDK8_uc001uqs.1_Intron|CDK8_uc001uqt.1_Intron	NM_001260	NP_001251			cyclin-dependent kinase 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)														---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27221533	27221534	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27221533_27221534insT	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)														---	---	---	---
PRHOXNB	646625	broad.mit.edu	37	13	28557364	28557364	+	Intron	DEL	T	-	-	rs77813429		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28557364delT	uc010aan.1	-							NM_001105577	NP_001099047			parahox cluster neighbor						allantoin biosynthetic process|purine base metabolic process	peroxisome	carboxy-lyase activity				0	all_cancers(110;0.12)|all_hematologic(3;0.0119)|Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0407)|all cancers(112;0.0491)|OV - Ovarian serous cystadenocarcinoma(117;0.199)														---	---	---	---
FLT1	2321	broad.mit.edu	37	13	29006396	29006398	+	Intron	DEL	CTC	-	-	rs72495719		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29006396_29006398delCTC	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010tdp.1_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	29048623	29048624	+	Intron	DEL	AC	-	-	rs71948121		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29048623_29048624delAC	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010tdp.1_Intron|FLT1_uc001usd.2_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	29308665	29308665	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29308665delA								SLC46A3 (15515 upstream) : MTUS2 (290083 downstream)																																			---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29778098	29778098	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29778098delT	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29964789	29964791	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29964789_29964791delAAA	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30866505	30866506	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30866505_30866506delTT	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402			katanin p60 subunit A-like 1							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
ALOX5AP	241	broad.mit.edu	37	13	31293981	31293981	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31293981delT	uc010tdr.1	+							NM_001629	NP_001620			arachidonate 5-lipoxygenase-activating protein						cellular response to calcium ion|leukotriene biosynthetic process|leukotriene production involved in inflammatory response|protein homotrimerization	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	arachidonic acid binding|protein N-terminus binding				0		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0187)|Epithelial(112;0.0803)|OV - Ovarian serous cystadenocarcinoma(117;0.0864)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	31591123	31591126	+	IGR	DEL	TTCT	-	-	rs66956577		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31591123_31591126delTTCT								C13orf26 (41972 upstream) : HSPH1 (119639 downstream)																																			---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32940963	32940963	+	Intron	DEL	A	-	-	rs112101824		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32940963delA	uc001uub.1	+							NM_000059	NP_000050			breast cancer 2, early onset						cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33054049	33054050	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33054049_33054050delGA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34820997	34820997	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34820997delA								RFC3 (280303 upstream) : NBEA (695459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34833357	34833357	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34833357delC								RFC3 (292663 upstream) : NBEA (683099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35047259	35047260	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35047259_35047260delTT								RFC3 (506565 upstream) : NBEA (469196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35169714	35169715	+	IGR	INS	-	GT	GT	rs148552978	by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35169714_35169715insGT								RFC3 (629020 upstream) : NBEA (346741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	36730591	36730592	+	IGR	INS	-	GA	GA	rs143230375	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36730591_36730592insGA								DCLK1 (25127 upstream) : SOHLH2 (11755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37161955	37161956	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37161955_37161956insT								CCNA1 (144937 upstream) : C13orf36 (86093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37180994	37180995	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37180994_37180995delTT								CCNA1 (163976 upstream) : C13orf36 (67054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37730126	37730126	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37730126delT								CSNK1A1L (50325 upstream) : POSTN (406594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38901953	38901954	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38901953_38901954delTC								TRPC4 (458014 upstream) : UFM1 (21988 downstream)																																			---	---	---	---
COG6	57511	broad.mit.edu	37	13	40268934	40268934	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40268934delT	uc001uxh.2	+						COG6_uc001uxi.2_Intron|COG6_uc010acb.2_Intron	NM_020751	NP_065802			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	40544246	40544247	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40544246_40544247delAT								COG6 (178444 upstream) : LOC646982 (377026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	40798133	40798136	+	IGR	DEL	GCGC	-	-	rs143138731	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40798133_40798136delGCGC								COG6 (432331 upstream) : LOC646982 (123137 downstream)																																			---	---	---	---
LOC646982	646982	broad.mit.edu	37	13	41032621	41032622	+	Intron	DEL	CA	-	-	rs72171511		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41032621_41032622delCA	uc010tfa.1	-						LOC646982_uc001uxj.3_Intron|LOC646982_uc001uxk.2_RNA	NR_024507				Homo sapiens cDNA, FLJ17553.												0																		---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41162944	41162945	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41162944_41162945delAA	uc001uxl.3	-						FOXO1_uc010acc.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41776236	41776236	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41776236delT	uc001uxv.1	+											Homo sapiens cDNA FLJ31620 fis, clone NT2RI2003184.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41864535	41864535	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41864535delT								MTRF1 (26793 upstream) : NAA16 (20806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	42118866	42118873	+	IGR	DEL	ACACACAC	-	-	rs149381373		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42118866_42118873delACACACAC								C13orf15 (73853 upstream) : KIAA0564 (22089 downstream)																																			---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42432748	42432748	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42432748delA	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	42545255	42545255	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42545255delT								KIAA0564 (10034 upstream) : DGKH (68917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	43271650	43271651	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43271650_43271651delTG								TNFSF11 (89501 upstream) : C13orf30 (84035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	43317779	43317780	+	IGR	INS	-	G	G	rs139427598	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43317779_43317780insG								TNFSF11 (135630 upstream) : C13orf30 (37906 downstream)																																			---	---	---	---
EPSTI1	94240	broad.mit.edu	37	13	43538282	43538282	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43538282delA	uc001uyw.1	-						EPSTI1_uc001uyx.1_Intron	NM_001002264	NP_001002264			epithelial stromal interaction 1 isoform 1											ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)														---	---	---	---
SERP2	387923	broad.mit.edu	37	13	44956245	44956245	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44956245delT	uc001uzj.2	+						SERP2_uc001uzk.2_Intron	NM_001010897	NP_001010897			stress-associated endoplasmic reticulum protein						protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane					0		all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123)														---	---	---	---
SIAH3	283514	broad.mit.edu	37	13	46365302	46365302	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46365302delA	uc001vap.2	-							NM_198849	NP_942146			seven in absentia homolog 3						multicellular organismal development|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	46438728	46438730	+	IGR	DEL	CTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46438728_46438730delCTC								SIAH3 (12882 upstream) : ZC3H13 (91075 downstream)																																			---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47219241	47219241	+	Intron	DEL	G	-	-	rs35014736		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47219241delG	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	47854547	47854547	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47854547delT								HTR2A (383497 upstream) : SUCLA2 (662245 downstream)																																			---	---	---	---
CYSLTR2	57105	broad.mit.edu	37	13	49253373	49253373	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49253373delA	uc010acx.1	+						CYSLTR2_uc010acy.1_Intron|CYSLTR2_uc010acz.1_Intron|CYSLTR2_uc010ada.1_Intron|CYSLTR2_uc010adb.1_Intron|CYSLTR2_uc010adc.1_Intron|CYSLTR2_uc010add.1_Intron|CYSLTR2_uc010acw.1_Intron	NM_020377	NP_065110			cysteinyl leukotriene receptor 2						immune response	integral to membrane|plasma membrane				lung(2)	2		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)													---	---	---	---
KPNA3	3839	broad.mit.edu	37	13	50296564	50296565	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50296564_50296565insA	uc001vdj.2	-							NM_002267	NP_002258			karyopherin alpha 3						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|protein complex assembly	cytoplasm|nuclear pore	nuclear localization sequence binding|protein transporter activity				0		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	50377401	50377402	+	IGR	INS	-	TT	TT	rs145147206		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50377401_50377402insTT								KPNA3 (10344 upstream) : LOC220429 (87143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	50393726	50393727	+	IGR	INS	-	T	T	rs144608950		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50393726_50393727insT								KPNA3 (26669 upstream) : LOC220429 (70818 downstream)																																			---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50662798	50662798	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50662798delT	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron|DLEU1_uc010adl.1_Intron|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|DLEU1_uc001vec.2_Intron|DLEU1_uc001ved.2_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50957092	50957093	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50957092_50957093delTT	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	52888659	52888659	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52888659delT								THSD1P1 (22979 upstream) : THSD1 (62646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53503340	53503341	+	IGR	DEL	AG	-	-	rs35026121		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53503340_53503341delAG								PCDH8 (80566 upstream) : OLFM4 (99631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54624440	54624441	+	IGR	DEL	AA	-	-	rs113548912		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54624440_54624441delAA								OLFM4 (998254 upstream) : MIR1297 (261666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55298784	55298784	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55298784delT								MIR1297 (412601 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56213128	56213128	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56213128delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56250522	56250522	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56250522delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57378163	57378163	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57378163delC								None (None upstream) : PRR20C (336889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57438158	57438158	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57438158delT								None (None upstream) : PRR20C (276894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58468529	58468529	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58468529delT								PCDH17 (165464 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59441832	59441832	+	IGR	DEL	A	-	-	rs76639871		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59441832delA								None (None upstream) : DIAPH3 (797893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60201530	60201530	+	IGR	DEL	A	-	-	rs79155239		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60201530delA								None (None upstream) : DIAPH3 (38195 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60301435	60301436	+	Intron	INS	-	C	C	rs342585	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60301435_60301436insC	uc001vht.2	-						DIAPH3_uc001vhs.2_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	61296505	61296506	+	IGR	DEL	GC	-	-	rs142779823	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61296505_61296506delGC								TDRD3 (148493 upstream) : PCDH20 (687315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61625181	61625181	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61625181delA								TDRD3 (477169 upstream) : PCDH20 (358640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61684660	61684660	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61684660delC								TDRD3 (536648 upstream) : PCDH20 (299161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61864266	61864266	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61864266delT								TDRD3 (716254 upstream) : PCDH20 (119555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62602501	62602501	+	IGR	DEL	A	-	-	rs113780503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62602501delA								PCDH20 (600422 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63407804	63407804	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63407804delT								None (None upstream) : OR7E156P (903764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63432038	63432038	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63432038delC								None (None upstream) : OR7E156P (879530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65083824	65083827	+	IGR	DEL	TTTG	-	-	rs72208063		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65083824_65083827delTTTG								OR7E156P (767123 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65779846	65779846	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65779846delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65986915	65986915	+	IGR	DEL	T	-	-	rs78222131		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65986915delT								None (None upstream) : PCDH9 (890052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66201857	66201858	+	IGR	INS	-	TG	TG	rs139924335	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66201857_66201858insTG								None (None upstream) : PCDH9 (675109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66422454	66422454	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66422454delA								None (None upstream) : PCDH9 (454513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66500774	66500774	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66500774delA								None (None upstream) : PCDH9 (376193 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67072572	67072572	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67072572delA	uc001vik.2	-						PCDH9_uc010aei.2_Intron|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)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67633891	67633891	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67633891delA	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	67914740	67914740	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67914740delT								PCDH9 (110272 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68232565	68232566	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68232565_68232566insA								PCDH9 (428097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68387623	68387625	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68387623_68387625delTTT								PCDH9 (583155 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69566297	69566297	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69566297delT								None (None upstream) : KLHL1 (708429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69723536	69723536	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69723536delT								None (None upstream) : KLHL1 (551190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71041374	71041375	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71041374_71041375insT								ATXN8OS (327489 upstream) : DACH1 (970723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71348261	71348264	+	IGR	DEL	CACA	-	-	rs36011852		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71348261_71348264delCACA								ATXN8OS (634376 upstream) : DACH1 (663834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	72823304	72823305	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72823304_72823305delGT								DACH1 (381974 upstream) : C13orf37 (459190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73687798	73687798	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73687798delA								KLF5 (36123 upstream) : KLF12 (572352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75160350	75160350	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75160350delT								KLF12 (451956 upstream) : LOC647288 (651540 downstream)																																			---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76112127	76112127	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76112127delA	uc001vjo.1	-						COMMD6_uc001vjn.1_5'Flank|COMMD6_uc010aet.1_5'Flank|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76634871	76634871	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76634871delA								LMO7 (200867 upstream) : KCTD12 (819433 downstream)																																			---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77700784	77700784	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77700784delA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron|MYCBP2_uc001vkg.1_5'Flank	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	77728552	77728552	+	Intron	DEL	A	-	-	rs144699563	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77728552delA	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	82226028	82226028	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82226028delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82368465	82368465	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82368465delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82626206	82626206	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82626206delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82903914	82903914	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82903914delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83142187	83142190	+	IGR	DEL	AAAA	-	-	rs77217172		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83142187_83142190delAAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83420933	83420934	+	IGR	INS	-	AGGA	AGGA	rs146884357	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83420933_83420934insAGGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83786220	83786221	+	IGR	INS	-	A	A	rs143426611	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83786220_83786221insA								None (None upstream) : SLITRK1 (665123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85836369	85836369	+	IGR	DEL	T	-	-	rs11368164		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85836369delT								None (None upstream) : SLITRK6 (530553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86020939	86020940	+	IGR	DEL	AC	-	-	rs10537458		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86020939_86020940delAC								None (None upstream) : SLITRK6 (345982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86400184	86400184	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86400184delA								SLITRK6 (26701 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86593146	86593146	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86593146delT								SLITRK6 (219663 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86649474	86649475	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86649474_86649475insT								SLITRK6 (275991 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87863040	87863041	+	IGR	INS	-	TCC	TCC	rs144228386	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87863040_87863041insTCC								None (None upstream) : SLITRK5 (461829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88183962	88183963	+	Intron	INS	-	A	A	rs34082274		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88183962_88183963insA	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88349243	88349244	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88349243_88349244delTG								SLITRK5 (17375 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89000326	89000327	+	IGR	INS	-	GAAG	GAAG	rs141385241	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89000326_89000327insGAAG								SLITRK5 (668458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89024190	89024191	+	IGR	INS	-	T	T	rs142954058		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89024190_89024191insT								SLITRK5 (692322 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89747030	89747030	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89747030delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90075741	90075741	+	IGR	DEL	T	-	-	rs36076298		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90075741delT								None (None upstream) : MIR622 (807695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90200114	90200114	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90200114delT								None (None upstream) : MIR622 (683322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91765960	91765960	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91765960delA								LOC144776 (187109 upstream) : MIR17HG (234114 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92826792	92826793	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92826792_92826793delAA	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)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	93977184	93977184	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93977184delT	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)																---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95809343	95809344	+	Intron	DEL	CA	-	-	rs142921361		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95809343_95809344delCA	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.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)													---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96621101	96621102	+	Intron	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96621101_96621102insGT	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																		---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97052567	97052568	+	Intron	INS	-	CG	CG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97052567_97052568insCG	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	97865568	97865568	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97865568delA								OXGR1 (218964 upstream) : MBNL2 (9006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98516419	98516419	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98516419delT								RAP2A (396168 upstream) : IPO5 (89510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98555837	98555838	+	IGR	DEL	TT	-	-	rs34083349		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98555837_98555838delTT								RAP2A (435586 upstream) : IPO5 (50091 downstream)																																			---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98910952	98910952	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98910952delA	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	99265075	99265078	+	IGR	DEL	TCTT	-	-	rs7320452		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99265075_99265078delTCTT								STK24 (35679 upstream) : SLC15A1 (70979 downstream)																																			---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	100027775	100027775	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100027775delG	uc001voa.3	+						UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron|UBAC2_uc001voh.2_Intron	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100977796	100977796	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100977796delA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100986352	100986354	+	Intron	DEL	AAC	-	-	rs75614130	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100986352_100986354delAAC	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	101598500	101598501	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101598500_101598501delAG								TMTC4 (271397 upstream) : NALCN (107629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101626667	101626667	+	IGR	DEL	T	-	-	rs72132261		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101626667delT								TMTC4 (299564 upstream) : NALCN (79463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101702246	101702246	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101702246delT								TMTC4 (375143 upstream) : NALCN (3884 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101781082	101781083	+	Intron	DEL	TT	-	-	rs71761907		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101781082_101781083delTT	uc001vox.1	-							NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102475291	102475291	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102475291delT	uc001vpe.2	-						FGF14_uc001vpf.2_Intron	NM_004115	NP_004106			fibroblast growth factor 14 isoform 1A						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	104357273	104357274	+	IGR	INS	-	T	T	rs112906506		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104357273_104357274insT								SLC10A2 (638077 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104369957	104369957	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104369957delA								SLC10A2 (650761 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106148111	106148114	+	IGR	DEL	CTTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106148111_106148114delCTTC								DAOA (4729 upstream) : EFNB2 (993984 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107893400	107893408	+	Intron	DEL	AAAAAAAAA	-	-	rs71713381		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107893400_107893408delAAAAAAAAA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109416135	109416136	+	Intron	INS	-	TG	TG	rs150965677	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109416135_109416136insTG	uc001vqt.1	+						MYO16_uc010agk.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109517046	109517046	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109517046delA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	110050086	110050087	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110050086_110050087insT								MYO16 (189731 upstream) : IRS2 (356099 downstream)																																			---	---	---	---
IRS2	8660	broad.mit.edu	37	13	110440824	110440824	+	5'Flank	DEL	A	-	-	rs11302101		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110440824delA	uc001vqv.2	-							NM_003749	NP_003740			insulin receptor substrate 2						fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|skin(1)|ovary(1)|kidney(1)	8	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	110665067	110665068	+	IGR	INS	-	ACT	ACT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110665067_110665068insACT								IRS2 (226153 upstream) : COL4A1 (136243 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110834981	110834981	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110834981delC	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)															---	---	---	---
CARKD	55739	broad.mit.edu	37	13	111288722	111288723	+	Intron	INS	-	CTT	CTT	rs146902351	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111288722_111288723insCTT	uc001vrb.2	+						CARKD_uc010tjj.1_Intron|CARKD_uc001vqz.2_Intron|CARKD_uc001vra.2_Intron|CARKD_uc010tjk.1_Intron|CARKD_uc010tjl.1_Intron|CARKD_uc001vrc.2_Intron					RecName: Full=Carbohydrate kinase domain-containing protein; Flags: Precursor;											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	111726766	111726766	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111726766delT								ANKRD10 (159350 upstream) : ARHGEF7 (40858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112049685	112049685	+	IGR	DEL	C	-	-	rs35031419		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112049685delC								C13orf16 (53092 upstream) : SOX1 (672228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	112197650	112197651	+	IGR	INS	-	T	T	rs141008703	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112197650_112197651insT								C13orf16 (201057 upstream) : SOX1 (524262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	113272703	113272704	+	IGR	INS	-	TCACAG	TCACAG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113272703_113272704insTCACAG								TUBGCP3 (30222 upstream) : C13orf35 (28654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	113924502	113924502	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113924502delT								CUL4A (5111 upstream) : LAMP1 (26967 downstream)																																			---	---	---	---
DCUN1D2	55208	broad.mit.edu	37	13	114123460	114123461	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114123460_114123461delCA	uc001vtr.1	-						DCUN1D2_uc001vts.1_Intron|DCUN1D2_uc010agw.1_Intron	NM_001014283	NP_001014305			DCN1, defective in cullin neddylation 1, domain												0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19404337	19404338	+	IGR	INS	-	AC	AC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19404337_19404338insAC								OR11H12 (25765 upstream) : POTEG (149027 downstream)																																			---	---	---	---
ANG	283	broad.mit.edu	37	14	21149361	21149361	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21149361delA	uc001vxw.3	+						RNASE4_uc001vxx.3_5'Flank	NM_001145	NP_001136			angiogenin, ribonuclease, RNase A family, 5						actin filament polymerization|activation of phospholipase A2 activity|activation of phospholipase C activity|activation of protein kinase B activity|angiogenesis|cell communication|cell death|cell migration|diacylglycerol biosynthetic process|homeostatic process|negative regulation of smooth muscle cell proliferation|negative regulation of translation|oocyte maturation|ovarian follicle development|placenta development|positive regulation of endothelial cell proliferation|positive regulation of phosphorylation|positive regulation of protein secretion|response to hormone stimulus|response to hypoxia|rRNA transcription	angiogenin-PRI complex|basal lamina|extracellular space|growth cone|neuronal cell body|nucleolus	actin binding|copper ion binding|heparin binding|pancreatic ribonuclease activity|peptide binding|receptor binding|rRNA binding			ovary(1)	1	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)														---	---	---	---
ANG	283	broad.mit.edu	37	14	21157252	21157252	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21157252delA	uc001vxw.3	+						RNASE4_uc001vxx.3_Intron|RNASE4_uc001vxy.3_Intron|ANG_uc001vxz.2_Intron|RNASE4_uc001vya.2_Intron	NM_001145	NP_001136			angiogenin, ribonuclease, RNase A family, 5						actin filament polymerization|activation of phospholipase A2 activity|activation of phospholipase C activity|activation of protein kinase B activity|angiogenesis|cell communication|cell death|cell migration|diacylglycerol biosynthetic process|homeostatic process|negative regulation of smooth muscle cell proliferation|negative regulation of translation|oocyte maturation|ovarian follicle development|placenta development|positive regulation of endothelial cell proliferation|positive regulation of phosphorylation|positive regulation of protein secretion|response to hormone stimulus|response to hypoxia|rRNA transcription	angiogenin-PRI complex|basal lamina|extracellular space|growth cone|neuronal cell body|nucleolus	actin binding|copper ion binding|heparin binding|pancreatic ribonuclease activity|peptide binding|receptor binding|rRNA binding			ovary(1)	1	all_cancers(95;0.00387)	all_cancers(140;0.196)|all_epithelial(140;0.156)	Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	OV - Ovarian serous cystadenocarcinoma(311;3.25e-17)|GBM - Glioblastoma multiforme(265;5.56e-07)														---	---	---	---
METT11D1	64745	broad.mit.edu	37	14	21461941	21461941	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21461941delT	uc001vyn.2	+						METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571			methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	21918845	21918845	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21918845delA								CHD8 (13441 upstream) : RAB2B (8335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22152206	22152208	+	IGR	DEL	TTT	-	-	rs71933448		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22152206_22152208delTTT								OR4E2 (17970 upstream) : DAD1 (881599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23211218	23211225	+	IGR	DEL	AGAAAGAG	-	-	rs72167420	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23211218_23211225delAGAAAGAG								ABHD4 (129961 upstream) : OXA1L (24506 downstream)																																			---	---	---	---
LRP10	26020	broad.mit.edu	37	14	23339788	23339788	+	5'Flank	DEL	A	-	-	rs78548411		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23339788delA	uc001whd.2	+							NM_014045	NP_054764			low density lipoprotein receptor-related protein						endocytosis	coated pit|integral to membrane				central_nervous_system(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)														---	---	---	---
PSMB5	5693	broad.mit.edu	37	14	23502434	23502434	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23502434delA	uc001wii.2	-						PSMB5_uc001wij.2_Intron|PSMB5_uc010tni.1_Intron	NM_002797	NP_002788			proteasome beta 5 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|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	protein binding|threonine-type endopeptidase activity			ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	25051909	25051910	+	IGR	INS	-	TG	TG	rs140297788	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25051909_25051910insTG								CTSG (6443 upstream) : GZMH (23783 downstream)																																			---	---	---	---
STXBP6	29091	broad.mit.edu	37	14	25418273	25418273	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25418273delA	uc001wpu.2	-						STXBP6_uc001wpv.2_Intron|STXBP6_uc001wpw.2_Intron|STXBP6_uc001wpx.1_Intron	NM_014178	NP_054897			amisyn						vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)														---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30069561	30069561	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30069561delA	uc001wqh.2	-							NM_002742	NP_002733			protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	30851899	30851899	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30851899delT								PRKD1 (455000 upstream) : G2E3 (176430 downstream)																																			---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31112379	31112379	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31112379delA	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010amd.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)														---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31175238	31175238	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31175238delT	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010amd.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	31256254	31256257	+	IGR	DEL	AAAC	-	-	rs111770450		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31256254_31256257delAAAC								SCFD1 (51236 upstream) : COCH (87484 downstream)																																			---	---	---	---
AP4S1	11154	broad.mit.edu	37	14	31496343	31496343	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31496343delT	uc001wqy.3	+						STRN3_uc001wqu.2_5'Flank|STRN3_uc001wqv.2_5'Flank|STRN3_uc010tpj.1_5'Flank|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)														---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32236913	32236914	+	Intron	INS	-	T	T	rs150860389	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32236913_32236914insT	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428			nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	32998571	32998571	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32998571delT	uc001wrq.2	+						AKAP6_uc010aml.2_Intron	NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33804243	33804244	+	Intron	INS	-	GC	GC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33804243_33804244insGC	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)														---	---	---	---
PPP2R3C	55012	broad.mit.edu	37	14	35564160	35564160	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35564160delA	uc001wss.2	-						PPP2R3C_uc001wst.2_Intron|PPP2R3C_uc010tpr.1_Intron|PPP2R3C_uc001wsu.2_Intron	NM_017917	NP_060387			serine/threonine-protein phosphatase 2A							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)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35641697	35641704	+	Intron	DEL	CCTCTCTC	-	-	rs71435864		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35641697_35641704delCCTCTCTC	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35649732	35649733	+	Intron	INS	-	TGTG	TGTG	rs140304917	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35649732_35649733insTGTG	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35934754	35934754	+	IGR	DEL	G	-	-	rs35730330		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35934754delG								NFKBIA (60794 upstream) : INSM2 (68494 downstream)																																			---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36123832	36123832	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36123832delA	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	36937525	36937525	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36937525delC								MBIP (147643 upstream) : SFTA3 (4971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40234543	40234543	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40234543delT								FBXO33 (332839 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41121764	41121764	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41121764delT								None (None upstream) : LRFN5 (955000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41161248	41161248	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41161248delT								None (None upstream) : LRFN5 (915516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44007714	44007714	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44007714delT								None (None upstream) : FSCB (965641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44075610	44075611	+	IGR	INS	-	T	T	rs147259046	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44075610_44075611insT								None (None upstream) : FSCB (897744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44468573	44468573	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44468573delA								None (None upstream) : FSCB (504782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45051558	45051558	+	IGR	DEL	A	-	-	rs62069593		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45051558delA								FSCB (75059 upstream) : C14orf28 (314949 downstream)																																			---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45407581	45407581	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45407581delT	uc001wvq.2	-						KLHL28_uc001wvr.2_Intron	NM_017658	NP_060128			BTB (POZ) domain containing 5											ovary(1)	1																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45541627	45541627	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45541627delT	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FKBP3	2287	broad.mit.edu	37	14	45588773	45588773	+	Intron	DEL	A	-	-	rs78439113		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45588773delA	uc010tqf.1	-							NM_002013	NP_002004			FK506 binding protein 3, 25kDa						protein folding	membrane|nucleus	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	46200520	46200520	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46200520delT								C14orf106 (477915 upstream) : RPL10L (919702 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47657121	47657122	+	Intron	DEL	TG	-	-	rs111509070		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47657121_47657122delTG	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970			MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	48505937	48505938	+	IGR	DEL	TT	-	-	rs75202332		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48505937_48505938delTT								MDGA2 (361949 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48651105	48651107	+	IGR	DEL	AGG	-	-	rs34406477		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48651105_48651107delAGG								MDGA2 (507117 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	48997983	48997983	+	IGR	DEL	T	-	-	rs142634506	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:48997983delT								MDGA2 (853995 upstream) : None (None downstream)																																			---	---	---	---
ATL1	51062	broad.mit.edu	37	14	51075197	51075198	+	Intron	INS	-	T	T	rs149684351	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51075197_51075198insT	uc001wyf.3	+						ATL1_uc001wyd.3_Intron|ATL1_uc001wye.3_Intron	NM_015915	NP_056999			atlastin GTPase 1 isoform a						axonogenesis|cell death|endoplasmic reticulum organization|protein homooligomerization	axon|endoplasmic reticulum membrane|Golgi cis cisterna|Golgi membrane|integral to membrane|microsome	GTP binding|GTPase activity|identical protein binding			skin(3)|central_nervous_system(1)	4																		---	---	---	---
SAV1	60485	broad.mit.edu	37	14	51117741	51117741	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51117741delA	uc001wyg.1	-						SAV1_uc001wyh.1_Intron	NM_021818	NP_068590			WW45 protein						hippo signaling cascade	cytoplasm|nucleus	identical protein binding			breast(1)	1	all_epithelial(31;0.000611)|Breast(41;0.0333)																	---	---	---	---
TRIM9	114088	broad.mit.edu	37	14	51532771	51532778	+	Intron	DEL	GAAGGAAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51532771_51532778delGAAGGAAG	uc001wyx.3	-						TRIM9_uc001wyy.2_Intron|TRIM9_uc001wyz.3_Intron	NM_015163	NP_055978			tripartite motif protein 9 isoform 1						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)																	---	---	---	---
TMX1	81542	broad.mit.edu	37	14	51706761	51706787	+	5'Flank	DEL	TCCTTCCCCCACAATATTGGGACACCC	-	-	rs28372741		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51706761_51706787delTCCTTCCCCCACAATATTGGGACACCC	uc001wza.3	+						TMX1_uc010tqr.1_5'Flank|TMX1_uc010aoa.2_5'Flank	NM_030755	NP_110382			thioredoxin domain containing 1 precursor						anti-apoptosis|cell proliferation|cell redox homeostasis|DNA replication|electron transport chain|ER to Golgi vesicle-mediated transport|leukocyte activation|positive regulation of growth|positive regulation of transcription, DNA-dependent|response to stress|signal transduction	endoplasmic reticulum membrane|integral to membrane|membrane fraction	arsenate reductase (thioredoxin) activity|disulfide oxidoreductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	51785761	51785762	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51785761_51785762delGT								TMX1 (61391 upstream) : FRMD6 (170093 downstream)																																			---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52030388	52030388	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52030388delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53935018	53935018	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53935018delT								DDHD1 (314972 upstream) : BMP4 (481439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54204250	54204251	+	IGR	INS	-	AG	AG	rs151107564	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54204250_54204251insAG								DDHD1 (584204 upstream) : BMP4 (212206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54454665	54454665	+	IGR	DEL	T	-	-	rs72061336		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54454665delT								BMP4 (31111 upstream) : CDKN3 (409008 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55227708	55227717	+	Intron	DEL	TGAAAGTGTT	-	-	rs33955557		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55227708_55227717delTGAAAGTGTT	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron|SAMD4A_uc001xbg.2_Intron	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
FBXO34	55030	broad.mit.edu	37	14	55770381	55770381	+	Intron	DEL	A	-	-	rs74502136		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55770381delA	uc001xbu.2	+						FBXO34_uc010aoo.2_Intron	NM_017943	NP_060413			F-box only protein 34											ovary(2)|lung(2)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	56296324	56296324	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56296324delT								C14orf34 (32932 upstream) : PELI2 (288769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56363953	56363954	+	IGR	INS	-	TG	TG	rs139210305	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56363953_56363954insTG								C14orf34 (100561 upstream) : PELI2 (221139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	58179013	58179014	+	IGR	INS	-	T	T	rs148947464	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58179013_58179014insT								SLC35F4 (115398 upstream) : C14orf37 (291795 downstream)																																			---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58911811	58911811	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58911811delA	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron|KIAA0586_uc010tru.1_Intron	NM_014749	NP_055564			talpid3 protein											ovary(1)	1																		---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60337772	60337772	+	5'Flank	DEL	A	-	-	rs35625104		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60337772delA	uc001xen.1	-							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)														---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60635821	60635821	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60635821delA	uc001xeq.2	+	10					DHRS7_uc001xet.2_Intron	NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	61168493	61168493	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61168493delT								SIX1 (52338 upstream) : SIX4 (7763 downstream)																																			---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61339588	61339589	+	Intron	DEL	AT	-	-	rs34701641		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61339588_61339589delAT	uc001xfd.2	+						MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
TRMT5	57570	broad.mit.edu	37	14	61443754	61443754	+	Intron	DEL	A	-	-	rs2296925	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61443754delA	uc001xff.3	-							NM_020810	NP_065861			tRNA methyltransferase 5							cytoplasm	tRNA (guanine-N1-)-methyltransferase activity			central_nervous_system(2)|large_intestine(1)	3				OV - Ovarian serous cystadenocarcinoma(108;0.0873)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61969720	61969727	+	Intron	DEL	TTTTTTTT	-	-	rs34050696		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61969720_61969727delTTTTTTTT	uc001xfn.2	+						PRKCH_uc010tsa.1_Intron|PRKCH_uc010tsb.1_Intron	NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62298445	62298445	+	IGR	DEL	T	-	-	rs77981820		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62298445delT								SNAPC1 (35300 upstream) : SYT16 (155358 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63277796	63277796	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63277796delA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63930215	63930215	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63930215delA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						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)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63966447	63966448	+	Intron	DEL	AA	-	-	rs71869605		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63966447_63966448delAA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						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)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	64003954	64003955	+	Intron	INS	-	A	A	rs11435884		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64003954_64003955insA	uc001xgd.1	-						PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						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)														---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64923994	64923994	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64923994delT	uc001xhb.2	+						MTHFD1_uc010aqf.2_Intron|ZBTB25_uc001xhc.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	65369666	65369671	+	IGR	DEL	ACACAT	-	-	rs59695685		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65369666_65369671delACACAT								SPTB (23065 upstream) : CHURC1 (11469 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66157348	66157349	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66157348_66157349delTC	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron|FUT8_uc001xis.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	66284367	66284368	+	IGR	DEL	AC	-	-	rs150233495		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66284367_66284368delAC								FUT8 (74406 upstream) : C14orf53 (668741 downstream)																																			---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67136322	67136322	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67136322delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.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								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67242648	67242648	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67242648delA	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.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								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67514046	67514051	+	Intron	DEL	TGTGTT	-	-	rs113754647		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67514046_67514051delTGTGTT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|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								---	---	---	---
RDH12	145226	broad.mit.edu	37	14	68199254	68199255	+	Intron	DEL	AA	-	-	rs146899432		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68199254_68199255delAA	uc001xjz.3	+							NM_152443	NP_689656			retinol dehydrogenase 12						photoreceptor cell maintenance|response to stimulus|retinol metabolic process	intracellular	binding|retinol dehydrogenase activity			ovary(1)	1				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)													---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68397059	68397060	+	Intron	DEL	TT	-	-	rs6573800	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68397059_68397060delTT	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					---	---	---	---
Unknown	0	broad.mit.edu	37	14	69323722	69323722	+	IGR	DEL	A	-	-	rs113748789		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69323722delA								C14orf181 (60532 upstream) : ACTN1 (17119 downstream)																																			---	---	---	---
SFRS5	6430	broad.mit.edu	37	14	70226016	70226016	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70226016delT	uc001xll.2	+							NM_006925	NP_008856			splicing factor, arginine/serine-rich 5						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding				0				all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70698963	70698964	+	IGR	DEL	GA	-	-	rs75770191		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70698963_70698964delGA								SLC8A3 (43176 upstream) : ADAM21P1 (13507 downstream)																																			---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71231571	71231571	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71231571delA	uc001xmm.2	-						MAP3K9_uc010ttk.1_Intron|MAP3K9_uc001xmk.2_Intron|MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71560039	71560041	+	Intron	DEL	AAA	-	-	rs76330730		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71560039_71560041delAAA	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	73095345	73095346	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73095345_73095346delAG	uc001xnc.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74095779	74095779	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74095779delA								ACOT6 (9189 upstream) : DNAL1 (15799 downstream)																																			---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74153808	74153808	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75264231	75264231	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75264231delT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75430096	75430097	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75430096_75430097delAA								PGF (7805 upstream) : EIF2B2 (39515 downstream)																																			---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76393236	76393236	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76393236delA	uc001xrx.2	+						TTLL5_uc001xsa.2_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	76484505	76484505	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76484505delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	77505132	77505133	+	IGR	INS	-	GTGT	GTGT	rs138326479	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77505132_77505133insGTGT								C14orf4 (10098 upstream) : KIAA1737 (59445 downstream)																																			---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	77990783	77990786	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77990783_77990786delAAAA	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)													---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78637684	78637685	+	Intron	INS	-	GT	GT	rs150864901	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78637684_78637685insGT	uc001xum.1	+											Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78999084	78999084	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78999084delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79345257	79345257	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79345257delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79487205	79487206	+	Intron	INS	-	AC	AC	rs138620447	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79487205_79487206insAC	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79655883	79655884	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79655883_79655884delAA	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81172783	81172784	+	Intron	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81172783_81172784insTG	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81951796	81951799	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81951796_81951799delTTTT	uc010tvv.1	-							NM_005065	NP_005056			sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81956168	81956168	+	Intron	DEL	G	-	-	rs4903983	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81956168delG	uc010tvv.1	-							NM_005065	NP_005056			sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	82480619	82480620	+	IGR	DEL	TG	-	-	rs113078191		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82480619_82480620delTG								SEL1L (480414 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82535701	82535702	+	IGR	INS	-	TCCC	TCCC	rs28394171		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82535701_82535702insTCCC								SEL1L (535496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82735551	82735551	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82735551delT								SEL1L (735346 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83392566	83392567	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83392566_83392567delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84129004	84129004	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84129004delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84222267	84222267	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84222267delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84238352	84238352	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84238352delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84286581	84286581	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84286581delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85281016	85281023	+	IGR	DEL	CCTCCCTC	-	-	rs76839618		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85281016_85281023delCCTCCCTC								None (None upstream) : FLRT2 (715465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85303849	85303850	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85303849_85303850insA								None (None upstream) : FLRT2 (692638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85804318	85804321	+	IGR	DEL	AAAA	-	-	rs76610624		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85804318_85804321delAAAA								None (None upstream) : FLRT2 (192167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86612610	86612617	+	IGR	DEL	TAGATGGA	-	-	rs72463703	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86612610_86612617delTAGATGGA								FLRT2 (518341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86673651	86673651	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86673651delC								FLRT2 (579382 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86753396	86753400	+	IGR	DEL	GGAAG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86753396_86753400delGGAAG								FLRT2 (659127 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87574411	87574412	+	IGR	INS	-	T	T	rs137866931	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87574411_87574412insT								None (None upstream) : GALC (729752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87620305	87620305	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87620305delC								None (None upstream) : GALC (683859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87749124	87749124	+	IGR	DEL	A	-	-	rs35864426		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87749124delA								None (None upstream) : GALC (555040 downstream)																																			---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89728452	89728452	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89728452delA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|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|protein C-terminus 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(2)|ovary(1)	3																		---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89823043	89823046	+	Intron	DEL	CATT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89823043_89823046delCATT	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|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|protein C-terminus 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(2)|ovary(1)	3																		---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91164595	91164595	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91164595delA	uc001xyp.2	-						uc001xyr.1_RNA	NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)														OREG0022866	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	14	91319828	91319828	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91319828delA								TTC7B (37067 upstream) : RPS6KA5 (17339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	91331398	91331398	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91331398delT								TTC7B (48637 upstream) : RPS6KA5 (5769 downstream)																																			---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91600785	91600785	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91600785delT	uc001xzb.2	+						C14orf159_uc010atu.1_Intron|C14orf159_uc010atv.1_Intron|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_uc010twj.1_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)														---	---	---	---
GPR68	8111	broad.mit.edu	37	14	91710563	91710570	+	Intron	DEL	ACACACAC	-	-	rs138684591		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91710563_91710570delACACACAC	uc001xzg.2	-						GPR68_uc001xzh.2_Intron	NM_003485	NP_003476			G protein-coupled receptor 68						inflammatory response	integral to plasma membrane	G-protein coupled receptor activity			kidney(1)	1		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)														---	---	---	---
CATSPERB	79820	broad.mit.edu	37	14	92078404	92078411	+	Intron	DEL	CTTTCTTC	-	-	rs72515246		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92078404_92078411delCTTTCTTC	uc001xzs.1	-						CATSPERB_uc010aub.1_Intron	NM_024764	NP_079040			cation channel, sperm-associated, beta						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				breast(2)|skin(2)|ovary(1)	5		all_cancers(154;0.0663)|all_epithelial(191;0.236)																---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92258906	92258906	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92258906delA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067			tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92347467	92347468	+	Intron	INS	-	CC	CC	rs113395651		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92347467_92347468insCC	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320			fibulin 5 precursor						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)																---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92359451	92359451	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92359451delA	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320			fibulin 5 precursor						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)														OREG0022874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92439370	92439373	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92439370_92439373delTTTT	uc001xzy.2	-						TRIP11_uc010auf.1_Intron	NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
SLC24A4	123041	broad.mit.edu	37	14	92954419	92954419	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92954419delT	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron|SLC24A4_uc010auj.2_Intron|SLC24A4_uc010twn.1_Intron|SLC24A4_uc001yan.2_Intron	NM_153646	NP_705932			solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	93368699	93368700	+	IGR	INS	-	TCTTCCTTCTCCTCCTCCTCC	TCTTCCTTCTCCTCCTCCTCC	rs146897982	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93368699_93368700insTCTTCCTTCTCCTCCTCCTCC								GOLGA5 (62395 upstream) : CHGA (20745 downstream)																																			---	---	---	---
CHGA	1113	broad.mit.edu	37	14	93387662	93387663	+	5'Flank	INS	-	CTCT	CTCT	rs145378031	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
ITPK1	3705	broad.mit.edu	37	14	93450166	93450167	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93450166_93450167delAA	uc001ybg.2	-						ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Intron|ITPK1_uc001ybh.2_Intron	NM_014216	NP_055031			inositol 1,3,4-triphosphate 5/6 kinase isoform						blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	94183111	94183111	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94183111delC								KIAA1409 (9422 upstream) : PRIMA1 (1533 downstream)																																			---	---	---	---
ASB2	51676	broad.mit.edu	37	14	94422870	94422871	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94422870_94422871insT	uc001ycc.1	-						ASB2_uc001ycd.2_Intron|ASB2_uc001yce.1_5'Flank	NM_016150	NP_057234			ankyrin repeat and SOCS box-containing protein						intracellular signal transduction					ovary(1)|pancreas(1)	2		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95983573	95983585	+	IGR	DEL	CCCACAGTCCGGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95983573_95983585delCCCACAGTCCGGG								C14orf49 (41400 upstream) : SNHG10 (15668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96344890	96344891	+	Intron	INS	-	TA	TA	rs138101563	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96344890_96344891insTA	uc001yfe.2	+											Homo sapiens cDNA FLJ12965 fis, clone NT2RP2005741.																														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96752443	96752443	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96752443delA	uc001yfi.2	-							NM_018036	NP_060506			ATG2 autophagy related 2 homolog B											ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97776409	97776409	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97776409delT								VRK1 (428459 upstream) : C14orf64 (615538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	97980586	97980593	+	IGR	DEL	TTCCTTTT	-	-	rs71883285	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97980586_97980593delTTCCTTTT								VRK1 (632636 upstream) : C14orf64 (411354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99302974	99302975	+	IGR	DEL	CA	-	-	rs111264056		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99302974_99302975delCA								C14orf177 (118877 upstream) : BCL11B (332652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99429704	99429706	+	IGR	DEL	GAG	-	-	rs2933338	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99429704_99429706delGAG								C14orf177 (245607 upstream) : BCL11B (205921 downstream)																																			---	---	---	---
BCL11B	64919	broad.mit.edu	37	14	99683708	99683709	+	Intron	INS	-	ACACACACATACAGACAC	ACACACACATACAGACAC	rs144037524	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99683708_99683709insACACACACATACAGACAC	uc001yga.2	-						BCL11B_uc001ygb.2_Intron	NM_138576	NP_612808			B-cell CLL/lymphoma 11B isoform 1							nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)				T	TLX3	T-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	14	99799224	99799225	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99799224_99799225delAT								BCL11B (61402 upstream) : SETD3 (64859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99800773	99800773	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99800773delT								BCL11B (62951 upstream) : SETD3 (63311 downstream)																																			---	---	---	---
CCDC85C	317762	broad.mit.edu	37	14	100044445	100044446	+	Intron	DEL	GT	-	-	rs111366848		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100044445_100044446delGT	uc010avr.2	-							NM_001144995	NP_001138467			coiled-coil domain containing 85C												0																		---	---	---	---
EVL	51466	broad.mit.edu	37	14	100492581	100492581	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100492581delA	uc001ygt.2	+						EVL_uc001ygv.2_Intron	NM_016337	NP_057421			Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)																---	---	---	---
EVL	51466	broad.mit.edu	37	14	100524992	100524992	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100524992delT	uc001ygt.2	+						EVL_uc001ygv.2_Intron	NM_016337	NP_057421			Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)																---	---	---	---
EVL	51466	broad.mit.edu	37	14	100535128	100535129	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100535128_100535129insT	uc001ygt.2	+						EVL_uc001ygv.2_Intron|EVL_uc001ygu.2_Intron|EVL_uc010avu.2_Intron	NM_016337	NP_057421			Enah/Vasp-like						actin polymerization or depolymerization|axon guidance|cell surface receptor linked signaling pathway|organ morphogenesis	cytoskeleton|cytosol|focal adhesion|lamellipodium	actin binding|profilin binding|SH3 domain binding			large_intestine(2)|ovary(1)	3		Melanoma(154;0.152)																---	---	---	---
DEGS2	123099	broad.mit.edu	37	14	100613996	100613998	+	Intron	DEL	CCC	-	-	rs66550225		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100613996_100613998delCCC	uc001ygx.2	-							NM_206918	NP_996801			degenerative spermatocyte homolog 2, lipid						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	sphingosine hydroxylase activity				0		Melanoma(154;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	101865241	101865241	+	IGR	DEL	T	-	-	rs141842002		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101865241delT								MIR656 (332103 upstream) : DIO3OS (153319 downstream)																																			---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102723062	102723062	+	Intron	DEL	A	-	-	rs11298006		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102723062delA	uc001ylm.2	-						RAGE_uc010txv.1_Intron|RAGE_uc001yln.2_Intron	NM_014226	NP_055041			MAPK/MAK/MRK overlapping kinase						signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103166093	103166094	+	Intron	DEL	TT	-	-	rs35514078		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103166093_103166094delTT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103187899	103187901	+	Intron	DEL	AAT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103187899_103187901delAAT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	103544456	103544456	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103544456delA								CDC42BPB (20714 upstream) : C14orf73 (22025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	103545068	103545068	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103545068delT								CDC42BPB (21326 upstream) : C14orf73 (21413 downstream)																																			---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103946464	103946464	+	Intron	DEL	A	-	-	rs113319948		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103946464delA	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron|MARK3_uc010tyb.1_Intron|MARK3_uc010awq.2_Intron	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104056251	104056251	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104056251delA	uc010tyd.1	+						C14orf153_uc001ynl.3_Intron|C14orf153_uc010tyc.1_Intron	NM_005552	NP_005543			kinesin light chain 1 isoform 1						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104116448	104116449	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104116448_104116449delTT	uc001yno.2	+						KLC1_uc010tyd.1_Intron|KLC1_uc010tye.1_Intron|KLC1_uc001ynm.1_Intron|KLC1_uc001ynn.1_Intron|KLC1_uc010tyf.1_Intron	NM_182923	NP_891553			kinesin light chain 1 isoform 2						blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104245519	104245519	+	Intron	DEL	G	-	-	rs67376559		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104245519delG	uc001yof.1	-						PPP1R13B_uc001yog.1_Intron	NM_015316	NP_056131			apoptosis-stimulating protein of p53, 1						apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)																---	---	---	---
TDRD9	122402	broad.mit.edu	37	14	104457738	104457739	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104457738_104457739insT	uc001yom.3	+						TDRD9_uc001yon.3_Intron	NM_153046	NP_694591			tudor domain containing 9						cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	104670280	104670283	+	IGR	DEL	CATC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104670280_104670283delCATC								KIF26A (23046 upstream) : C14orf180 (375773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	104767708	104767719	+	IGR	DEL	ACCACCACCGCC	-	-	rs72234717		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104767708_104767719delACCACCACCGCC								KIF26A (120474 upstream) : C14orf180 (278337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	104910749	104910756	+	IGR	DEL	CATTCACC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104910749_104910756delCATTCACC								KIF26A (263515 upstream) : C14orf180 (135300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	104975520	104975520	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104975520delT								KIF26A (328286 upstream) : C14orf180 (70536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105080897	105080898	+	IGR	INS	-	GATA	GATA	rs28410345		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105080897_105080898insGATA								TMEM179 (9800 upstream) : INF2 (75045 downstream)																																			---	---	---	---
INF2	64423	broad.mit.edu	37	14	105153797	105153798	+	5'Flank	INS	-	CA	CA	rs149398466	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105153797_105153798insCA	uc001ypb.2	+						INF2_uc001ypc.2_5'Flank|INF2_uc001yoy.3_5'Flank	NM_022489	NP_071934			inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105729281	105729282	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105729281_105729282delAA	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqr.2_Intron	NM_001519	NP_001510			transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
PACS2	23241	broad.mit.edu	37	14	105810037	105810038	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105810037_105810038delTT	uc001yqt.2	+						PACS2_uc001yqs.2_Intron|PACS2_uc001yqv.2_Intron|PACS2_uc001yqu.2_Intron	NM_015197	NP_056012			phosphofurin acidic cluster sorting protein 2						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)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106337612	106337612	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106337612delT	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107153437	107153438	+	Intron	INS	-	A	A	rs141277239	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107153437_107153438insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107163851	107163851	+	Intron	DEL	C	-	-	rs34857857		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107163851delC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20283123	20283123	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20283123delT								None (None upstream) : GOLGA6L6 (453971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20475850	20475851	+	IGR	DEL	TT	-	-	rs141348814	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20475850_20475851delTT								None (None upstream) : GOLGA6L6 (261243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20477298	20477298	+	IGR	DEL	T	-	-	rs113877718		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20477298delT								None (None upstream) : GOLGA6L6 (259796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20559225	20559225	+	IGR	DEL	T	-	-	rs60113640		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20559225delT								None (None upstream) : GOLGA6L6 (177869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20579178	20579179	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20579178_20579179insA								None (None upstream) : GOLGA6L6 (157915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20601044	20601044	+	Intron	DEL	A	-	-	rs10716282		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20601044delA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	21905915	21905916	+	IGR	INS	-	A	A	rs113231430		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21905915_21905916insA								NF1P1 (771290 upstream) : LOC646214 (26598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22490720	22490721	+	IGR	DEL	AA	-	-	rs55759728	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22490720_22490721delAA								OR4N3P (76335 upstream) : MIR1268 (22508 downstream)																																			---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22945350	22945351	+	Intron	INS	-	A	A	rs141360543	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22945350_22945351insA	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron	NM_014608	NP_055423			cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23685218	23685220	+	IGR	DEL	CTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23685218_23685220delCTC								GOLGA8E (236795 upstream) : MKRN3 (125234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23981358	23981358	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23981358delC								NDN (48908 upstream) : PWRN2 (428568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24305025	24305025	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24305025delT								NDN (372575 upstream) : PWRN2 (104901 downstream)																																			---	---	---	---
PAR-SN	347746	broad.mit.edu	37	15	25249824	25249824	+	Intron	DEL	T	-	-	rs34856417		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25249824delT	uc001yxc.2	+											Homo sapiens RT-LII mRNA, complete sequence.												0																		---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	26090477	26090478	+	Intron	INS	-	TT	TT	rs149922723	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26090477_26090478insTT	uc010ayu.2	-						ATP10A_uc001zax.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	26284504	26284504	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26284504delT								ATP10A (174187 upstream) : GABRB3 (504191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26571833	26571833	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26571833delA								ATP10A (461516 upstream) : GABRB3 (216862 downstream)																																			---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27275843	27275844	+	Intron	INS	-	ACTT	ACTT	rs10648433		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27275843_27275844insACTT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	27939217	27939217	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27939217delG								GABRG3 (161083 upstream) : OCA2 (60808 downstream)																																			---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28517891	28517892	+	Intron	DEL	TA	-	-	rs75694916		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28517891_28517892delTA	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						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)														---	---	---	---
APBA2	321	broad.mit.edu	37	15	29148153	29148154	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29148153_29148154delGA	uc010uat.1	+						APBA2_uc010azj.2_Intron|APBA2_uc010uas.1_Intron	NM_001130414	NP_001123886			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)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29524868	29524869	+	Intron	INS	-	TTGT	TTGT	rs142062866	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29524868_29524869insTTGT	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	29892675	29892675	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29892675delA								FAM189A1 (29748 upstream) : TJP1 (99684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31010765	31010765	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31010765delT	uc001zev.2	+											Homo sapiens hypothetical LOC440261, mRNA (cDNA clone IMAGE:7479697), complete cds.																														---	---	---	---
MTMR10	54893	broad.mit.edu	37	15	31253444	31253445	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31253444_31253445delTT	uc001zfh.1	-						MTMR10_uc010azx.1_Intron|MTMR10_uc001zfi.1_Intron|MTMR10_uc001zfj.2_Intron|MTMR10_uc001zfk.2_Intron|MTMR10_uc010ubl.1_Intron	NM_017762	NP_060232			myotubularin related protein 10								phosphatase activity			ovary(1)	1		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	31552769	31552769	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31552769delA								TRPM1 (158845 upstream) : KLF13 (66314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31711152	31711155	+	IGR	DEL	ATAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31711152_31711155delATAC								KLF13 (41051 upstream) : OTUD7A (64175 downstream)																																			---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33820276	33820276	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33820276delT	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)														---	---	---	---
AVEN	57099	broad.mit.edu	37	15	34213637	34213638	+	Intron	INS	-	GA	GA	rs147298140	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34213637_34213638insGA	uc001zhj.2	-							NM_020371	NP_065104			cell death regulator aven						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)														---	---	---	---
AVEN	57099	broad.mit.edu	37	15	34250795	34250797	+	Intron	DEL	AAA	-	-	rs74709155		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34250795_34250797delAAA	uc001zhj.2	-							NM_020371	NP_065104			cell death regulator aven						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)														---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34528550	34528550	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	34757331	34757331	+	IGR	DEL	T	-	-	rs34113006		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34757331delT								GOLGA8A (75330 upstream) : GOLGA8B (60154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35294202	35294202	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35294202delA								ZNF770 (13748 upstream) : LOC723972 (235325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36179317	36179317	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36179317delA								ATPBD4 (340913 upstream) : C15orf41 (692495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	36697242	36697242	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36697242delA								ATPBD4 (858838 upstream) : C15orf41 (174570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37885483	37885484	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37885483_37885484insA								MEIS2 (491983 upstream) : TMCO5A (341343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38689144	38689144	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38689144delT								SPRED1 (39695 upstream) : FAM98B (57184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39800658	39800659	+	IGR	INS	-	CA	CA	rs147152883	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39800658_39800659insCA								C15orf54 (253610 upstream) : THBS1 (72621 downstream)																																			---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40235231	40235234	+	Intron	DEL	TTTT	-	-	rs34513040	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40235231_40235234delTTTT	uc001zkm.1	+						EIF2AK4_uc001zkl.2_Intron	NM_001013703	NP_001013725			eukaryotic translation initiation factor 2 alpha						translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)														---	---	---	---
FAM82A2	55177	broad.mit.edu	37	15	41050555	41050556	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41050555_41050556insT	uc001zmq.1	-							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	41310325	41310325	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41310325delA	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	41984100	41984100	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41984100delT	uc001zog.1	+						MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	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)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42073265	42073267	+	Intron	DEL	TTT	-	-	rs5812203		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42073265_42073267delTTT	uc001zok.3	+						MAPKBP1_uc001zoj.3_Intron|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Intron|MAPKBP1_uc010udb.1_Intron|MAPKBP1_uc010bck.2_Intron	NM_001128608	NP_001122080			mitogen-activated protein kinase binding protein											central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)														---	---	---	---
SPTBN5	51332	broad.mit.edu	37	15	42171798	42171799	+	Intron	INS	-	G	G	rs141761744	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42171798_42171799insG	uc001zos.2	-							NM_016642	NP_057726			spectrin, beta, non-erythrocytic 5						actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42750919	42750919	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42750919delA	uc001zpw.2	-						ZFP106_uc001zpv.2_5'Flank|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_5'Flank|ZFP106_uc001zpy.1_Intron	NM_022473	NP_071918			zinc finger protein 106 homolog							nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
SNAP23	8773	broad.mit.edu	37	15	42797297	42797297	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42797297delT	uc001zpz.1	+						SNAP23_uc001zqa.1_Intron	NM_003825	NP_003816			synaptosomal-associated protein 23 isoform						cellular membrane fusion|post-Golgi vesicle-mediated transport|protein transport|vesicle targeting	azurophil granule|cell junction|Golgi apparatus|nucleus|plasma membrane enriched fraction|specific granule|synapse|synaptosome	protein binding				0		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)														---	---	---	---
TMEM62	80021	broad.mit.edu	37	15	43473707	43473707	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43473707delT	uc001zqr.2	+						TMEM62_uc010bda.2_Intron|TMEM62_uc001zqt.2_Intron	NM_024956	NP_079232			transmembrane protein 62							integral to membrane				ovary(1)|breast(1)	2		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)														---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44285810	44285810	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44285810delT	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281			FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44599411	44599411	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44599411delT	uc001zto.1	+						CASC4_uc001ztp.2_Intron|CASC4_uc001ztq.2_Intron|CASC4_uc010bdu.1_Intron	NM_138423	NP_612432			cancer susceptibility candidate 4 isoform a							integral to membrane				ovary(1)	1		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)														---	---	---	---
TRIM69	140691	broad.mit.edu	37	15	45041703	45041703	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45041703delT	uc001zuf.2	+						TRIM69_uc001zui.1_Intron|TRIM69_uc010bdy.1_Intron|TRIM69_uc001zug.1_Intron|TRIM69_uc001zuh.1_Intron	NM_182985	NP_892030			tripartite motif-containing 69 isoform a						apoptosis	nuclear speck	zinc ion binding				0		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	46628580	46628580	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46628580delA								SQRDL (645102 upstream) : SEMA6D (847823 downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47702350	47702350	+	Intron	DEL	T	-	-	rs67382888		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47702350delT	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47946908	47946908	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47946908delC	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	48198789	48198790	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48198789_48198790delAC								SEMA6D (132370 upstream) : SLC24A5 (214379 downstream)																																			---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48571818	48571818	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48571818delA	uc001zwn.3	+						SLC12A1_uc010uew.1_Intron|SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329			sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
ATP8B4	79895	broad.mit.edu	37	15	50252231	50252231	+	Intron	DEL	T	-	-	rs72407155		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50252231delT	uc001zxu.2	-						ATP8B4_uc010ber.2_Intron|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113			ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)														---	---	---	---
GABPB1	2553	broad.mit.edu	37	15	50571062	50571063	+	Intron	DEL	AA	-	-	rs71993721		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50571062_50571063delAA	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron	NM_005254	NP_005245			GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1																		---	---	---	---
USP8	9101	broad.mit.edu	37	15	50784069	50784070	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50784069_50784070insT	uc001zym.3	+						USP8_uc001zyl.3_Intron|USP8_uc001zyn.3_Intron|USP8_uc010ufh.1_Intron|USP8_uc001zyp.3_5'Flank	NM_001128611	NP_001122083			ubiquitin specific peptidase 8						cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	50851256	50851256	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50851256delT								USP50 (12354 upstream) : TRPM7 (1235 downstream)																																			---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51858410	51858410	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51858410delA	uc002abf.2	-						DMXL2_uc010ufy.1_Intron|DMXL2_uc010bfa.2_Intron	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)														---	---	---	---
KIAA1370	56204	broad.mit.edu	37	15	52892478	52892478	+	Intron	DEL	T	-	-	rs35694811		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52892478delT	uc002acg.3	-						KIAA1370_uc002ach.3_Intron|KIAA1370_uc010bfg.1_Intron|KIAA1370_uc010ugf.1_Intron	NM_019600	NP_062546			hypothetical protein LOC56204												0				all cancers(107;0.0803)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53569730	53569733	+	IGR	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53569730_53569733delAAAA								ONECUT1 (487521 upstream) : WDR72 (236205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	53779809	53779809	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53779809delT								ONECUT1 (697600 upstream) : WDR72 (26129 downstream)																																			---	---	---	---
WDR72	256764	broad.mit.edu	37	15	54027487	54027487	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54027487delA	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435			WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54616850	54616850	+	Intron	DEL	A	-	-	rs36107767		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54616850delA	uc002ack.2	+						UNC13C_uc002acl.2_Intron	NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	55097113	55097113	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55097113delA								UNC13C (176308 upstream) : RSL24D1 (376408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55367915	55367916	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55367915_55367916delAT								UNC13C (447110 upstream) : RSL24D1 (105605 downstream)																																			---	---	---	---
RAB27A	5873	broad.mit.edu	37	15	55532338	55532338	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55532338delC	uc002aco.2	-						RAB27A_uc002acr.2_Intron|RAB27A_uc002acp.2_Intron|RAB27A_uc002acq.2_Intron	NM_183234	NP_899057			Ras-related protein Rab-27A						small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity			ovary(1)	1				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56168551	56168551	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56168551delT	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	56965476	56965476	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56965476delA	uc002adu.2	-						ZNF280D_uc002adv.2_Intron|ZNF280D_uc010bfq.2_Intron|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfr.1_Intron|ZNF280D_uc010bfp.2_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)														---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57746965	57746965	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57746965delA	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	58241851	58241851	+	IGR	DEL	A	-	-	rs34888844		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58241851delA								GCOM1 (232099 upstream) : ALDH1A2 (3777 downstream)																																			---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58965027	58965027	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58965027delA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59297871	59297871	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59297871delA	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron	NM_017610	NP_060080			ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59332319	59332319	+	Intron	DEL	T	-	-	rs34594493		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59332319delT	uc002afv.2	+						RNF111_uc002afs.2_Intron|RNF111_uc002aft.2_Intron|RNF111_uc002afu.2_Intron|RNF111_uc002afw.2_Intron	NM_017610	NP_060080			ring finger protein 111						multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	60134701	60134701	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60134701delA								BNIP2 (153059 upstream) : FOXB1 (161720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60470848	60470850	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60470848_60470850delAAA								FOXB1 (142440 upstream) : ANXA2 (168501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	61826561	61826561	+	IGR	DEL	A	-	-	rs12913921	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61826561delA								RORA (305059 upstream) : VPS13C (318031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62745426	62745427	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62745426_62745427delAG								C2CD4B (287944 upstream) : MGC15885 (183944 downstream)																																			---	---	---	---
HERC1	8925	broad.mit.edu	37	15	64013237	64013237	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64013237delT	uc002amp.2	-						HERC1_uc010uil.1_Intron	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																		---	---	---	---
DAPK2	23604	broad.mit.edu	37	15	64217878	64217881	+	Intron	DEL	CACA	-	-	rs72280699		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64217878_64217881delCACA	uc002amr.2	-						DAPK2_uc010uim.1_Intron	NM_014326	NP_055141			death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)														---	---	---	---
TRIP4	9325	broad.mit.edu	37	15	64702165	64702166	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64702165_64702166insA	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																		---	---	---	---
RBPMS2	348093	broad.mit.edu	37	15	65046811	65046811	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65046811delA	uc002anq.2	-							NM_194272	NP_919248			RNA binding protein with multiple splicing 2								nucleic acid binding|nucleotide binding				0																		---	---	---	---
PARP16	54956	broad.mit.edu	37	15	65575608	65575608	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65575608delC	uc002aoo.2	-						PARP16_uc002aop.2_Intron|PARP16_uc002aoq.2_Intron	NM_017851	NP_060321			poly (ADP-ribose) polymerase family, member 16							integral to membrane	NAD+ ADP-ribosyltransferase activity			lung(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65611547	65611549	+	IGR	DEL	TCC	-	-	rs34111694		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65611547_65611549delTCC								PARP16 (32529 upstream) : IGDCC3 (7916 downstream)																																			---	---	---	---
IGDCC4	57722	broad.mit.edu	37	15	65697009	65697010	+	Intron	INS	-	TGAATGAA	TGAATGAA	rs142664210	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65697009_65697010insTGAATGAA	uc002aou.1	-							NM_020962	NP_066013			immunoglobulin superfamily, DCC subclass, member							integral to membrane|plasma membrane				ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66120255	66120256	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66120255_66120256delTT								DENND4A (35624 upstream) : RAB11A (41540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	66658492	66658492	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66658492delA								TIPIN (9438 upstream) : MAP2K1 (20719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	66895749	66895750	+	Intron	INS	-	TC	TC	rs148529377	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66895749_66895750insTC	uc002aqe.2	+											Homo sapiens cDNA FLJ38816 fis, clone LIVER2007568.																														---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	67936116	67936116	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67936116delT	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron|MAP2K5_uc002aqx.2_Intron	NM_145160	NP_660143			mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2																		---	---	---	---
PIAS1	8554	broad.mit.edu	37	15	68411780	68411780	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68411780delA	uc002aqz.2	+						PIAS1_uc010ujx.1_Intron	NM_016166	NP_057250			protein inhibitor of activated STAT, 1						androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
CORO2B	10391	broad.mit.edu	37	15	68932851	68932851	+	Intron	DEL	A	-	-	rs34183929		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68932851delA	uc002arj.3	+						CORO2B_uc010bic.2_Intron	NM_006091	NP_006082			coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69126634	69126634	+	IGR	DEL	C	-	-	rs59781278		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69126634delC								ANP32A (13373 upstream) : NOX5 (96230 downstream)																																			---	---	---	---
GLCE	26035	broad.mit.edu	37	15	69474608	69474609	+	Intron	INS	-	TG	TG	rs34135980		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69474608_69474609insTG	uc002ary.1	+						GLCE_uc002arw.2_Intron|GLCE_uc002arx.2_Intron	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																		---	---	---	---
CT62	196993	broad.mit.edu	37	15	71410668	71410668	+	5'Flank	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71410668delC	uc002ata.2	-							NM_001102658	NP_001096128			cancer/testis antigen 62												0																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71679546	71679546	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71679546delA	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71876813	71876813	+	Intron	DEL	G	-	-	rs34807823		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71876813delG	uc002atb.1	+						THSD4_uc002atd.1_Intron|THSD4_uc010ukg.1_Intron|THSD4_uc002ate.2_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72553349	72553349	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72553349delA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599			poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	72620125	72620126	+	Intron	INS	-	AA	AA	rs34405853		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72620125_72620126insAA	uc002aug.2	+						CELF6_uc002auk.3_Intron					Homo sapiens hexosaminidase A (alpha polypeptide), mRNA (cDNA clone IMAGE:4823589).																														---	---	---	---
C15orf60	283677	broad.mit.edu	37	15	73820231	73820231	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73820231delA	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74793177	74793177	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74793177delA								UBL7 (39648 upstream) : ARID3B (40371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74815279	74815279	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74815279delA								UBL7 (61750 upstream) : ARID3B (18269 downstream)																																			---	---	---	---
COX5A	9377	broad.mit.edu	37	15	75216560	75216560	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75216560delT	uc002azi.3	-							NM_004255	NP_004246			cytochrome c oxidase subunit Va precursor						respiratory electron transport chain	mitochondrial inner membrane	cytochrome-c oxidase activity|electron carrier activity|metal ion binding				0																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75702784	75702784	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75702784delA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	76039782	76039784	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76039782_76039784delAAA								DNM1P35 (7280 upstream) : UBE2Q2 (95838 downstream)																																			---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76849995	76849995	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76849995delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	77845249	77845249	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77845249delA								HMG20A (67306 upstream) : LINGO1 (60120 downstream)																																			---	---	---	---
CIB2	10518	broad.mit.edu	37	15	78405859	78405860	+	Intron	INS	-	TTCTTTCT	TTCTTTCT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78405859_78405860insTTCTTTCT	uc002bdb.1	-						CIB2_uc002bdc.1_Intron|CIB2_uc010ums.1_Intron	NM_006383	NP_006374			DNA-dependent protein kinase catalytic								calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78983222	78983223	+	IGR	DEL	AA	-	-	rs71448814		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78983222_78983223delAA								CHRNB4 (30348 upstream) : ADAMTS7 (68323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79936787	79936787	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79936787delA								KIAA1024 (172145 upstream) : MTHFS (200533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80048454	80048454	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80048454delG								KIAA1024 (283812 upstream) : MTHFS (88866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80347766	80347766	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80347766delA								BCL2A1 (84123 upstream) : ZFAND6 (4255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80608639	80608639	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80608639delA	uc002bfo.2	-											Homo sapiens cDNA FLJ40463 fis, clone TESTI2042149.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	80899814	80899814	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80899814delG								ARNT2 (9542 upstream) : FAM108C1 (87838 downstream)																																			---	---	---	---
FAM108C1	58489	broad.mit.edu	37	15	81005427	81005428	+	Intron	DEL	TT	-	-	rs76214096		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81005427_81005428delTT	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037			hypothetical protein LOC58489								hydrolase activity				0																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81193359	81193359	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81193359delA	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	82134058	82134059	+	IGR	DEL	AA	-	-	rs80042069		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82134058_82134059delAA								TMC3 (467640 upstream) : MEX3B (200069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	83640121	83640122	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83640121_83640122delGA	uc002bjk.1	-											Homo sapiens, clone IMAGE:5164756, mRNA.																														---	---	---	---
BTBD1	53339	broad.mit.edu	37	15	83705985	83705985	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83705985delA	uc002bjn.2	-						BTBD1_uc002bjo.2_Intron	NM_025238	NP_079514			BTB (POZ) domain containing 1 isoform 1							cytoplasmic mRNA processing body|protein complex	protein binding			ovary(1)|central_nervous_system(1)	2				all cancers(203;0.000186)														---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84227163	84227163	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84227163delT	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018			SH3-domain GRB2-like 3						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	85159949	85159949	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85159949delA	uc002bkr.2	+						ZSCAN2_uc010bmz.1_Intron|ZSCAN2_uc010bna.2_Intron|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992			zinc finger protein 29 isoform 1						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)														---	---	---	---
SEC11A	23478	broad.mit.edu	37	15	85233849	85233849	+	Intron	DEL	A	-	-	rs11321670		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85233849delA	uc002blb.1	-						SEC11A_uc002blc.1_Intron	NM_014300	NP_055115			SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85282393	85282396	+	IGR	DEL	TGTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85282393_85282396delTGTG								SEC11A (22719 upstream) : ZNF592 (9422 downstream)																																			---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85442416	85442416	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85442416delA	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85587594	85587595	+	Intron	INS	-	AA	AA	rs145758763	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85587594_85587595insAA	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron	NM_002605	NP_002596			phosphodiesterase 8A 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			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86758454	86758455	+	Intron	DEL	GC	-	-	rs34695258		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86758454_86758455delGC	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	88039970	88039970	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88039970delA								AGBL1 (467687 upstream) : NCRNA00052 (80190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88385522	88385523	+	IGR	INS	-	GAAT	GAAT	rs148350151	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88385522_88385523insGAAT								NCRNA00052 (262605 upstream) : NTRK3 (34465 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88423337	88423338	+	Intron	DEL	TT	-	-	rs71851481		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88423337_88423338delTT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.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)			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88801205	88801205	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88801205delA	uc002bme.1	-						NTRK3_uc002bmh.2_5'Flank|NTRK3_uc002bmf.1_5'Flank|NTRK3_uc010bnh.1_5'Flank|NTRK3_uc002bmg.2_5'Flank	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88873489	88873489	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88873489delT								NTRK3 (73828 upstream) : MRPL46 (129219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88921451	88921451	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88921451delA								NTRK3 (121790 upstream) : MRPL46 (81257 downstream)																																			---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89723517	89723517	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89723517delT	uc002bnj.2	+						ABHD2_uc002bnk.2_Intron	NM_007011	NP_008942			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
Unknown	0	broad.mit.edu	37	15	90479328	90479335	+	IGR	DEL	ACACACAG	-	-	rs10541504		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90479328_90479335delACACACAG								AP3S2 (23106 upstream) : ZNF710 (65417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90669414	90669414	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90669414delA								IDH2 (23706 upstream) : SEMA4B (58738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90868742	90868742	+	IGR	DEL	A	-	-	rs78745053	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90868742delA								TTLL13 (53299 upstream) : GABARAPL3 (21023 downstream)																																			---	---	---	---
CRTC3	64784	broad.mit.edu	37	15	91167695	91167695	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91167695delC	uc002bpp.2	+						CRTC3_uc002bpo.2_Intron	NM_022769	NP_073606			transducer of regulated CREB protein 3 isoform						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus			CRTC3/MAML2(26)	salivary_gland(26)|ovary(1)	27	Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163)		BRCA - Breast invasive adenocarcinoma(143;0.0745)					T	MAML2	salivary gland mucoepidermoid								---	---	---	---
BLM	641	broad.mit.edu	37	15	91308328	91308329	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91308328_91308329delTT	uc002bpr.2	+						BLM_uc010uqh.1_Intron|BLM_uc010uqi.1_Intron|BLM_uc010bnx.2_Intron|BLM_uc002bps.1_Intron	NM_000057	NP_000048			Bloom syndrome protein						double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)|skin(2)|breast(1)	6	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)					Mis|N|F			leukemia|lymphoma|skin squamous cell |other cancers		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Bloom_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	15	91378356	91378358	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91378356_91378358delTTT								BLM (19672 upstream) : FURIN (33527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	91570571	91570571	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91570571delA	uc002bqr.1	+						uc002bqs.1_Intron					Homo sapiens cDNA FLJ30789 fis, clone FEBRA2000937.																														---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91812339	91812340	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91812339_91812340delAA	uc002bqv.2	+						SV2B_uc010uqv.1_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663			synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	92292862	92292867	+	IGR	DEL	TGGAGA	-	-	rs145621440		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92292862_92292867delTGGAGA								SV2B (454214 upstream) : SLCO3A1 (104071 downstream)																																			---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92596925	92596926	+	Intron	DEL	TG	-	-	rs66533251		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92596925_92596926delTG	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	92807739	92807739	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92807739delT								SLCO3A1 (92074 upstream) : ST8SIA2 (129401 downstream)																																			---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93558308	93558308	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93558308delT	uc002bsp.2	+						CHD2_uc002bso.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	93693431	93693433	+	IGR	DEL	AGC	-	-	rs10522231		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93693431_93693433delAGC								RGMA (60998 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93853777	93853777	+	5'Flank	DEL	T	-	-	rs66464641		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93853777delT	uc002bsu.1	+											Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94558101	94558101	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94558101delA								RGMA (925668 upstream) : MCTP2 (216700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95280302	95280305	+	IGR	DEL	CATC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95280302_95280305delCATC								MCTP2 (253122 upstream) : LOC145820 (696017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95959460	95959460	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95959460delG								MCTP2 (932280 upstream) : LOC145820 (16862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97358918	97358919	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97358918_97358919insT								SPATA8 (30074 upstream) : LOC91948 (926927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97610889	97610896	+	IGR	DEL	TTCCTTCT	-	-	rs72438368		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97610889_97610896delTTCCTTCT								SPATA8 (282045 upstream) : LOC91948 (674950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98120666	98120667	+	IGR	DEL	TG	-	-	rs10542793		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98120666_98120667delTG								SPATA8 (791822 upstream) : LOC91948 (165179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98229122	98229123	+	IGR	DEL	AC	-	-	rs3995778		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98229122_98229123delAC								SPATA8 (900278 upstream) : LOC91948 (56723 downstream)																																			---	---	---	---
ARRDC4	91947	broad.mit.edu	37	15	98508660	98508661	+	Intron	DEL	CG	-	-	rs28380454	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98508660_98508661delCG	uc010bom.2	+						ARRDC4_uc002bui.3_Intron	NM_183376	NP_899232			arrestin domain containing 4						signal transduction						0	Melanoma(26;0.00539)|Lung NSC(78;0.0125)|all_lung(78;0.0222)		OV - Ovarian serous cystadenocarcinoma(32;0.0417)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	98747166	98747167	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98747166_98747167delTT								ARRDC4 (230099 upstream) : FAM169B (233224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99577805	99577805	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99577805delT								PGPEP1L (26781 upstream) : SYNM (67481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	100036472	100036472	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100036472delA								LRRC28 (109192 upstream) : MEF2A (69661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	100324442	100324442	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100324442delA								LYSMD4 (50816 upstream) : C15orf51 (5919 downstream)																																			---	---	---	---
LASS3	204219	broad.mit.edu	37	15	100978817	100978818	+	Intron	INS	-	T	T	rs150497304	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100978817_100978818insT	uc002bvz.2	-						LASS3_uc002bwa.2_Intron|LASS3_uc002bwb.2_Intron	NM_178842	NP_849164			LAG1 longevity assurance homolog 3							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(2)|pancreas(1)|skin(1)	4	Lung NSC(78;0.0018)|all_lung(78;0.00278)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000867)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)															---	---	---	---
LASS3	204219	broad.mit.edu	37	15	101072811	101072812	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101072811_101072812delAA	uc002bvz.2	-						LASS3_uc002bwa.2_Intron|LASS3_uc002bwb.2_Intron	NM_178842	NP_849164			LAG1 longevity assurance homolog 3							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(2)|pancreas(1)|skin(1)	4	Lung NSC(78;0.0018)|all_lung(78;0.00278)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000867)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)															---	---	---	---
RAB11FIP3	9727	broad.mit.edu	37	16	531512	531512	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:531512delA	uc002chf.2	+						RAB11FIP3_uc010uuf.1_Intron|RAB11FIP3_uc010uug.1_5'Flank	NM_014700	NP_055515			rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)																---	---	---	---
LOC146336	146336	broad.mit.edu	37	16	1118403	1118404	+	Intron	INS	-	GTC	GTC	rs150395080	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1118403_1118404insGTC	uc002cko.2	-							NR_027242				SubName: Full=cDNA FLJ32252 fis, clone PROST1000167, weakly similar to SYNAPSIN I;												0																		---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1235646	1235649	+	Intron	DEL	CGGT	-	-	rs72095483		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1235646_1235649delCGGT	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron	NM_021098	NP_066921			calcium channel, voltage-dependent, T type,						aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
HN1L	90861	broad.mit.edu	37	16	1751590	1751590	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1751590delT	uc002cmg.2	+	5					HN1L_uc010uvi.1_3'UTR|HN1L_uc010brt.2_RNA|HN1L_uc010bru.2_3'UTR|HN1L_uc010uvj.1_3'UTR|HN1L_uc010uvk.1_3'UTR	NM_144570	NP_653171			hematological and neurological expressed 1-like							cytoplasm|nucleus				upper_aerodigestive_tract(1)	1																		---	---	---	---
PGP	283871	broad.mit.edu	37	16	2262925	2262926	+	3'UTR	INS	-	TGTT	TGTT	rs145363269	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2262925_2262926insTGTT	uc002cpk.1	-	2					C16orf79_uc002cpi.1_5'Flank|C16orf79_uc010bsh.2_5'Flank|PGP_uc010uvz.1_Intron	NM_001042371	NP_001035830			phosphoglycolate phosphatase						carbohydrate metabolic process		phosphoglycolate phosphatase activity			skin(1)	1																		---	---	---	---
ZNF213	7760	broad.mit.edu	37	16	3189629	3189630	+	Intron	INS	-	TCTGTCCAGA	TCTGTCCAGA	rs144107498	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3189629_3189630insTCTGTCCAGA	uc010uws.1	+						ZNF213_uc002cud.2_Intron|ZNF213_uc010btf.2_3'UTR|ZNF213_uc010bth.2_Intron|ZNF213_uc010uwt.1_Intron	NM_004220	NP_004211			zinc finger protein 213						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3464768	3464769	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3464768_3464769delAA								ZNF174 (5406 upstream) : ZNF597 (21342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	4201214	4201214	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4201214delA								ADCY9 (35028 upstream) : SRL (38163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	4237310	4237311	+	IGR	INS	-	C	C	rs144985552	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4237310_4237311insC								ADCY9 (71124 upstream) : SRL (2066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	4348115	4348115	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4348115delT								TFAP4 (25114 upstream) : GLIS2 (34110 downstream)																																			---	---	---	---
CORO7	79585	broad.mit.edu	37	16	4407754	4407755	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4407754_4407755delGT	uc002cwh.3	-						CORO7_uc002cwe.2_Intron|CORO7_uc002cwf.2_Intron|CORO7_uc002cwg.3_Intron|CORO7_uc010uxh.1_Intron|CORO7_uc010uxi.1_Intron|CORO7_uc002cwi.1_3'UTR	NM_024535	NP_078811			coronin 7							cytoplasmic membrane-bounded vesicle|cytosol|Golgi membrane|integral to membrane of membrane fraction|soluble fraction					0																		---	---	---	---
DNAJA3	9093	broad.mit.edu	37	16	4487633	4487633	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4487633delA	uc002cwk.2	+						DNAJA3_uc002cwl.2_Intron|DNAJA3_uc010uxk.1_Intron	NM_005147	NP_005138			DnaJ (Hsp40) homolog, subfamily A, member 3						activation of caspase activity|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of cell proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein kinase activity|neuromuscular junction development|positive regulation of apoptosis|positive regulation of protein ubiquitination|protein folding|protein folding|protein stabilization|response to heat|response to interferon-gamma	cytosol|mitochondrial matrix|mitochondrial nucleoid|nucleus	ATP binding|heat shock protein binding|interferon-gamma receptor binding|metal ion binding|NF-kappaB binding|protein kinase binding			ovary(2)|breast(2)	4																		---	---	---	---
MGRN1	23295	broad.mit.edu	37	16	4715364	4715365	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4715364_4715365delTT	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	5618226	5618227	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5618226_5618227insT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6155999	6155999	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6155999delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.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	6584083	6584083	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6584083delA	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	7438046	7438046	+	Intron	DEL	T	-	-	rs74811464		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7438046delT	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)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7633151	7633151	+	Intron	DEL	T	-	-	rs138191898		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7633151delT	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	8029953	8029954	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8029953_8029954delTT								A2BP1 (266613 upstream) : TMEM114 (589549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8259193	8259194	+	IGR	INS	-	A	A	rs145780765	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8259193_8259194insA								A2BP1 (495853 upstream) : TMEM114 (360309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8438639	8438639	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8438639delA								A2BP1 (675299 upstream) : TMEM114 (180864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8510365	8510368	+	IGR	DEL	GAGG	-	-	rs12709231		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8510365_8510368delGAGG								A2BP1 (747025 upstream) : TMEM114 (109135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9093757	9093759	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9093757_9093759delTTT								USP7 (36416 upstream) : C16orf72 (91778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9262253	9262253	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9262253delA								C16orf72 (48708 upstream) : GRIN2A (585014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9269344	9269345	+	IGR	INS	-	T	T	rs147601496		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9269344_9269345insT								C16orf72 (55799 upstream) : GRIN2A (577922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9291011	9291014	+	IGR	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9291011_9291014delTTTT								C16orf72 (77466 upstream) : GRIN2A (556253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9584575	9584576	+	IGR	DEL	GA	-	-	rs112935656		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9584575_9584576delGA								C16orf72 (371030 upstream) : GRIN2A (262691 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10142622	10142623	+	Intron	INS	-	A	A	rs141752459	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10142622_10142623insA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10499230	10499230	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10499230delA	uc002czu.2	+						ATF7IP2_uc002czv.2_Intron|ATF7IP2_uc010uyo.1_Intron|ATF7IP2_uc010uyp.1_Intron	NM_024997	NP_079273			activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	10613650	10613651	+	IGR	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10613650_10613651delCT								ATF7IP2 (36156 upstream) : EMP2 (8629 downstream)																																			---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10741329	10741329	+	Intron	DEL	A	-	-	rs71404409		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10741329delA	uc002czz.1	-							NM_144674	NP_653275			tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	11295404	11295404	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11295404delT								CLEC16A (19360 upstream) : C16orf75 (48102 downstream)																																			---	---	---	---
C16orf75	116028	broad.mit.edu	37	16	11374528	11374528	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11374528delA	uc002daq.1	+											Homo sapiens cDNA FLJ41770 fis, clone IMR322007225.						DNA replication	nucleus	DNA binding				0								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
Unknown	0	broad.mit.edu	37	16	11714024	11714024	+	IGR	DEL	A	-	-	rs75686446		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11714024delA								LITAF (32702 upstream) : SNN (48277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12031883	12031883	+	IGR	DEL	G	-	-	rs116770375		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12031883delG								GSPT1 (21364 upstream) : TNFRSF17 (27081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12702224	12702225	+	IGR	INS	-	AG	AG	rs111675940		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12702224_12702225insAG								SNX29 (34079 upstream) : CPPED1 (51432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	12724170	12724170	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12724170delC								SNX29 (56025 upstream) : CPPED1 (29487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14416445	14416445	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14416445delA								MIR365-1 (13217 upstream) : PARN (113114 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15076412	15076412	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15076412delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.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)													---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15108788	15108789	+	Intron	DEL	TA	-	-	rs5816113		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15108788_15108789delTA	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	15790244	15790244	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15790244delA	uc002ddt.1	+						NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron	NM_017668	NP_060138			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																		---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16091841	16091841	+	Intron	DEL	A	-	-	rs371941	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16091841delA	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	17641681	17641684	+	IGR	DEL	ATCT	-	-	rs66504203		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17641681_17641684delATCT								XYLT1 (76943 upstream) : NOMO2 (869499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17842621	17842621	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17842621delA								XYLT1 (277883 upstream) : NOMO2 (668562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18033900	18033900	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18033900delC								XYLT1 (469162 upstream) : NOMO2 (477283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18323858	18323858	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18323858delA								XYLT1 (759120 upstream) : NOMO2 (187325 downstream)																																			---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18880244	18880244	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18880244delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	18982103	18982103	+	IGR	DEL	T	-	-	rs66462019		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18982103delT								SMG1 (44377 upstream) : TMC7 (13153 downstream)																																			---	---	---	---
SYT17	51760	broad.mit.edu	37	16	19192125	19192125	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19192125delT	uc002dfw.2	+						SYT17_uc002dfx.2_Intron|SYT17_uc002dfy.2_Intron|SYT17_uc002dfv.1_Intron	NM_016524	NP_057608			B/K protein							membrane|synaptic vesicle	transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	20195634	20195635	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20195634_20195635delTC								GPR139 (110534 upstream) : GP2 (126177 downstream)																																			---	---	---	---
ACSM2A	123876	broad.mit.edu	37	16	20481194	20481194	+	Intron	DEL	A	-	-	rs60365080		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20481194delA	uc010bwe.2	+						ACSM2A_uc010bwd.1_Intron|ACSM2A_uc010vax.1_Intron|ACSM2A_uc002dhf.3_Intron|ACSM2A_uc002dhg.3_Intron|ACSM2A_uc010vay.1_Intron	NM_001010845	NP_001010845			acyl-CoA synthetase medium-chain family member						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			skin(2)|breast(1)	3																		---	---	---	---
ERI2	112479	broad.mit.edu	37	16	20875803	20875803	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20875803delA	uc002dht.3	-						DCUN1D3_uc002dhz.2_Intron	NM_001142725	NP_001136197			exoribonuclease 2 isoform 1							intracellular	exonuclease activity|nucleic acid binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
ERI2	112479	broad.mit.edu	37	16	20902322	20902323	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20902322_20902323delTT	uc002dht.3	-						DCUN1D3_uc002dhz.2_Intron	NM_001142725	NP_001136197			exoribonuclease 2 isoform 1							intracellular	exonuclease activity|nucleic acid binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20983561	20983561	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20983561delT	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21036218	21036218	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21036218delT	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21107456	21107457	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21107456_21107457delTT	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21107459	21107460	+	Intron	INS	-	C	C	rs77719133	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21107459_21107460insC	uc010vbe.1	-							NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21119184	21119184	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21119184delT	uc010vbe.1	-						DNAH3_uc002die.2_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
CRYM	1428	broad.mit.edu	37	16	21281070	21281070	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21281070delC	uc002dik.2	-						CRYM_uc010bwq.1_Intron|CRYM_uc002dil.2_Intron|CRYM_uc002dim.2_Intron	NM_001888	NP_001879			crystallin, mu isoform 1						negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity				0				GBM - Glioblastoma multiforme(48;0.0573)	Levothyroxine(DB00451)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	21598985	21598985	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21598985delT	uc002diq.3	+											Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21740531	21740531	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21740531delT	uc002djh.2	+						uc002diq.3_Intron|OTOA_uc010vbj.1_Intron|OTOA_uc002dji.2_Intron|OTOA_uc010vbk.1_Intron	NM_144672	NP_653273			otoancorin isoform 1						sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21828346	21828346	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21828346delT	uc010vbl.1	-						uc002diq.3_Intron|RRN3P1_uc002djl.2_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	21831680	21831680	+	Intron	DEL	A	-	-	rs3830664		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21831680delA	uc002diq.3	+						RRN3P1_uc010vbl.1_5'Flank|RRN3P1_uc002djl.2_RNA					Homo sapiens cDNA FLJ59829 complete cds.																														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22264985	22264985	+	Intron	DEL	T	-	-	rs71926662		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22264985delT	uc002dki.2	+						EEF2K_uc002dkh.2_Intron	NM_013302	NP_037434			elongation factor-2 kinase						insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22971044	22971064	+	IGR	DEL	TTCTTCTTCTTCTTCTTCTTA	-	-	rs2369685		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22971044_22971064delTTCTTCTTCTTCTTCTTCTTA								HS3ST2 (43387 upstream) : USP31 (101665 downstream)																																			---	---	---	---
COG7	91949	broad.mit.edu	37	16	23406132	23406132	+	Intron	DEL	T	-	-	rs5816212		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23406132delT	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24104478	24104478	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24104478delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24149879	24149879	+	Intron	DEL	T	-	-	rs66797029		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24149879delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24199016	24199020	+	Intron	DEL	TTTTA	-	-	rs67861779		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24199016_24199020delTTTTA	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
CACNG3	10368	broad.mit.edu	37	16	24297167	24297167	+	Intron	DEL	T	-	-	rs144279970		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24297167delT	uc002dmf.2	+							NM_006539	NP_006530			voltage-dependent calcium channel gamma-3						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	24847467	24847468	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24847467_24847468delTT								TNRC6A (9922 upstream) : SLC5A11 (9848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25279127	25279127	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25279127delA								ZKSCAN2 (10272 upstream) : HS3ST4 (424220 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25722908	25722908	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25722908delT	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)														---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	26085985	26085985	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26085985delT	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	26813874	26813877	+	IGR	DEL	TTTT	-	-	rs34867076		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26813874_26813877delTTTT								HS3ST4 (664866 upstream) : C16orf82 (264342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26832454	26832454	+	IGR	DEL	G	-	-	rs112795176		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26832454delG								HS3ST4 (683446 upstream) : C16orf82 (245765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27088704	27088705	+	IGR	INS	-	CTTT	CTTT	rs143025532	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27088704_27088705insCTTT								C16orf82 (8218 upstream) : JMJD5 (126102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	28479769	28479770	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28479769_28479770delAA	uc010vct.1	-						uc002dpk.2_Intron|CLN3_uc002dpl.2_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28929977	28929978	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28929977_28929978delTT	uc002drq.2	-						uc010vct.1_Intron|RABEP2_uc010vdf.1_Intron|RABEP2_uc010byn.2_Intron|RABEP2_uc002drr.2_Intron	NM_024816	NP_079092			rabaptin, RAB GTPase binding effector protein 2						endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29371855	29371855	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29371855delT	uc010vct.1	-						RUNDC2C_uc010bys.1_Intron|RUNDC2C_uc002dsj.1_Intron|RUNDC2C_uc010vdo.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
MVP	9961	broad.mit.edu	37	16	29852258	29852258	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29852258delA	uc002dui.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc010vdz.1_Intron|MVP_uc002duj.2_Intron|MVP_uc010vea.1_Intron	NM_005115	NP_005106			major vault protein						mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30082576	30082576	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30082576delT	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	30450413	30450414	+	IGR	INS	-	T	T	rs146345731	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30450413_30450414insT								DCTPP1 (9040 upstream) : SEPHS2 (4539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32320426	32320427	+	Intron	DEL	CG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32320426_32320427delCG	uc002edb.2	-											Homo sapiens similar to protein phosphatase 2A 48 kDa regulatory subunit isoform 1; serine/threonine protein phosphatase 2A, 48kDa regulatory subunit; PP2A, subunit B, PR48 isoform; PP2A B subunit PR48; NY-REN-8 antigen, mRNA (cDNA clone IMAGE:5272051).																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	32494367	32494368	+	IGR	INS	-	T	T	rs143786075	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32494367_32494368insT								HERC2P4 (330493 upstream) : TP53TG3B (190473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32520111	32520111	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32520111delT								HERC2P4 (356237 upstream) : TP53TG3B (164730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32521408	32521408	+	IGR	DEL	T	-	-	rs111943548		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32521408delT								HERC2P4 (357534 upstream) : TP53TG3B (163433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32531286	32531286	+	IGR	DEL	A	-	-	rs111403972		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32531286delA								HERC2P4 (367412 upstream) : TP53TG3B (153555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32532115	32532116	+	IGR	INS	-	A	A	rs141107018		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32532115_32532116insA								HERC2P4 (368241 upstream) : TP53TG3B (152725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32554319	32554319	+	IGR	DEL	A	-	-	rs142875489		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32554319delA								HERC2P4 (390445 upstream) : TP53TG3B (130522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32653255	32653256	+	IGR	INS	-	G	G	rs149287842	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32653255_32653256insG								HERC2P4 (489381 upstream) : TP53TG3B (31585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33378446	33378446	+	IGR	DEL	A	-	-	rs111647005		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33378446delA								SLC6A10P (481983 upstream) : MIR1826 (587062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33530019	33530019	+	IGR	DEL	T	-	-	rs111564755		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	33606803	33606804	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33606803_33606804insT								SLC6A10P (710340 upstream) : MIR1826 (358704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33821436	33821437	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33821436_33821437insT								SLC6A10P (924973 upstream) : MIR1826 (144071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33829008	33829008	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33829008delC								SLC6A10P (932545 upstream) : MIR1826 (136500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34002212	34002212	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34002212delA								MIR1826 (36620 upstream) : UBE2MP1 (401590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34007734	34007735	+	IGR	INS	-	AA	AA	rs141266293		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34007734_34007735insAA								MIR1826 (42142 upstream) : UBE2MP1 (396067 downstream)																																			---	---	---	---
LOC283914	283914	broad.mit.edu	37	16	34617194	34617195	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34617194_34617195insT	uc010vgc.1	+						LOC283914_uc002edw.2_RNA	NR_027080				Homo sapiens cDNA clone IMAGE:5271062.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	46493871	46493872	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46493871_46493872delTG								None (None upstream) : ANKRD26P1 (9377 downstream)																																			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47205338	47205338	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47205338delT	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)																---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47292700	47292700	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	47709429	47709432	+	Intron	DEL	CACT	-	-	rs60526044		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47709429_47709432delCACT	uc002eev.3	+						PHKB_uc002eeu.3_Intron|PHKB_uc002eew.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	47877405	47877405	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47877405delC								PHKB (141972 upstream) : ABCC12 (239479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48074739	48074740	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48074739_48074740delTT								PHKB (339306 upstream) : ABCC12 (42144 downstream)																																			---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48172717	48172717	+	Intron	DEL	T	-	-	rs112593695		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48172717delT	uc002efc.1	-						ABCC12_uc002eey.1_Intron|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_Intron|ABCC12_uc002efd.1_Intron|ABCC12_uc002efe.1_Intron|ABCC12_uc010vgj.1_Intron	NM_033226	NP_150229			ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	49496270	49496271	+	IGR	INS	-	A	A	rs35451941		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49496270_49496271insA								C16orf78 (62953 upstream) : ZNF423 (28251 downstream)																																			---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53471221	53471221	+	Intron	DEL	T	-	-	rs78410252		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53471221delT	uc002ehi.3	+						RBL2_uc010vgv.1_Intron	NM_005611	NP_005602			retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54183810	54183813	+	IGR	DEL	TTTT	-	-	rs76452906		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54183810_54183813delTTTT								FTO (35432 upstream) : IRX3 (133399 downstream)																																			---	---	---	---
BBS2	583	broad.mit.edu	37	16	56532619	56532620	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56532619_56532620delAA	uc002ejd.2	-						BBS2_uc010ccg.2_3'UTR	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				---	---	---	---
SLC12A3	6559	broad.mit.edu	37	16	56924815	56924817	+	Intron	DEL	AAA	-	-	rs35897513		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56924815_56924817delAAA	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580			solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)													---	---	---	---
CETP	1071	broad.mit.edu	37	16	57010691	57010692	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57010691_57010692delTC	uc002eki.2	+						CETP_uc002ekj.2_Intron	NM_000078	NP_000069			cholesteryl ester transfer protein, plasma						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	57066156	57066157	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57066156_57066157delAA	uc002ekk.1	+						NLRC5_uc010ccq.1_Intron|NLRC5_uc002ekn.2_Intron|NLRC5_uc002ekl.2_Intron|NLRC5_uc002ekm.2_Intron|NLRC5_uc010ccr.1_Intron|NLRC5_uc010ccs.1_5'Flank	NM_032206	NP_115582			nucleotide-binding oligomerization domains 27						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	58122807	58122807	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58122807delT								MMP15 (42005 upstream) : C16orf80 (24690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58175432	58175432	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58175432delT								C16orf80 (12136 upstream) : CSNK2A2 (16384 downstream)																																			---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58647056	58647056	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58647056delA	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	58670626	58670626	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58670626delT								CNOT1 (6876 upstream) : SLC38A7 (29672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59463502	59463502	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59463502delT								GOT2 (695256 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59639905	59639906	+	IGR	DEL	AC	-	-	rs112132509		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59639905_59639906delAC								GOT2 (871659 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60279537	60279537	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60279537delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60572240	60572242	+	IGR	DEL	GGA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60572240_60572242delGGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61102559	61102560	+	IGR	DEL	AG	-	-	rs72008791		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61102559_61102560delAG								None (None upstream) : CDH8 (584675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61348294	61348294	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61348294delA								None (None upstream) : CDH8 (338941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61442316	61442317	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61442316_61442317insT								None (None upstream) : CDH8 (244918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62378244	62378244	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62378244delA								CDH8 (308208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62891467	62891474	+	IGR	DEL	ACACACAC	-	-	rs143646977		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62891467_62891474delACACACAC								CDH8 (821431 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63022418	63022418	+	IGR	DEL	T	-	-	rs57324389		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63022418delT								CDH8 (952382 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63809099	63809099	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63809099delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64060373	64060373	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64060373delA								None (None upstream) : CDH11 (920312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64241641	64241641	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64241641delA								None (None upstream) : CDH11 (739044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64923042	64923043	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64923042_64923043delTT								None (None upstream) : CDH11 (57642 downstream)																																			---	---	---	---
CDH11	1009	broad.mit.edu	37	16	65078615	65078616	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65078615_65078616insA	uc002eoi.2	-						CDH11_uc002eoj.2_Intron|CDH11_uc010vin.1_Intron|CDH11_uc010vio.1_Intron	NM_001797	NP_001788			cadherin 11, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
LOC283867	283867	broad.mit.edu	37	16	65417291	65417292	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65417291_65417292insA	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	65714770	65714772	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65714770_65714772delAAA								LOC283867 (104567 upstream) : CDH5 (685753 downstream)																																			---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66732522	66732522	+	5'Flank	DEL	T	-	-	rs112276947		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66732522delT	uc002epz.2	-						CMTM4_uc002eqa.2_5'Flank	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)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66811036	66811036	+	Intron	DEL	A	-	-	rs71671589		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66811036delA	uc010viv.1	-						CCDC79_uc002eqc.1_Intron|CCDC79_uc002eqd.1_Intron	NM_001136505	NP_001129977			coiled-coil domain containing 79						regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
CBFB	865	broad.mit.edu	37	16	67104591	67104592	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67104591_67104592delAA	uc002era.2	+						CBFB_uc002erb.2_Intron|CBFB_uc010vja.1_Intron	NM_001755	NP_001746			core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)				T	MYH11	AML								---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67355554	67355555	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67355554_67355555delTT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
ATP6V0D1	9114	broad.mit.edu	37	16	67488438	67488439	+	Intron	INS	-	TTTTGT	TTTTGT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67488438_67488439insTTTTGT	uc002ete.1	-						ATP6V0D1_uc010vjo.1_Intron|ATP6V0D1_uc010vjn.1_Intron	NM_004691	NP_004682			ATPase, H+ transporting, lysosomal, V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	67586326	67586326	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67586326delC								FAM65A (5638 upstream) : CTCF (10138 downstream)																																			---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67615232	67615232	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67615232delT	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)														---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67769671	67769672	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67769671_67769672delAA	uc002eud.2	-						RANBP10_uc010ceo.2_Intron|RANBP10_uc010vju.1_Intron|RANBP10_uc010vjv.1_Intron|RANBP10_uc010vjx.1_Intron|RANBP10_uc010vjy.1_Intron	NM_020850	NP_065901			RAN binding protein 10											ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)														---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67778725	67778726	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67778725_67778726insT	uc002eud.2	-						RANBP10_uc010ceo.2_Intron|RANBP10_uc010vju.1_Intron|RANBP10_uc010vjv.1_Intron|RANBP10_uc010vjx.1_Intron|RANBP10_uc010vjy.1_Intron	NM_020850	NP_065901			RAN binding protein 10											ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)														---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68707819	68707819	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68707819delA	uc002ewf.2	+						CDH3_uc010vli.1_Intron	NM_001793	NP_001784			cadherin 3, type 1 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)														---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	68906125	68906125	+	Intron	DEL	A	-	-	rs74784219		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68906125delA	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)														---	---	---	---
SNTB2	6645	broad.mit.edu	37	16	69339663	69339663	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69339663delT	uc002ewu.2	+	7						NM_006750	NP_006741			basic beta 2 syntrophin							cell junction|dystrophin-associated glycoprotein complex|membrane fraction|microtubule|transport vesicle membrane	actin binding|calmodulin binding|protein binding				0		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)														---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70112545	70112545	+	Intron	DEL	T	-	-	rs74482750		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70112545delT	uc002exy.2	+							NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70178854	70178855	+	Intron	INS	-	A	A	rs149555664		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70178854_70178855insA	uc002eyf.1	+						CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Intron|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_5'Flank|PDPR_uc010vls.1_5'Flank	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)														---	---	---	---
DDX19B	11269	broad.mit.edu	37	16	70327157	70327157	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70327157delA	uc010vlv.1	+						DDX19B_uc010vlw.1_5'Flank	NM_001014451	NP_001014451			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						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)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70988702	70988702	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70988702delT	uc002ezr.2	-							NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70993832	70993832	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70993832delT	uc002ezr.2	-							NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71061896	71061896	+	Intron	DEL	T	-	-	rs142337199		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71061896delT	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_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	71269955	71269955	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71269955delT								HYDIN (5330 upstream) : FTSJD1 (46249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	71353977	71353981	+	IGR	DEL	GCATG	-	-	rs72437812		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71353977_71353981delGCATG								FTSJD1 (30464 upstream) : CALB2 (38645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	71556027	71556028	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71556027_71556028insA								ZNF19 (32773 upstream) : CHST4 (4033 downstream)																																			---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	71994067	71994067	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71994067delA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	72028454	72028454	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72028454delA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	72534798	72534798	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72534798delC	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	73521307	73521308	+	IGR	INS	-	T	T	rs71956866		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73521307_73521308insT								HTA (393637 upstream) : PSMD7 (809373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74018598	74018598	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74018598delA								HTA (890928 upstream) : PSMD7 (312083 downstream)																																			---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74514459	74514459	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74514459delT	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	75127283	75127286	+	Intron	DEL	AAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75127283_75127286delAAAA	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																		---	---	---	---
ZFP1	162239	broad.mit.edu	37	16	75201295	75201295	+	Intron	DEL	T	-	-	rs35744641		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75201295delT	uc002fdo.2	+						ZFP1_uc002fdp.2_Intron|ZFP1_uc010cgt.2_Intron|ZFP1_uc010cgs.2_Intron|ZFP1_uc002fdq.2_Intron	NM_153688	NP_710155			zinc finger protein 1 homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75784804	75784804	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75784804delT								TERF2IP (93476 upstream) : CNTNAP4 (526372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76099237	76099237	+	IGR	DEL	T	-	-	rs11309658		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76099237delT								TERF2IP (407909 upstream) : CNTNAP4 (211939 downstream)																																			---	---	---	---
CNTNAP4	85445	broad.mit.edu	37	16	76429634	76429634	+	Intron	DEL	T	-	-	rs66722954		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76429634delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	76962169	76962170	+	IGR	DEL	TG	-	-	rs139669534		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76962169_76962170delTG								CNTNAP4 (369034 upstream) : MON1B (262666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77275109	77275109	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77275109delA								SYCE1L (28133 upstream) : ADAMTS18 (40917 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78338845	78338846	+	Intron	INS	-	T	T	rs140986697	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78338845_78338846insT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_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)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78483302	78483302	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78483302delG	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_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)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78862984	78862987	+	Intron	DEL	GATG	-	-	rs72383986		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78862984_78862987delGATG	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_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)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78911176	78911176	+	Intron	DEL	C	-	-	rs113657530		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78911176delC	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_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	79687930	79687931	+	IGR	INS	-	GTGT	GTGT	rs145484295	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79687930_79687931insGTGT								MAF (53308 upstream) : DYNLRB2 (886923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80924340	80924340	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80924340delA	uc002fft.1	-											Homo sapiens cDNA FLJ35683 fis, clone SPLEN2019131.																														---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81578538	81578538	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81578538delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	81759345	81759346	+	IGR	INS	-	CCTTCCTTCCTTCC	CCTTCCTTCCTTCC	rs67564461		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81759345_81759346insCCTTCCTTCCTTCC								CMIP (13980 upstream) : PLCG2 (53584 downstream)																																			---	---	---	---
PLCG2	5336	broad.mit.edu	37	16	81817438	81817438	+	Intron	DEL	T	-	-	rs74908827		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81817438delT	uc002fgt.2	+						PLCG2_uc010chg.1_5'Flank	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	82311975	82311976	+	IGR	INS	-	ACACACAC	ACACACAC	rs28641500		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82311975_82311976insACACACAC								MPHOSPH6 (108146 upstream) : CDH13 (348602 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82706408	82706409	+	Intron	DEL	AC	-	-	rs150321182		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82706408_82706409delAC	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82813464	82813465	+	Intron	INS	-	TA	TA	rs144345801	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82813464_82813465insTA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82893170	82893172	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82893170_82893172delAAA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82969060	82969060	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82969060delT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83765943	83765943	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83765943delG	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83772137	83772137	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83772137delC	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
HSBP1	3281	broad.mit.edu	37	16	83843047	83843047	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83843047delT	uc002fgy.1	+							NM_001537	NP_001528			heat shock factor binding protein 1						negative regulation of transcription from RNA polymerase II promoter	nucleus	transcription corepressor activity				0		all_cancers(2;0.00573)|all_epithelial(2;0.0309)		BRCA - Breast invasive adenocarcinoma(80;0.0404)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	83854422	83854423	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83854422_83854423delTC								HSBP1 (7828 upstream) : MLYCD (78307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	84246517	84246519	+	IGR	DEL	TTT	-	-	rs35521888		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84246517_84246519delTTT								ADAD2 (15745 upstream) : KCNG4 (9306 downstream)																																			---	---	---	---
WFDC1	58189	broad.mit.edu	37	16	84352358	84352358	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84352358delG	uc002fhw.2	+						WFDC1_uc002fhv.2_Intron	NM_021197	NP_067020			WAP four-disulfide core domain 1 precursor						negative regulation of cell growth	extracellular space	serine-type endopeptidase inhibitor activity			breast(1)	1																		---	---	---	---
COTL1	23406	broad.mit.edu	37	16	84636457	84636458	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84636457_84636458delAA	uc002fid.2	-						COTL1_uc002fie.2_Intron|COTL1_uc010chk.2_Intron	NM_021149	NP_066972			coactosin-like 1							cytoplasm|cytoskeleton	actin binding|enzyme binding			skin(1)	1																		---	---	---	---
USP10	9100	broad.mit.edu	37	16	84799083	84799083	+	Intron	DEL	T	-	-	rs67261206		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84799083delT	uc002fii.2	+						USP10_uc010voe.1_Intron|USP10_uc010vof.1_Intron|USP10_uc002fij.2_Intron	NM_005153	NP_005144			ubiquitin specific protease 10						DNA damage response, signal transduction by p53 class mediator|DNA repair|protein deubiquitination|ubiquitin-dependent protein catabolic process	early endosome|intermediate filament cytoskeleton|nucleus	cystic fibrosis transmembrane conductance regulator binding|p53 binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0																		---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84855711	84855711	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84855711delC	uc010voh.1	+						CRISPLD2_uc010vog.1_Intron|CRISPLD2_uc002fio.2_Intron|CRISPLD2_uc002fik.3_Intron|CRISPLD2_uc002fil.2_Intron|CRISPLD2_uc002fim.2_Intron|CRISPLD2_uc002fin.3_Intron	NM_031476	NP_113664			cysteine-rich secretory protein LCCL domain							extracellular region|transport vesicle					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	85397857	85397857	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85397857delC								FAM92B (251743 upstream) : KIAA0182 (247172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85502858	85502859	+	IGR	INS	-	A	A	rs113931439		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85502858_85502859insA								FAM92B (356744 upstream) : KIAA0182 (142170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86404944	86404945	+	IGR	INS	-	A	A	rs144800460	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86404944_86404945insA								LOC732275 (25659 upstream) : FOXF1 (139188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86436870	86436871	+	IGR	INS	-	C	C	rs147084195	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86436870_86436871insC								LOC732275 (57585 upstream) : FOXF1 (107262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86737117	86737118	+	IGR	INS	-	AGT	AGT	rs150538830	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86737117_86737118insAGT								FOXL1 (121814 upstream) : FBXO31 (625826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88269737	88269737	+	IGR	DEL	G	-	-	rs77723947		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88269737delG								BANP (158814 upstream) : ZNF469 (224142 downstream)																																			---	---	---	---
FAM38A	9780	broad.mit.edu	37	16	88806255	88806260	+	Intron	DEL	CCTGGC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88806255_88806260delCCTGGC	uc010vpb.1	-						uc010vpc.1_RNA|uc010cic.1_5'Flank	NM_001142864	NP_001136336			family with sequence similarity 38, member A							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	89104804	89104805	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89104804_89104805delTG								CBFA2T3 (61403 upstream) : ACSF3 (55449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	89308110	89308114	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89308110_89308114delTTTTT								ZNF778 (8610 upstream) : ANKRD11 (25921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	89747195	89747199	+	IGR	DEL	TTTTC	-	-	rs147140115	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89747195_89747199delTTTTC								C16orf55 (9520 upstream) : CDK10 (5877 downstream)																																			---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89809062	89809072	+	Intron	DEL	AAAAAAAAAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89809062_89809072delAAAAAAAAAAA	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc010vpo.1_Intron	NM_000135	NP_000126			Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89818179	89818181	+	Intron	DEL	TTT	-	-	rs68008076		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89818179_89818181delTTT	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc010vpo.1_Intron	NM_000135	NP_000126			Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89872325	89872325	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89872325delT	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc002fov.1_Intron|FANCA_uc002fow.1_Intron|FANCA_uc002fox.1_Intron|FANCA_uc010ciu.1_Intron|FANCA_uc002foy.2_Intron	NM_000135	NP_000126			Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	16	89980552	89980553	+	RNA	DEL	TG	-	-	rs72318787		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89980552_89980553delTG	uc010ciy.1	+	2		c.1055_1056delTG								Homo sapiens cDNA clone IMAGE:40002380.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	90188413	90188413	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90188413delA	uc002fqr.2	+											Homo sapiens cDNA FLJ35239 fis, clone PROST2002212.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	213870	213873	+	IGR	DEL	ATAG	-	-	rs138290841		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:213870_213873delATAG								RPH3AL (11294 upstream) : C17orf97 (46245 downstream)																																			---	---	---	---
FAM57A	79850	broad.mit.edu	37	17	639051	639051	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:639051delA	uc002frp.2	+						FAM57A_uc002frq.2_Intron|FAM57A_uc002frr.2_Intron	NM_024792	NP_079068			family with sequence similarity 57, member A							integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0217)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	744843	744844	+	Intron	INS	-	T	T	rs149671291		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:744843_744844insT	uc002fsa.2	-						NXN_uc002fsb.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)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1009430	1009431	+	Intron	INS	-	C	C	rs148330284	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1009430_1009431insC	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc002fsg.2_Intron|ABR_uc010cjq.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
SMYD4	114826	broad.mit.edu	37	17	1698614	1698633	+	Intron	DEL	ATCTATCTATCTATCTAATC	-	-	rs71375545		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1698614_1698633delATCTATCTATCTATCTAATC	uc002ftm.3	-						SMYD4_uc002ftn.1_Intron	NM_052928	NP_443160			SET and MYND domain containing 4								zinc ion binding			skin(3)|kidney(2)	5																		---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1865574	1865575	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1865574_1865575delAA	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
METT10D	79066	broad.mit.edu	37	17	2333573	2333573	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2333573delT	uc002fut.2	-						METT10D_uc002fuu.3_Intron|METT10D_uc010cka.2_Intron|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_Intron|METT10D_uc010vqy.1_Intron	NM_024086	NP_076991			methyltransferase 10 domain containing								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	2422012	2422012	+	IGR	DEL	G	-	-	rs74311742		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2422012delG								METT10D (6812 upstream) : PAFAH1B1 (74911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	2673521	2673521	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2673521delA								MIR1253 (22045 upstream) : RAP1GAP2 (26211 downstream)																																			---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2790975	2790975	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2790975delT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
SHPK	23729	broad.mit.edu	37	17	3522330	3522330	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3522330delT	uc002fvz.1	-							NM_013276	NP_037408			carbohydrate kinase-like						carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3928682	3928682	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3928682delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_Intron|ZZEF1_uc002fxi.2_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4397012	4397013	+	IGR	DEL	TG	-	-	rs55748804	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4397012_4397013delTG								SPNS3 (5514 upstream) : SPNS2 (5116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5714018	5714018	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5714018delT	uc002gcm.2	+											Homo sapiens hypothetical protein LOC339166, mRNA (cDNA clone IMAGE:5163423), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	5848555	5848555	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5848555delC								NLRP1 (360723 upstream) : WSCD1 (123882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5959163	5959164	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5959163_5959164delAG								NLRP1 (471331 upstream) : WSCD1 (13273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	6824079	6824080	+	IGR	INS	-	TG	TG	rs147171995	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6824079_6824080insTG								ALOX12P2 (20412 upstream) : ALOX12 (75304 downstream)																																			---	---	---	---
ASGR1	432	broad.mit.edu	37	17	7079170	7079171	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7079170_7079171delCA	uc002ges.3	-						ASGR1_uc010clx.1_Intron	NM_001671	NP_001662			asialoglycoprotein receptor 1						receptor-mediated endocytosis	integral to plasma membrane	asialoglycoprotein receptor activity|metal ion binding|sugar binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7603866	7603867	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7603866_7603867delAA	uc010vuh.1	+						WRAP53_uc010vui.1_Intron|WRAP53_uc002gip.2_Intron|WRAP53_uc002gir.2_Intron|WRAP53_uc002giq.2_Intron|WRAP53_uc010cnl.2_Intron|WRAP53_uc010vuj.1_5'Flank	NM_001143990	NP_001137462			WD repeat domain 79 isoform 2						positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0																		---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7713720	7713720	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7713720delT	uc002giu.1	+						DNAH2_uc010cnm.1_Intron	NM_020877	NP_065928			dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	7871232	7871232	+	IGR	DEL	A	-	-	rs62856660		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7871232delA								CNTROB (18337 upstream) : GUCY2D (34756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	7934205	7934206	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7934205_7934206delTT								GUCY2D (10547 upstream) : ALOX15B (8152 downstream)																																			---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7990546	7990557	+	Intron	DEL	ACACACACAGAC	-	-	rs72449480		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7990546_7990557delACACACACAGAC	uc002gjy.1	-						hsa-mir-4314|MI0015846_5'Flank	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)			---	---	---	---
C17orf68	80169	broad.mit.edu	37	17	8134459	8134459	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8134459delA	uc002gkq.3	-						C17orf68_uc010cnv.2_Intron	NM_025099	NP_079375			alpha accessory factor 132						positive regulation of DNA replication|telomere maintenance	Stn1-Ten1 complex	protein binding|single-stranded DNA binding				0																		---	---	---	---
PFAS	5198	broad.mit.edu	37	17	8164558	8164558	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8164558delT	uc002gkr.2	+						PFAS_uc010vuv.1_Intron|PFAS_uc010cnw.1_5'Flank	NM_012393	NP_036525			phosphoribosylformylglycinamidine synthase						'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process	cytosol	ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding			ovary(2)|central_nervous_system(2)|pancreas(1)	5					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
STX8	9482	broad.mit.edu	37	17	9253270	9253270	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9253270delC	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9422186	9422189	+	Intron	DEL	AAAA	-	-	rs35000731		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9422186_9422189delAAAA	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
WDR16	146845	broad.mit.edu	37	17	9509388	9509388	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9509388delA	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																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9619287	9619288	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9619287_9619288delTG	uc010cod.2	+						USP43_uc002gma.3_Intron|USP43_uc010vva.1_Intron|USP43_uc010coe.2_Intron|USP43_uc002gmc.3_Intron	NM_153210	NP_694942			ubiquitin specific protease 43						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	9702910	9702911	+	IGR	INS	-	TG	TG	rs147256412	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9702910_9702911insTG								DHRS7C (8309 upstream) : GLP2R (26470 downstream)																																			---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9993487	9993488	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9993487_9993488delAA	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
GAS7	8522	broad.mit.edu	37	17	10006069	10006069	+	Intron	DEL	T	-	-	rs142011191		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10006069delT	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10446084	10446084	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10446084delA	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																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11528394	11528395	+	Intron	DEL	CA	-	-	rs71679095		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11528394_11528395delCA	uc002gne.2	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12164929	12164930	+	IGR	INS	-	TC	TC	rs10646465		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12164929_12164930insTC								MAP2K4 (117879 upstream) : MYOCD (404277 downstream)																																			---	---	---	---
RICH2	9912	broad.mit.edu	37	17	12766162	12766162	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12766162delA	uc002gnr.3	+						RICH2_uc010vvk.1_Intron|RICH2_uc010vvl.1_Intron|RICH2_uc002gns.3_Intron|RICH2_uc010vvm.1_Intron|RICH2_uc010vvn.1_Intron	NM_014859	NP_055674			Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	13251708	13251708	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13251708delT								ELAC2 (330349 upstream) : HS3ST3A1 (147298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13639194	13639195	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13639194_13639195insT								HS3ST3A1 (133950 upstream) : CDRT15P (288620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14454738	14454739	+	IGR	DEL	AC	-	-	rs72169255		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14454738_14454739delAC								HS3ST3B1 (205246 upstream) : PMP22 (678358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14533734	14533734	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14533734delA								HS3ST3B1 (284242 upstream) : PMP22 (599363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14608988	14608989	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14608988_14608989delTT								HS3ST3B1 (359496 upstream) : PMP22 (524108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	15058758	15058759	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15058758_15058759delAA								HS3ST3B1 (809266 upstream) : PMP22 (74338 downstream)																																			---	---	---	---
TRIM16	10626	broad.mit.edu	37	17	15496417	15496417	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15496417delA	uc002gor.1	-						CDRT1_uc010vvy.1_Intron|CDRT1_uc010vvz.1_Intron|CDRT1_uc002gov.3_Intron					SubName: Full=Putative uncharacterized protein; Flags: Fragment;						histone H3 acetylation|histone H4 acetylation|positive regulation of interleukin-1 beta secretion|positive regulation of keratinocyte differentiation|positive regulation of retinoic acid receptor signaling pathway|positive regulation of transcription, DNA-dependent|response to growth hormone stimulus|response to organophosphorus|response to retinoic acid	cytoplasm|plasma membrane|PML body	DNA binding|interleukin-1 binding|NACHT domain binding|zinc ion binding			ovary(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	16420421	16420421	+	IGR	DEL	T	-	-	rs5819576		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16420421delT								C17orf76 (24941 upstream) : ZNF287 (33210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	16429788	16429789	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16429788_16429789insT								C17orf76 (34308 upstream) : ZNF287 (23842 downstream)																																			---	---	---	---
ZNF624	57547	broad.mit.edu	37	17	16532090	16532091	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16532090_16532091delAA	uc010cpi.1	-							NM_020787	NP_065838			zinc finger protein 624						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)														---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17703480	17703481	+	Intron	INS	-	TCTGTCTCTC	TCTGTCTCTC	rs35020141		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17703480_17703481insTCTGTCTCTC	uc002grm.2	+							NM_030665	NP_109590			retinoic acid induced 1							cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	17982340	17982340	+	IGR	DEL	A	-	-	rs142867503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17982340delA								C17orf39 (10622 upstream) : DRG2 (8943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	18398885	18398886	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18398885_18398886insA								LGALS9C (627 upstream) : LOC220594 (15691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19403645	19403645	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19403645delT								RNF112 (83058 upstream) : SLC47A1 (33522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19431159	19431159	+	IGR	DEL	A	-	-	rs35747845		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19431159delA								RNF112 (110572 upstream) : SLC47A1 (6008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19492329	19492331	+	IGR	DEL	ACT	-	-	rs60144002		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19492329_19492331delACT								SLC47A1 (9983 upstream) : ALDH3A2 (59733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19499510	19499510	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19499510delA								SLC47A1 (17164 upstream) : ALDH3A2 (52554 downstream)																																			---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20189133	20189134	+	Intron	DEL	TT	-	-	rs112146667		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20189133_20189134delTT	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	20382948	20382948	+	IGR	DEL	T	-	-	rs56272040		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20382948delT								LGALS9B (12100 upstream) : CCDC144NL (383762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20606137	20606137	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20606137delT								LGALS9B (235289 upstream) : CCDC144NL (160573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21164377	21164377	+	IGR	DEL	T	-	-	rs11304155		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21164377delT								C17orf103 (7799 upstream) : MAP2K3 (23591 downstream)																																			---	---	---	---
MAP2K3	5606	broad.mit.edu	37	17	21190473	21190473	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21190473delC	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron	NM_145109	NP_659731			mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|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|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	21230585	21230586	+	IGR	INS	-	ATAAT	ATAAT	rs149209781		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21230585_21230586insATAAT								MAP2K3 (12036 upstream) : KCNJ12 (49113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21341833	21341833	+	IGR	DEL	G	-	-	rs63315060		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21341833delG								KCNJ12 (18654 upstream) : C17orf51 (89739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21408420	21408420	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21408420delA								KCNJ12 (85241 upstream) : C17orf51 (23152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21520240	21520241	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21520240_21520241insA								C17orf51 (42509 upstream) : FAM27L (305129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21525263	21525263	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21525263delT								C17orf51 (47532 upstream) : FAM27L (300107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21527523	21527528	+	IGR	DEL	TGTGCG	-	-	rs150010584		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21527523_21527528delTGTGCG								C17orf51 (49792 upstream) : FAM27L (297842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21531402	21531402	+	IGR	DEL	T	-	-	rs75040995		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21531402delT								C17orf51 (53671 upstream) : FAM27L (293968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21541903	21541904	+	IGR	INS	-	G	G	rs146783355		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21541903_21541904insG								C17orf51 (64172 upstream) : FAM27L (283466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21981676	21981676	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21981676delT								FLJ36000 (68606 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	22055916	22055917	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22055916_22055917insC								FLJ36000 (142846 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	22176132	22176132	+	IGR	DEL	A	-	-	rs112062309		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:22176132delA								FLJ36000 (263062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25270417	25270417	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25270417delG								None (None upstream) : WSB1 (350689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25293982	25293983	+	IGR	INS	-	AAT	AAT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25293982_25293983insAAT								None (None upstream) : WSB1 (327123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25299920	25299923	+	IGR	DEL	TTAC	-	-	rs113874200		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25299920_25299923delTTAC								None (None upstream) : WSB1 (321183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25310849	25310849	+	IGR	DEL	A	-	-	rs33937773		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25310849delA								None (None upstream) : WSB1 (310257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25317773	25317774	+	IGR	INS	-	T	T	rs143994876	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25317773_25317774insT								None (None upstream) : WSB1 (303332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25327560	25327561	+	IGR	INS	-	T	T	rs145728212		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25327560_25327561insT								None (None upstream) : WSB1 (293545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25740051	25740052	+	IGR	DEL	AC	-	-	rs58859577		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25740051_25740052delAC								WSB1 (99406 upstream) : KSR1 (58984 downstream)																																			---	---	---	---
TMEM97	27346	broad.mit.edu	37	17	26654164	26654164	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26654164delT	uc002hat.2	+	3						NM_014573	NP_055388			transmembrane protein 97						cholesterol homeostasis|regulation of cell growth	integral to membrane|lysosome|nuclear membrane|plasma membrane|rough endoplasmic reticulum	protein binding				0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)														---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26959820	26959820	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26959820delA	uc002hbu.2	-							NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26964371	26964371	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26964371delA	uc002hbu.2	-							NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	27354030	27354030	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27354030delA								SEZ6 (20572 upstream) : PIPOX (15888 downstream)																																			---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27475062	27475062	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27475062delA	uc002hdt.1	-						MYO18A_uc010csa.1_Intron|MYO18A_uc002hdu.1_Intron	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	27685135	27685135	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27685135delT								NUFIP2 (63969 upstream) : TAOK1 (32808 downstream)																																			---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28320516	28320516	+	Intron	DEL	A	-	-	rs78216599		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28320516delA	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron|EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
TMIGD1	388364	broad.mit.edu	37	17	28652583	28652583	+	Intron	DEL	A	-	-	rs34218272		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28652583delA	uc002hfa.1	-						TMIGD1_uc010csh.1_Intron	NM_206832	NP_996663			transmembrane and immunoglobulin domain							integral to membrane					0																		---	---	---	---
TBC1D29	26083	broad.mit.edu	37	17	28885450	28885451	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28885450_28885451insT	uc002hfh.2	+						uc002hfg.1_5'Flank|TBC1D29_uc002hfi.2_5'Flank	NM_015594	NP_056409			TBC1 domain family, member 29							intracellular	Rab GTPase activator activity				0		Myeloproliferative disorder(56;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	29013542	29013543	+	IGR	DEL	AC	-	-	rs71970549		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29013542_29013543delAC								LRRC37B2 (20827 upstream) : SUZ12P (22171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29338460	29338461	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29338460_29338461delAC								RNF135 (11535 upstream) : NF1 (83534 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	17	29380687	29380688	+	IGR	INS	-	A	A	rs149866235	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29380687_29380688insA								RNF135 (53762 upstream) : NF1 (41307 downstream)																																			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29575850	29575851	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29575850_29575851delTT	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron|NF1_uc002hgi.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	p.?(2)		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)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29943811	29943811	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29943811delG								MIR365-2 (41271 upstream) : C17orf79 (235074 downstream)																																			---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30502481	30502481	+	Intron	DEL	T	-	-	rs149208196		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30502481delT	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)																---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31487699	31487699	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31487699delC	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)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31696456	31696456	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31696456delT	uc002hhu.2	-							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	32633171	32633171	+	IGR	DEL	A	-	-	rs112391295		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32633171delA								CCL11 (17972 upstream) : CCL8 (12895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	33144351	33144351	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33144351delA								TMEM132E (178015 upstream) : CCT6B (110589 downstream)																																			---	---	---	---
RFFL	117584	broad.mit.edu	37	17	33358136	33358136	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33358136delT	uc002hin.1	-						RFFL_uc002hiq.2_Intron|RFFL_uc010cti.1_Intron|RFFL_uc002hip.1_Intron|RFFL_uc002hio.1_Intron	NM_001017368	NP_001017368			rififylin						apoptosis	membrane	ligase activity|zinc ion binding				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)														---	---	---	---
CCL5	6352	broad.mit.edu	37	17	34203939	34203940	+	Intron	INS	-	T	T	rs138597635	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34203939_34203940insT	uc002hkf.2	-							NM_002985	NP_002976			small inducible cytokine A5 precursor						activation of phospholipase D activity|cell-cell signaling|cellular protein complex assembly|chemokine-mediated signaling pathway|dendritic cell chemotaxis|eosinophil chemotaxis|immune response|leukocyte cell-cell adhesion|macrophage chemotaxis|negative regulation of T cell apoptosis|negative regulation of viral genome replication|neutrophil activation|positive regulation of activation of JAK2 kinase activity|positive regulation of cell-cell adhesion mediated by integrin|positive regulation of homotypic cell-cell adhesion|positive regulation of innate immune response|positive regulation of macrophage chemotaxis|positive regulation of monocyte chemotaxis|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of T cell apoptosis|positive regulation of T cell chemotaxis|positive regulation of T cell proliferation|positive regulation of translational initiation|positive regulation of tyrosine phosphorylation of STAT protein|positive regulation of viral genome replication|protein tetramerization|regulation of chronic inflammatory response|response to virus	extracellular space	CCR1 chemokine receptor binding|CCR4 chemokine receptor binding|CCR5 chemokine receptor binding|chemoattractant activity|chemokine activity|chemokine receptor antagonist activity|protein homodimerization activity|protein self-association|receptor signaling protein tyrosine kinase activator activity				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0183)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	34481815	34481815	+	IGR	DEL	C	-	-	rs75088276		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34481815delC								CCL4 (48801 upstream) : TBC1D3B (11246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	35008310	35008311	+	IGR	INS	-	GTGC	GTGC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35008310_35008311insGTGC								MRM1 (42904 upstream) : LHX1 (286188 downstream)																																			---	---	---	---
C17orf78	284099	broad.mit.edu	37	17	35749618	35749619	+	3'UTR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35749618_35749619delAA	uc002hns.2	+	7					ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc002hnq.2_Intron	NM_173625	NP_775896			hypothetical protein LOC284099							integral to membrane					0		Breast(25;0.00295)|Ovarian(249;0.15)																---	---	---	---
TADA2A	6871	broad.mit.edu	37	17	35804503	35804504	+	Intron	INS	-	A	A	rs146647296	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35804503_35804504insA	uc002hnt.2	+						TADA2A_uc002hnu.1_Intron|TADA2A_uc002hnv.2_Intron|TADA2A_uc010wdd.1_Intron|TADA2A_uc002hnw.2_Intron|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479			transcriptional adaptor 2A isoform a						histone H3 acetylation|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)|skin(1)	4																		---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35989272	35989273	+	Intron	INS	-	ACAC	ACAC	rs10661586		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35989272_35989273insACAC	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941			ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	36812532	36812533	+	IGR	DEL	GG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36812532_36812533delGG								SRCIN1 (50349 upstream) : C17orf96 (15428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	37078102	37078103	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37078102_37078103delTG								LASP1 (80 upstream) : FBXO47 (14582 downstream)																																			---	---	---	---
KRT28	162605	broad.mit.edu	37	17	38956830	38956830	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38956830delA	uc002hvh.1	-							NM_181535	NP_853513			keratin 25D							cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)																---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41224585	41224586	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41224585_41224586delTT	uc002icq.2	-						BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Intron|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Intron|BRCA1_uc002ict.2_Intron|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron	NM_007294	NP_009225			breast cancer 1, early onset isoform 1						androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	43059666	43059704	+	IGR	DEL	GGTGGTGGTGGTAATGATATTGGTGGTGGTGATGGAGGA	-	-	rs116364318	by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43059666_43059704delGGTGGTGGTGGTAATGATATTGGTGGTGGTGATGGAGGA								C1QL1 (14022 upstream) : DCAKD (41002 downstream)																																			---	---	---	---
CRHR1	1394	broad.mit.edu	37	17	43895168	43895169	+	Intron	INS	-	G	G	rs147741634	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43895168_43895169insG	uc010dap.2	+						CRHR1_uc010wjx.1_Intron|CRHR1_uc002ijp.2_Intron|CRHR1_uc002ijm.2_Intron|CRHR1_uc002ijn.2_Intron|CRHR1_uc010dar.2_Intron|CRHR1_uc010dao.2_Intron|CRHR1_uc010daq.2_Intron|CRHR1_uc010das.1_Intron|CRHR1_uc002ijo.1_Intron	NM_001145146	NP_001138618			corticotropin releasing hormone receptor 1						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44285983	44285987	+	Intron	DEL	AAAAA	-	-	rs149187563		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44285983_44285987delAAAAA	uc010dav.2	-							NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	44309250	44309251	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44309250_44309251insA								KIAA1267 (6533 upstream) : ARL17B (54612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45148043	45148043	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45148043delT	uc002ilc.1	-											full-length cDNA clone CS0DH004YI07 of T cells (Jurkat cell line) of Homo sapiens (human).																														---	---	---	---
CDC27	996	broad.mit.edu	37	17	45241565	45241565	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45241565delA	uc002ild.3	-						CDC27_uc002ile.3_Intron|CDC27_uc002ilf.3_Intron|CDC27_uc010wkp.1_Intron|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247			cell division cycle protein 27 isoform 2						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	46095149	46095150	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46095149_46095150delTT								CDK5RAP3 (36003 upstream) : COPZ2 (8385 downstream)																																			---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46213539	46213540	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46213539_46213540delTT	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
HOXB7	3217	broad.mit.edu	37	17	46685066	46685066	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46685066delT	uc002inv.2	-	2					HOXB6_uc002ins.1_5'Flank|HOXB6_uc010dbh.1_5'Flank	NM_004502	NP_004493			homeobox B7							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
TTLL6	284076	broad.mit.edu	37	17	46855994	46855999	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46855994_46855999delAAAAAA	uc010wlo.1	-						TTLL6_uc002iob.2_Intron|TTLL6_uc010dbi.2_Intron|TTLL6_uc002ioc.2_Intron|TTLL6_uc002iod.2_Intron	NM_001130918	NP_001124390			tubulin tyrosine ligase-like family, member 6							cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0																		---	---	---	---
IGF2BP1	10642	broad.mit.edu	37	17	47112099	47112099	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47112099delA	uc002iom.2	+						IGF2BP1_uc010dbj.2_Intron	NM_006546	NP_006537			insulin-like growth factor 2 mRNA binding						CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1																		---	---	---	---
ABI3	51225	broad.mit.edu	37	17	47295005	47295005	+	Intron	DEL	C	-	-	rs113223751		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47295005delC	uc002iop.1	+						ABI3_uc002ioq.1_Intron	NM_016428	NP_057512			NESH protein isoform 1						cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)												HNSCC(55;0.14)			---	---	---	---
ZNF652	22834	broad.mit.edu	37	17	47421563	47421563	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47421563delA	uc002iov.3	-						ZNF652_uc002iow.2_Intron|ZNF652_uc002iou.3_Intron	NM_001145365	NP_001138837			zinc finger protein 652						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)															---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47701841	47701841	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47701841delT	uc010dbk.2	-						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)			---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47704049	47704049	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47704049delA	uc010dbk.2	-						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)			---	---	---	---
ACSF2	80221	broad.mit.edu	37	17	48500652	48500653	+	5'Flank	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48500652_48500653delTT	uc002iqu.2	+						ACSF2_uc010wml.1_5'Flank|ACSF2_uc010wmm.1_5'Flank|ACSF2_uc010wmn.1_5'Flank|ACSF2_uc010wmo.1_5'Flank	NM_025149	NP_079425			acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
MYCBPAP	84073	broad.mit.edu	37	17	48602072	48602073	+	Intron	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48602072_48602073insGT	uc010wmr.1	+						MYCBPAP_uc002iqz.2_Intron	NM_032133	NP_115509			Myc-binding protein-associated protein						cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|skin(2)|ovary(1)|pancreas(1)	6	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49177990	49177991	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49177990_49177991delAA	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	49452314	49452316	+	IGR	DEL	AGG	-	-	rs3029086		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49452314_49452316delAGG								UTP18 (77024 upstream) : CA10 (255359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	49536992	49536992	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49536992delA								UTP18 (161702 upstream) : CA10 (170683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50843676	50843676	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50843676delA								CA10 (606299 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51787708	51787708	+	IGR	DEL	A	-	-	rs75813544		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51787708delA								None (None upstream) : KIF2B (112531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51913120	51913120	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51913120delT								KIF2B (10547 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52595479	52595480	+	IGR	INS	-	T	T	rs139578277	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52595479_52595480insT								KIF2B (692906 upstream) : TOM1L1 (382572 downstream)																																			---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54228221	54228222	+	5'Flank	INS	-	C	C	rs141238490	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54228221_54228222insC	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	54648689	54648689	+	IGR	DEL	A	-	-	rs75617500		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54648689delA								ANKFN1 (88682 upstream) : NOG (22371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54782839	54782841	+	IGR	DEL	CCG	-	-	rs57046237	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54782839_54782841delCCG								NOG (109888 upstream) : C17orf67 (86434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54812998	54812998	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54812998delT								NOG (140047 upstream) : C17orf67 (56277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	56100072	56100073	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56100072_56100073delTT								SFRS1 (15365 upstream) : DYNLL2 (60707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57396690	57396690	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57396690delA								GDPD1 (44817 upstream) : YPEL2 (12363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57539309	57539309	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57539309delA								YPEL2 (60214 upstream) : DHX40 (103577 downstream)																																			---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59450813	59450813	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59450813delT	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.3_Intron|BCAS3_uc002izc.3_Intron|BCAS3_uc002izd.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-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60162867	60162867	+	IGR	DEL	C	-	-	rs8075080	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60162867delC								MED13 (20224 upstream) : TBC1D3P2 (179202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	60267840	60267841	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60267840_60267841insT								MED13 (125197 upstream) : TBC1D3P2 (74228 downstream)																																			---	---	---	---
TBC1D3P2	440452	broad.mit.edu	37	17	60347260	60347260	+	Intron	DEL	T	-	-	rs71934275		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60347260delT	uc002izq.2	-						TBC1D3P2_uc010woz.1_Intron|uc010wpa.1_5'Flank					SubName: Full=Putative uncharacterized protein TBC1D3E;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60369419	60369420	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60369419_60369420insA								TBC1D3P2 (16403 upstream) : EFCAB3 (78159 downstream)																																			---	---	---	---
MAP3K3	4215	broad.mit.edu	37	17	61761354	61761354	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61761354delA	uc002jbg.2	+						MAP3K3_uc002jbe.2_Intron|MAP3K3_uc002jbf.2_Intron|MAP3K3_uc002jbh.2_Intron|MAP3K3_uc010wpo.1_Intron|MAP3K3_uc010wpp.1_Intron	NM_002401	NP_002392			mitogen-activated protein kinase kinase kinase 3						MAPKKK cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autophosphorylation	cytosol	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			lung(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)	6																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61888619	61888619	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61888619delA	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron|DDX42_uc002jbx.2_Intron|DDX42_uc002jby.2_5'Flank	NM_007372	NP_031398			DEAD box polypeptide 42 protein						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																		---	---	---	---
ICAM2	3384	broad.mit.edu	37	17	62089964	62089965	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62089964_62089965insA	uc002jdw.3	-						ICAM2_uc010ded.2_Intron|ICAM2_uc002jdx.3_Intron|ICAM2_uc002jdv.3_Intron|ICAM2_uc010wpx.1_Intron	NM_001099788	NP_001093258			intercellular adhesion molecule 2 precursor						cell-cell adhesion|regulation of immune response	integral to plasma membrane	integrin binding			ovary(1)	1																		---	---	---	---
ERN1	2081	broad.mit.edu	37	17	62182356	62182356	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62182356delA	uc002jdz.2	-							NM_001433	NP_001424			endoplasmic reticulum to nucleus signalling 1						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																		---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64125854	64125854	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64125854delT	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)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64467117	64467118	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64467117_64467118delTT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64517248	64517250	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64517248_64517250delAAA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64659991	64659991	+	Intron	DEL	T	-	-	rs34996655		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64659991delT	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64661622	64661623	+	Intron	INS	-	GGTCTCA	GGTCTCA	rs138595473	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64661622_64661623insGGTCTCA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	64903474	64903474	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64903474delG								CACNG5 (22118 upstream) : CACNG4 (57539 downstream)																																			---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65104310	65104310	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65104310delA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron|HELZ_uc010der.2_3'UTR	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65156546	65156547	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65156546_65156547delAA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	65993785	65993785	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65993785delA								C17orf58 (4020 upstream) : KPNA2 (38063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66622126	66622127	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66622126_66622127delTT								FAM20A (25031 upstream) : ABCA8 (241306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	67344497	67344498	+	IGR	INS	-	TA	TA	rs71144680		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67344497_67344498insTA								ABCA5 (21174 upstream) : MAP2K6 (66340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	67824236	67824236	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67824236delA								MAP2K6 (285774 upstream) : KCNJ16 (247190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68155057	68155057	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68155057delT								KCNJ16 (23313 upstream) : KCNJ2 (9757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68217288	68217288	+	IGR	DEL	A	-	-	rs56942540		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68217288delA								KCNJ2 (41107 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68227377	68227378	+	IGR	INS	-	AAAC	AAAC	rs139875741	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68227377_68227378insAAAC								KCNJ2 (51196 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68342299	68342299	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68342299delC								KCNJ2 (166118 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68427510	68427510	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68427510delA								KCNJ2 (251329 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70063744	70063744	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70063744delG								None (None upstream) : SOX9 (53417 downstream)																																			---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70722649	70722650	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70722649_70722650delAC	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71853829	71853829	+	IGR	DEL	C	-	-	rs112346711		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71853829delC								C17orf54 (29153 upstream) : RPL38 (345966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71908818	71908819	+	IGR	DEL	TC	-	-	rs10542426		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71908818_71908819delTC								C17orf54 (84142 upstream) : RPL38 (290976 downstream)																																			---	---	---	---
RAB37	326624	broad.mit.edu	37	17	72674822	72674823	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72674822_72674823delAC	uc010dfu.2	+						RAB37_uc002jlc.2_Intron|RAB37_uc002jld.2_Intron	NM_175738	NP_783865			RAB37, member RAS oncogene family isoform 3						protein transport|small GTPase mediated signal transduction	ER-Golgi intermediate compartment	GTP binding			ovary(1)	1																		---	---	---	---
SLC16A5	9121	broad.mit.edu	37	17	73086558	73086558	+	Intron	DEL	T	-	-	rs142390788		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73086558delT	uc002jmr.2	+						SLC16A5_uc002jms.1_Intron|SLC16A5_uc002jmt.2_Intron|SLC16A5_uc002jmu.2_Intron|SLC16A5_uc010wrt.1_5'Flank	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)													---	---	---	---
NUP85	79902	broad.mit.edu	37	17	73211395	73211395	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73211395delC	uc002jng.1	+						NUP85_uc010dgd.1_Intron|NUP85_uc010wrv.1_Intron	NM_024844	NP_079120			nucleoporin 85						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	73576829	73576829	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73576829delA								LLGL2 (5540 upstream) : MYO15B (7310 downstream)																																			---	---	---	---
UBE2O	63893	broad.mit.edu	37	17	74447857	74447858	+	Intron	DEL	GG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74447857_74447858delGG	uc002jrm.3	-						UBE2O_uc002jrn.3_Intron	NM_022066	NP_071349			ubiquitin-conjugating enzyme E2O								ATP binding|ubiquitin-protein ligase activity			breast(2)|skin(2)|lung(1)	5																		---	---	---	---
MFSD11	79157	broad.mit.edu	37	17	74759952	74759953	+	Intron	INS	-	T	T	rs4789354		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74759952_74759953insT	uc002jta.2	+						MFSD11_uc002jtb.2_Intron|MFSD11_uc010dha.2_Intron|MFSD11_uc002jtc.2_Intron|MFSD11_uc002jtd.3_Intron|MFSD11_uc010dhb.2_Intron|MFSD11_uc002jte.2_Intron	NM_024311	NP_077287			major facilitator superfamily domain containing							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	74950519	74950521	+	IGR	DEL	AGA	-	-	rs112238959		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74950519_74950521delAGA								MGAT5B (4049 upstream) : C17orf86 (134204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75221001	75221001	+	IGR	DEL	T	-	-	rs112820603		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75221001delT								SEC14L1 (7822 upstream) : SEPT9 (56491 downstream)																																			---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75371036	75371036	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75371036delT	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_5'Flank	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)															---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75441608	75441609	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75441608_75441609delGT	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc002jtx.1_Intron|SEPT9_uc010wtl.1_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	75869640	75869641	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75869640_75869641delTT								SEPT9 (372964 upstream) : FLJ45079 (5468 downstream)																																			---	---	---	---
AFMID	125061	broad.mit.edu	37	17	76188082	76188083	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76188082_76188083insT	uc002jva.3	+						AFMID_uc002juy.3_Intron|AFMID_uc010dhj.2_Intron|AFMID_uc002jvb.3_Intron|AFMID_uc002juz.3_Intron	NM_001010982	NP_001010982			arylformamidase isoform 1							cytosol|nucleus	arylformamidase activity			large_intestine(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77086852	77086852	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77086852delT	uc010dhs.2	-	14						NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77216680	77216681	+	Intron	INS	-	GT	GT	rs146139080	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77216680_77216681insGT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	77902337	77902337	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77902337delA								CBX4 (89124 upstream) : TBC1D16 (11484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77910716	77910717	+	RNA	INS	-	GTGC	GTGC	rs894870		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77910716_77910717insGTGC	uc002jxg.1	-	1		c.1561_1562insGCAC								Homo sapiens cDNA FLJ20748 fis, clone HEP05772.																														---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77958504	77958504	+	Intron	DEL	A	-	-	rs10528420		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77958504delA	uc002jxj.2	-							NM_019020	NP_061893			TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)															---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	77981821	77981826	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77981821_77981826delAAAAAA	uc002jxj.2	-							NM_019020	NP_061893			TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)															---	---	---	---
TBC1D16	125058	broad.mit.edu	37	17	78007182	78007182	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78007182delT	uc002jxj.2	-							NM_019020	NP_061893			TBC1 domain family, member 16							intracellular	Rab GTPase activator activity				0	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78299477	78299478	+	Intron	INS	-	A	A	rs141307834	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78299477_78299478insA	uc002jyg.1	+							NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78844910	78844910	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78844910delT	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	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																		---	---	---	---
FLJ90757	440465	broad.mit.edu	37	17	79005508	79005508	+	3'UTR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79005508delC	uc002jyy.2	-	2						NR_026857				Homo sapiens cDNA FLJ14444 fis, clone HEMBB1001153.												0																		---	---	---	---
AZI1	22994	broad.mit.edu	37	17	79187359	79187359	+	Intron	DEL	A	-	-	rs139229130		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79187359delA	uc002jzp.1	-						AZI1_uc002jzn.1_Intron|AZI1_uc002jzo.1_Intron|AZI1_uc010wum.1_Intron	NM_014984	NP_055799			5-azacytidine induced 1 isoform a						cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	79366052	79366052	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79366052delA								TMEM105 (61578 upstream) : BAHCC1 (7488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	79840684	79840684	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79840684delA								ARHGDIA (11446 upstream) : THOC4 (5027 downstream)																																			---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80140996	80140997	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80140996_80140997insG	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron|CCDC57_uc010dik.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	80262803	80262803	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80262803delA								CSNK1D (31230 upstream) : CD7 (9943 downstream)																																			---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	81001553	81001556	+	Intron	DEL	AAAC	-	-	rs111504889		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:81001553_81001556delAAAC	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	92770	92771	+	IGR	INS	-	AG	AG	rs141470439	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:92770_92771insAG								None (None upstream) : USP14 (65712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1250079	1250079	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1250079delT								ADCYAP1 (337908 upstream) : C18orf2 (4311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2413422	2413422	+	IGR	DEL	A	-	-	rs79228797	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2413422delA								None (None upstream) : METTL4 (124103 downstream)																																			---	---	---	---
LOC727896	727896	broad.mit.edu	37	18	2943456	2943457	+	3'UTR	INS	-	TGTT	TGTT	rs55747910		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2943456_2943457insTGTT	uc010wyu.1	-	1					LPIN2_uc002klo.2_Intron	NR_026659				Homo sapiens cDNA clone IMAGE:4614712, containing frame-shift errors.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3053907	3053912	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3053907_3053912delTTTTTT								LPIN2 (41962 upstream) : MYOM1 (12894 downstream)																																			---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3198789	3198789	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3198789delA	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	3618610	3618611	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3618610_3618611insT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.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	3675081	3675081	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3675081delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.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	4105010	4105011	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4105010_4105011delCA	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	4455732	4455732	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4455732delT	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	4587909	4587910	+	IGR	INS	-	AATCTG	AATCTG	rs146904464	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4587909_4587910insAATCTG								DLGAP1 (132643 upstream) : LOC642597 (555762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5705555	5705556	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5705555_5705556delCA								EPB41L3 (74913 upstream) : TMEM200C (184628 downstream)																																			---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6311118	6311119	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6311118_6311119delTC	uc002kmz.3	-						L3MBTL4_uc010dkt.2_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)																---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6912351	6912351	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6912351delT	uc010wzi.1	+	17					ARHGAP28_uc002kne.2_3'UTR					SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7067470	7067470	+	Intron	DEL	A	-	-	rs112704142		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7067470delA	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8384458	8384458	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8384458delA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	8493753	8493753	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8493753delT								PTPRM (86895 upstream) : RAB12 (115682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	9293579	9293579	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9293579delT								ANKRD12 (8373 upstream) : TWSG1 (41186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	9301391	9301394	+	IGR	DEL	ACAG	-	-	rs72024558		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9301391_9301394delACAG								ANKRD12 (16185 upstream) : TWSG1 (33371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10970659	10970660	+	IGR	DEL	CA	-	-	rs113164434		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10970659_10970660delCA								FAM38B (268680 upstream) : GNAL (718476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11608446	11608446	+	IGR	DEL	T	-	-	rs35024613		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11608446delT								FAM38B (906467 upstream) : GNAL (80690 downstream)																																			---	---	---	---
SPIRE1	56907	broad.mit.edu	37	18	12478560	12478561	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12478560_12478561delGT	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098			spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0																		---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12867627	12867628	+	Intron	INS	-	CG	CG	rs146731662	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12867627_12867628insCG	uc002krp.2	-						PTPN2_uc002krl.2_Intron|PTPN2_uc002krn.2_Intron|PTPN2_uc002kro.2_Intron|PTPN2_uc002krm.2_Intron	NM_002828	NP_002819			protein tyrosine phosphatase, non-receptor type						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	15026275	15026276	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15026275_15026276delAA								ANKRD30B (173538 upstream) : LOC644669 (287279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15059372	15059373	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15059372_15059373delTG								ANKRD30B (206635 upstream) : LOC644669 (254182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15208048	15208049	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15208048_15208049insT								ANKRD30B (355311 upstream) : LOC644669 (105506 downstream)																																			---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	18963670	18963670	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	19064356	19064356	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19064356delA	uc010xam.1	+						GREB1L_uc010dlp.1_Intron|GREB1L_uc010xan.1_Intron|GREB1L_uc010dlr.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19296813	19296813	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19296813delA	uc002ktp.2	+							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)															---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19303841	19303843	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19303841_19303843delTTT	uc002ktp.2	+							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	19563248	19563248	+	IGR	DEL	A	-	-	rs35289964		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19563248delA								MIB1 (112338 upstream) : GATA6 (186168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	19598192	19598194	+	IGR	DEL	AAA	-	-	rs72264469		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19598192_19598194delAAA								MIB1 (147282 upstream) : GATA6 (151222 downstream)																																			---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20805398	20805398	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20805398delT	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)																	---	---	---	---
C18orf8	29919	broad.mit.edu	37	18	21096683	21096685	+	Intron	DEL	TTC	-	-	rs10538811		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21096683_21096685delTTC	uc010xax.1	+						C18orf8_uc010xau.1_Intron|C18orf8_uc010xav.1_Intron|C18orf8_uc010xaw.1_Intron|C18orf8_uc002kul.2_Intron	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)																	---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21394232	21394232	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21394232delT	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)													---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21462573	21462574	+	Intron	INS	-	A	A	rs113890059		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21462573_21462574insA	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_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)													---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21942209	21942209	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21942209delA	uc002kve.2	-							NM_080597	NP_542164			oxysterol-binding protein-like 1A isoform B						cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)																	---	---	---	---
OSBPL1A	114876	broad.mit.edu	37	18	21959484	21959486	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21959484_21959486delAAA	uc002kve.2	-							NM_080597	NP_542164			oxysterol-binding protein-like 1A isoform B						cholesterol metabolic process|lipid transport|vesicle-mediated transport		phospholipid binding			ovary(4)	4	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	22097066	22097075	+	IGR	DEL	GTGTGTGCGC	-	-	rs34702784	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22097066_22097075delGTGTGTGCGC								HRH4 (37146 upstream) : ZNF521 (544813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22210655	22210655	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22210655delT	uc002kvj.1	+											Homo sapiens cDNA FLJ42358 fis, clone UTERU2023262.																														---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22824714	22824714	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22824714delT	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276			zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
SS18	6760	broad.mit.edu	37	18	23651929	23651929	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23651929delA	uc002kvm.2	-						SS18_uc002kvn.2_Intron|SS18_uc010xbf.1_Intron|SS18_uc010xbg.1_Intron|SS18_uc010xbh.1_Intron|SS18_uc010xbi.1_Intron|SS18_uc010dlz.1_Intron	NM_001007559	NP_001007560			synovial sarcoma translocation, chromosome 18						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	ligand-dependent nuclear receptor transcription coactivator activity|protein binding		SS18/SSX1(1169)|SS18/SSX2(702)|SS18/SSX4(12)	soft_tissue(1883)|ovary(1)	1884	all_cancers(21;0.000194)|Lung NSC(5;0.000413)|all_lung(6;0.00118)|Ovarian(20;0.124)							T	SSX1| SSX2	synovial sarcoma								---	---	---	---
TAF4B	6875	broad.mit.edu	37	18	23843676	23843677	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23843676_23843677delTC	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	24195763	24195763	+	Intron	DEL	T	-	-	rs35195194		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24195763delT	uc010xbk.1	-							NM_198991	NP_945342			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	24390483	24390483	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24390483delT								LOC728606 (106881 upstream) : AQP4 (41527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	25196007	25196007	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25196007delT								C18orf16 (425357 upstream) : CDH2 (334923 downstream)																																			---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25610310	25610310	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25610310delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	27103320	27103321	+	IGR	INS	-	AC	AC	rs144026061	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27103320_27103321insAC								None (None upstream) : MIR302F (775555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28254584	28254584	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28254584delT								MIR302F (375658 upstream) : DSC3 (315469 downstream)																																			---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29237269	29237269	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29237269delT	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766			beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	29301844	29301845	+	IGR	DEL	TG	-	-	rs11665507		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29301844_29301845delTG								B4GALT6 (37158 upstream) : MCART2 (37814 downstream)																																			---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29512390	29512391	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29512390_29512391insA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29796832	29796833	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29796832_29796833delAA	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																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	30047774	30047774	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30047774delG	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30273377	30273380	+	Intron	DEL	AGAG	-	-	rs2021552	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30273377_30273380delAGAG	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	30909395	30909395	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30909395delA	uc002kxn.2	-						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																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31189908	31189908	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31189908delA	uc010dmg.1	+						ASXL3_uc002kxq.2_Intron	NM_030632	NP_085135			additional sex combs like 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32692149	32692151	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32692149_32692151delTTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32897133	32897133	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32897133delT								ZNF271 (6404 upstream) : ZNF24 (15045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33308726	33308726	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33308726delA								GALNT1 (16929 upstream) : MIR187 (176055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35274463	35274463	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35274463delT								CELF4 (128463 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35279334	35279339	+	IGR	DEL	TGTGTA	-	-	rs71862275		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35279334_35279339delTGTGTA								CELF4 (133334 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35395466	35395466	+	IGR	DEL	T	-	-	rs117355260	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35395466delT								CELF4 (249466 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35509794	35509794	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35509794delT								CELF4 (363794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37872246	37872246	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37872246delT								LOC647946 (491964 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38038242	38038249	+	IGR	DEL	ACACACAC	-	-	rs71895008		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38038242_38038249delACACACAC								LOC647946 (657960 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38104157	38104157	+	IGR	DEL	T	-	-	rs71855866		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38104157delT								LOC647946 (723875 upstream) : KC6 (956081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39033530	39033530	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39033530delT								None (None upstream) : KC6 (26708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39240654	39240654	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39240654delA								KC6 (140093 upstream) : PIK3C3 (294545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	40297364	40297365	+	IGR	INS	-	CA	CA	rs138990255	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40297364_40297365insCA								PIK3C3 (635920 upstream) : RIT2 (25828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	40999865	40999865	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40999865delT								SYT4 (142250 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41432470	41432471	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41432470_41432471delGT								SYT4 (574855 upstream) : SETBP1 (827667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41743216	41743216	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41743216delT								SYT4 (885601 upstream) : SETBP1 (516922 downstream)																																			---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43212094	43212097	+	Intron	DEL	GTGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43212094_43212097delGTGT	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	43553469	43553470	+	IGR	INS	-	A	A	rs75339079		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43553469_43553470insA								KIAA1632 (6164 upstream) : PSTPIP2 (10033 downstream)																																			---	---	---	---
ATP5A1	498	broad.mit.edu	37	18	43664802	43664803	+	Intron	DEL	AC	-	-	rs147667560		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43664802_43664803delAC	uc002lbr.1	-						ATP5A1_uc010dnl.1_Intron|ATP5A1_uc002lbs.1_Intron|ATP5A1_uc002lbt.1_Intron	NM_004046	NP_004037			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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	45011403	45011406	+	Intron	DEL	GGCA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45011403_45011406delGGCA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45199670	45199672	+	IGR	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45199670_45199672delAAA								IER3IP1 (496925 upstream) : SMAD2 (159795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45319840	45319840	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45319840delT								IER3IP1 (617095 upstream) : SMAD2 (39627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45464515	45464516	+	IGR	DEL	GC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45464515_45464516delGC								SMAD2 (7000 upstream) : ZBTB7C (89232 downstream)																																			---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45904510	45904510	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45904510delA	uc010dnw.2	-						ZBTB7C_uc010dob.1_5'Flank|ZBTB7C_uc010doc.1_5'Flank|ZBTB7C_uc010dod.1_5'Flank|ZBTB7C_uc010doe.1_5'Flank|ZBTB7C_uc010dof.1_5'Flank|ZBTB7C_uc010dog.1_5'Flank|ZBTB7C_uc010doh.1_5'Flank|ZBTB7C_uc010doi.1_5'Flank|ZBTB7C_uc010doj.1_5'Flank|ZBTB7C_uc010dok.1_5'Flank|ZBTB7C_uc010dol.1_5'Flank|ZBTB7C_uc010doa.1_5'Flank|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	46005697	46005697	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46005697delT								ZBTB7C (70034 upstream) : KIAA0427 (59730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47079256	47079256	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47079256delT								RPL17 (60350 upstream) : LIPG (9171 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47480391	47480392	+	Intron	DEL	TA	-	-	rs72483170	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47480391_47480392delTA	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)														---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47564262	47564262	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48398124	48398126	+	IGR	DEL	AAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48398124_48398126delAAC								MRO (46370 upstream) : ME2 (7309 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50053166	50053167	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50053166_50053167delAC	uc002lfe.1	+							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	50853678	50853678	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50853678delA	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)														---	---	---	---
MBD2	8932	broad.mit.edu	37	18	51752800	51752801	+	5'Flank	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51752800_51752801delAA	uc002lfg.1	-						MBD2_uc002lfh.1_5'Flank	NM_003927	NP_003918			methyl-CpG binding domain protein 2 isoform 1						transcription, DNA-dependent		C2H2 zinc finger domain binding|methyl-CpG binding|satellite DNA binding				0				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)	Hexobarbital(DB01355)													---	---	---	---
STARD6	147323	broad.mit.edu	37	18	51878499	51878500	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51878499_51878500insT	uc010xdt.1	-							NM_139171	NP_631910			START domain containing protein 6						lipid transport		lipid binding			ovary(1)	1				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	52377941	52377946	+	IGR	DEL	ATGATG	-	-	rs139291089		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52377941_52377946delATGATG								C18orf26 (111217 upstream) : RAB27B (117894 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	52891869	52891869	+	3'UTR	DEL	A	-	-	rs111302418		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52891869delA	uc002lfz.2	-	20					TCF4_uc002lfw.3_3'UTR|TCF4_uc010xdu.1_3'UTR|TCF4_uc010xdv.1_3'UTR|TCF4_uc002lfx.2_3'UTR|TCF4_uc010xdw.1_3'UTR|TCF4_uc002lfy.2_3'UTR|TCF4_uc010xdx.1_3'UTR|TCF4_uc010dph.1_3'UTR|TCF4_uc010xdy.1_3'UTR|TCF4_uc002lga.2_3'UTR|TCF4_uc002lfv.2_3'UTR	NM_003199	NP_003190			transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|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|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	53833327	53833328	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53833327_53833328delTT								TCF4 (530142 upstream) : TXNL1 (436727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54231106	54231106	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54231106delT								TCF4 (927921 upstream) : TXNL1 (38949 downstream)																																			---	---	---	---
TXNL1	9352	broad.mit.edu	37	18	54273777	54273777	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54273777delC	uc002lgg.2	-						TXNL1_uc010xdz.1_Intron|TXNL1_uc002lgh.2_Intron|TXNL1_uc002lgi.2_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	54500122	54500122	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54500122delA	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	54817563	54817566	+	IGR	DEL	TGCC	-	-	rs71991845	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54817563_54817566delTGCC								WDR7 (120527 upstream) : ST8SIA3 (202155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55293974	55293974	+	IGR	DEL	A	-	-	rs80142684		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55293974delA								NARS (4797 upstream) : ATP8B1 (19687 downstream)																																			---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55880139	55880139	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55880139delA	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	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56459323	56459323	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56459323delA								MALT1 (41953 upstream) : ZNF532 (70738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56459708	56459708	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56459708delA								MALT1 (42338 upstream) : ZNF532 (70353 downstream)																																			---	---	---	---
ZNF532	55205	broad.mit.edu	37	18	56563090	56563090	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56563090delT	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron	NM_018181	NP_060651			zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56837951	56837952	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56837951_56837952insA								SEC11C (11890 upstream) : GRP (49448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58582359	58582359	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58582359delA								MC4R (542358 upstream) : CDH20 (418629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58764315	58764315	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58764315delA								MC4R (724314 upstream) : CDH20 (236673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58790045	58790045	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58790045delT								MC4R (750044 upstream) : CDH20 (210943 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59048496	59048496	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59048496delT	uc002lif.2	+							NM_031891	NP_114097			cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	60075601	60075601	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60075601delT								TNFRSF11A (22099 upstream) : ZCCHC2 (115057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60076520	60076520	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60076520delT								TNFRSF11A (23018 upstream) : ZCCHC2 (114138 downstream)																																			---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60598432	60598433	+	Intron	INS	-	ACAAC	ACAAC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60598432_60598433insACAAC	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																		---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61646113	61646114	+	Intron	INS	-	T	T	rs145325883	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61646113_61646114insT	uc002ljv.2	+						SERPINB8_uc002ljs.1_Intron|SERPINB8_uc002ljt.2_Intron|SERPINB8_uc002lju.2_Intron|SERPINB8_uc010xex.1_Intron	NM_198833	NP_942130			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	62231738	62231739	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62231738_62231739insT								C18orf20 (415478 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62307235	62307236	+	IGR	DEL	TA	-	-	rs150694766		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62307235_62307236delTA								C18orf20 (490975 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63743175	63743175	+	IGR	DEL	T	-	-	rs35962952		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63743175delT								CDH7 (195001 upstream) : CDH19 (428146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64665619	64665619	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64665619delA								CDH19 (394403 upstream) : DSEL (508200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65187669	65187669	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65187669delT								DSEL (3702 upstream) : None (None downstream)																																			---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67677149	67677149	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67677149delA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron|RTTN_uc002lkn.2_Intron|RTTN_uc010dqp.2_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67708616	67708617	+	Intron	INS	-	CA	CA	rs140930073	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67708616_67708617insCA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron|RTTN_uc010dqp.2_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67774030	67774030	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67774030delA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	69317502	69317503	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69317502_69317503delAA								None (None upstream) : CBLN2 (886412 downstream)																																			---	---	---	---
FBXO15	201456	broad.mit.edu	37	18	71745830	71745831	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71745830_71745831insG	uc002lle.2	-						FBXO15_uc002lld.2_Intron|FBXO15_uc002llf.2_Intron	NM_152676	NP_689889			F-box protein 15 isoform 1											ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	71901606	71901606	+	IGR	DEL	G	-	-	rs8094280	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71901606delG								C18orf55 (75402 upstream) : CYB5A (18922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	72057056	72057056	+	IGR	DEL	A	-	-	rs142828698		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72057056delA								CYB5A (97835 upstream) : FAM69C (45908 downstream)																																			---	---	---	---
ZADH2	284273	broad.mit.edu	37	18	72913186	72913186	+	3'UTR	DEL	T	-	-	rs67264905		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72913186delT	uc002llx.2	-	2					ZADH2_uc010dqv.2_3'UTR	NM_175907	NP_787103			zinc binding alcohol dehydrogenase domain							peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73171083	73171084	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73171083_73171084delGA								C18orf62 (31494 upstream) : ZNF516 (900535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73886703	73886703	+	IGR	DEL	A	-	-	rs77447385		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73886703delA								C18orf62 (747114 upstream) : ZNF516 (184916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75209550	75209551	+	IGR	DEL	TT	-	-	rs72363543		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75209550_75209551delTT								GALR1 (227456 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75530146	75530147	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75530146_75530147delTG								GALR1 (548052 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76776475	76776476	+	IGR	INS	-	T	T	rs143149433	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	77030300	77030301	+	Intron	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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	77393498	77393518	+	IGR	DEL	TGATGGTGGTGGTGACGGTGA	-	-	rs78670059		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77393498_77393518delTGATGGTGGTGGTGACGGTGA								NFATC1 (104176 upstream) : CTDP1 (46283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77407098	77407099	+	IGR	INS	-	GGA	GGA	rs143485142	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77407098_77407099insGGA								NFATC1 (117776 upstream) : CTDP1 (32702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77413294	77413295	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77413294_77413295delAC								NFATC1 (123972 upstream) : CTDP1 (26506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	77611173	77611173	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77611173delA								CTDP1 (96666 upstream) : KCNG2 (12495 downstream)																																			---	---	---	---
SHC2	25759	broad.mit.edu	37	19	434538	434539	+	Intron	INS	-	CATA	CATA	rs112764935		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:434538_434539insCATA	uc002loq.3	-						SHC2_uc002lop.3_Intron	NM_012435	NP_036567			SHC (Src homology 2 domain containing)						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol					0		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)														---	---	---	---
ODF3L2	284451	broad.mit.edu	37	19	468371	468371	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:468371delA	uc002lor.2	-						ODF3L2_uc010drp.2_Intron	NM_182577	NP_872383			outer dense fiber of sperm tails 3-like 2												0																		---	---	---	---
HCN2	610	broad.mit.edu	37	19	613827	613828	+	Intron	INS	-	C	C	rs143893727	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:613827_613828insC	uc002lpe.2	+							NM_001194	NP_001185			hyperpolarization activated cyclic						cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel 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)														---	---	---	---
C19orf22	91300	broad.mit.edu	37	19	902440	902441	+	Intron	DEL	AA	-	-	rs74421507		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:902440_902441delAA	uc002lqg.2	-						C19orf22_uc002lqh.2_Intron|C19orf22_uc002lqi.2_Intron|C19orf22_uc002lqj.2_Intron	NM_138774	NP_620129			hypothetical protein LOC91300							nucleus	nucleic acid binding			pancreas(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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	1997185	1997185	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1997185delA	uc002lup.1	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	3131446	3131446	+	IGR	DEL	C	-	-	rs66993077		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3131446delC								GNA11 (9994 upstream) : GNA15 (4745 downstream)																																			---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3263574	3263575	+	Intron	INS	-	AAC	AAC	rs143211627	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3263574_3263575insAAC	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																		---	---	---	---
ITGB1BP3	27231	broad.mit.edu	37	19	3934245	3934245	+	Intron	DEL	A	-	-	rs76497904		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3934245delA	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778			integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SIRT6	51548	broad.mit.edu	37	19	4179560	4179561	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4179560_4179561delAG	uc002lzo.2	-						SIRT6_uc002lzn.2_Intron|SIRT6_uc002lzp.2_Intron|SIRT6_uc010xid.1_Intron|SIRT6_uc002lzq.2_Intron|SIRT6_uc002lzr.2_Intron	NM_016539	NP_057623			sirtuin 6						chromatin silencing|protein ADP-ribosylation	nuclear telomeric heterochromatin|nucleoplasm	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|protein binding|zinc ion binding			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.023)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
UBXN6	80700	broad.mit.edu	37	19	4449823	4449823	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4449823delA	uc002man.1	-						UBXN6_uc010dty.1_Intron|UBXN6_uc002mam.1_Intron	NM_025241	NP_079517			UBX domain protein 6							microtubule organizing center|nucleus	protein binding				0																		---	---	---	---
TICAM1	148022	broad.mit.edu	37	19	4828715	4828719	+	Intron	DEL	TTTTT	-	-	rs142006219		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4828715_4828719delTTTTT	uc002mbi.2	-							NM_182919	NP_891549			toll-like receptor adaptor molecule 1						apoptosis|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 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein kinase binding|signal transducer activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5179898	5179901	+	Intron	DEL	CCTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5179898_5179901delCCTT	uc002mbu.1	-							NM_130853	NP_570923			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)														---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5746448	5746448	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5746448delT	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
FUT6	2528	broad.mit.edu	37	19	5834825	5834826	+	Intron	INS	-	A	A	rs138656591	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5834825_5834826insA	uc002mdf.1	-						FUT6_uc002mdg.1_Intron|FUT6_uc002mdh.1_Intron|FUT6_uc010dul.1_5'Flank	NM_001040701	NP_001035791			fucosyltransferase 6						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity				0																		---	---	---	---
RFX2	5990	broad.mit.edu	37	19	6035860	6035865	+	Intron	DEL	GGGTGT	-	-	rs34235787		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6035860_6035865delGGGTGT	uc002meb.2	-						RFX2_uc002mec.2_Intron	NM_000635	NP_000626			regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6562609	6562609	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6562609delT								TNFSF9 (26670 upstream) : CD70 (20526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	6603568	6603568	+	IGR	DEL	T	-	-	rs66469607		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6603568delT								CD70 (12405 upstream) : TNFSF14 (60998 downstream)																																			---	---	---	---
INSR	3643	broad.mit.edu	37	19	7142022	7142022	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7142022delT	uc002mgd.1	-						INSR_uc002mge.1_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7153197	7153198	+	Intron	INS	-	CA	CA	rs140195352		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7153197_7153198insCA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7229340	7229343	+	Intron	DEL	GATA	-	-	rs71944075		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7229340_7229343delGATA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
C19orf45	374877	broad.mit.edu	37	19	7566797	7566798	+	Intron	INS	-	AG	AG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7566797_7566798insAG	uc002mgm.2	+							NM_198534	NP_940936			hypothetical protein LOC374877												0																		---	---	---	---
PNPLA6	10908	broad.mit.edu	37	19	7623628	7623629	+	Intron	INS	-	CTC	CTC	rs149281719		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7623628_7623629insCTC	uc010xjq.1	+						PNPLA6_uc002mgq.1_Intron|PNPLA6_uc010xjp.1_Intron|PNPLA6_uc002mgr.1_Intron|PNPLA6_uc002mgs.2_Intron|PNPLA6_uc002mgt.1_Intron	NM_006702	NP_006693			neuropathy target esterase isoform b						cell death|lipid catabolic process|phosphatidylcholine metabolic process	endoplasmic reticulum membrane|integral to membrane	lysophospholipase activity			ovary(3)	3																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8185361	8185368	+	Intron	DEL	CTTCCTTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8185361_8185368delCTTCCTTC	uc002mjf.2	-							NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9223507	9223508	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9223507_9223508insA								OR7G2 (9525 upstream) : OR7G1 (1766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9246281	9246281	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9246281delA								OR7G3 (8655 upstream) : ZNF317 (4805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9663001	9663002	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9663001_9663002delAA								ZNF426 (13698 upstream) : ZNF121 (13290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9818053	9818053	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9818053delA								ZNF562 (32277 upstream) : ZNF846 (44763 downstream)																																			---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10089452	10089452	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10089452delT	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)															---	---	---	---
RDH8	50700	broad.mit.edu	37	19	10130993	10130994	+	Intron	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10130993_10130994delAG	uc002mmr.2	+							NM_015725	NP_056540			retinol dehydrogenase 8 (all-trans)						estrogen biosynthetic process|response to stimulus|visual perception	cytoplasm|integral to plasma membrane	binding|estradiol 17-beta-dehydrogenase activity|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(3)|pancreas(1)	4			Epithelial(33;4.24e-05)		Vitamin A(DB00162)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	10378194	10378195	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10378194_10378195delAA								MRPL4 (7460 upstream) : ICAM1 (3322 downstream)																																			---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11502456	11502457	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11502456_11502457delTT	uc002mrn.2	-						RGL3_uc002mrm.2_Intron					SubName: Full=FLJ00153 protein; Flags: Fragment;						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
CNN1	1264	broad.mit.edu	37	19	11660769	11660769	+	3'UTR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11660769delG	uc002msc.1	+	7					CNN1_uc010xmb.1_3'UTR|CNN1_uc010xmc.1_3'UTR	NM_001299	NP_001290			calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0																		---	---	---	---
ELOF1	84337	broad.mit.edu	37	19	11664370	11664375	+	3'UTR	DEL	CACACC	-	-	rs112156914		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11664370_11664375delCACACC	uc002mse.1	-	4					ELOF1_uc002msd.1_3'UTR	NM_032377	NP_115753			elongation factor 1 homolog (ELF1, S.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	11950258	11950258	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11950258delT								ZNF440 (4242 upstream) : ZNF439 (9321 downstream)																																			---	---	---	---
ZNF44	51710	broad.mit.edu	37	19	12396845	12396845	+	Intron	DEL	A	-	-	rs34745883		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12396845delA	uc010xmj.1	-						ZNF44_uc002mtl.2_Intron|ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_Intron|ZNF44_uc002mtn.3_Intron|ZNF44_uc010dys.2_Intron	NM_001164276	NP_001157748			zinc finger protein 44 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)														---	---	---	---
ZNF799	90576	broad.mit.edu	37	19	12514368	12514369	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12514368_12514369insT	uc010dyt.2	-						ZNF799_uc002mts.3_5'Flank	NM_001080821	NP_001074290			zinc finger protein 799						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|ovary(2)|skin(1)	6																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12968230	12968230	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12968230delT	uc002mvm.2	+						MAST1_uc002mvk.2_Intron	NM_014975	NP_055790			microtubule associated serine/threonine kinase						cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13137538	13137539	+	Intron	INS	-	TCTC	TCTC	rs143842064	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13137538_13137539insTCTC	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)															---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13158053	13158054	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13158053_13158054delTT	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	13679666	13679667	+	IGR	INS	-	G	G	rs78137106		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13679666_13679667insG								CACNA1A (62392 upstream) : CCDC130 (162907 downstream)																																			---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13940638	13940639	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13940638_13940639insA	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560			zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	14396967	14396968	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14396967_14396968delTT								LPHN1 (79970 upstream) : CD97 (95245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	14450005	14450006	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14450005_14450006delTC	uc002myk.2	+											Homo sapiens cDNA clone IMAGE:4303615, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	15269381	15269384	+	IGR	DEL	AAAA	-	-	rs36011879		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15269381_15269384delAAAA								ILVBL (32804 upstream) : NOTCH3 (1061 downstream)																																			---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15273579	15273584	+	Intron	DEL	TGTGTT	-	-	rs3071617	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15273579_15273584delTGTGTT	uc002nan.2	-							NM_000435	NP_000426			Notch homolog 3 precursor						Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	15829451	15829452	+	IGR	INS	-	A	A	rs147949612	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15829451_15829452insA								CYP4F12 (21467 upstream) : OR10H2 (9382 downstream)																																			---	---	---	---
CYP4F2	8529	broad.mit.edu	37	19	16006876	16006883	+	Intron	DEL	ATCTATCC	-	-	rs112559375		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16006876_16006883delATCTATCC	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																		---	---	---	---
EPS15L1	58513	broad.mit.edu	37	19	16494980	16494980	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16494980delC	uc002ndz.1	-						EPS15L1_uc002ndx.2_Intron|EPS15L1_uc002ndy.2_Intron|EPS15L1_uc010xpe.1_Intron|EPS15L1_uc010xpf.1_Intron|EPS15L1_uc002nea.1_Intron|EPS15L1_uc010eah.1_Intron	NM_021235	NP_067058			epidermal growth factor receptor pathway						endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|nucleus|plasma membrane	calcium ion binding			ovary(3)|skin(2)	5																OREG0025333	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	17153980	17153980	+	IGR	DEL	A	-	-	rs11313415		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17153980delA								CPAMD8 (16355 upstream) : HAUS8 (6593 downstream)																																			---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17308205	17308208	+	Intron	DEL	GATA	-	-	rs146276386		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17308205_17308208delGATA	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron|MYO9B_uc002nfl.1_5'Flank	NM_004145	NP_004136			myosin IXB isoform 1						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																		---	---	---	---
SLC5A5	6528	broad.mit.edu	37	19	17995657	17995657	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17995657delT	uc002nhr.3	+							NM_000453	NP_000444			solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	18786022	18786022	+	IGR	DEL	T	-	-	rs66966117		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18786022delT								KLHL26 (4720 upstream) : CRTC1 (8403 downstream)																																			---	---	---	---
MEF2B	100271849	broad.mit.edu	37	19	19280405	19280408	+	Intron	DEL	AGGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19280405_19280408delAGGG	uc002nlm.2	-						MEF2B_uc002nln.2_Intron|MEF2B_uc002nll.2_Intron|LOC729991-MEF2B_uc010xqo.1_Intron|LOC729991-MEF2B_uc010xqp.1_Intron|LOC729991-MEF2B_uc002nlo.2_Intron|LOC729991-MEF2B_uc002nlp.2_Intron|MEF2B_uc002nlk.2_Intron	NM_001145785	NP_001139257			myocyte enhancer factor 2B isoform a											skin(1)	1			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)															---	---	---	---
ZNF101	94039	broad.mit.edu	37	19	19780721	19780721	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19780721delA	uc002nni.1	+						ZNF101_uc010ecg.1_Intron|ZNF101_uc002nnj.1_Intron	NM_033204	NP_149981			zinc finger protein 101						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF506	440515	broad.mit.edu	37	19	19903297	19903297	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19903297delA	uc002nog.2	-											Homo sapiens cDNA FLJ38256 fis, clone FCBBF3001081, highly similar to Zinc finger protein 506.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF626	199777	broad.mit.edu	37	19	20828056	20828056	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20828056delA	uc002npb.1	-						ZNF626_uc002npc.1_Intron|ZNF626_uc002npd.1_3'UTR	NM_001076675	NP_001070143			zinc finger protein 626 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	21147559	21147560	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21147559_21147560insA								ZNF85 (14058 upstream) : ZNF430 (55937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21817605	21817605	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21817605delG								ZNF429 (78537 upstream) : ZNF100 (89239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22341872	22341872	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22341872delG								ZNF257 (67971 upstream) : ZNF676 (20031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22718617	22718618	+	IGR	INS	-	A	A	rs145181805	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22718617_22718618insA								ZNF98 (113469 upstream) : ZNF492 (98508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22793578	22793587	+	IGR	DEL	AAAAAAAAAA	-	-	rs144732623		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22793578_22793587delAAAAAAAAAA								ZNF98 (188430 upstream) : ZNF492 (23539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23309536	23309536	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23309536delT	uc002nrb.1	+											Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	27854484	27854485	+	IGR	INS	-	A	A	rs145439722		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27854484_27854485insA								None (None upstream) : LOC148189 (426917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28267968	28267968	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28267968delT								None (None upstream) : LOC148189 (13434 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29359987	29359988	+	IGR	DEL	CA	-	-	rs72261991		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29359987_29359988delCA								None (None upstream) : LOC148145 (96052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29651941	29651941	+	IGR	DEL	A	-	-	rs80147324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29651941delA								LOC148145 (191886 upstream) : UQCRFS1 (46226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29982896	29982897	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29982896_29982897insA	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30212185	30212185	+	IGR	DEL	A	-	-	rs72101351		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30212185delA								C19orf12 (5733 upstream) : CCNE1 (90716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30242552	30242552	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30242552delA								C19orf12 (36100 upstream) : CCNE1 (60349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30798151	30798151	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30798151delC								C19orf2 (291540 upstream) : ZNF536 (65177 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30981068	30981068	+	Intron	DEL	T	-	-	rs3837960		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30981068delT	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532			zinc finger protein 536						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	31388825	31388825	+	IGR	DEL	T	-	-	rs112024794		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31388825delT								ZNF536 (339860 upstream) : DKFZp566F0947 (251958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32668613	32668614	+	IGR	INS	-	GAAA	GAAA	rs78373305	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32668613_32668614insGAAA								TSHZ3 (828423 upstream) : ZNF507 (167900 downstream)																																			---	---	---	---
ANKRD27	84079	broad.mit.edu	37	19	33133275	33133275	+	Intron	DEL	A	-	-	rs71747098		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33133275delA	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515			ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34967341	34967344	+	IGR	DEL	AGGA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34967341_34967344delAGGA								UBA2 (6544 upstream) : WTIP (5536 downstream)																																			---	---	---	---
ZNF792	126375	broad.mit.edu	37	19	35457503	35457504	+	5'Flank	INS	-	A	A	rs145269516	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35457503_35457504insA	uc002nxh.1	-							NM_175872	NP_787068			zinc finger protein 792						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	35473882	35473882	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35473882delT								ZNF792 (18929 upstream) : GRAMD1A (11806 downstream)																																			---	---	---	---
LOC100128675	100128675	broad.mit.edu	37	19	35559692	35559692	+	Intron	DEL	G	-	-	rs34554426		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35559692delG	uc010xsi.1	-							NR_024562				SubName: Full=cDNA FLJ57934;												0																		---	---	---	---
ATP4A	495	broad.mit.edu	37	19	36042957	36042957	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36042957delT	uc002oal.1	-						ATP4A_uc010eee.1_Intron	NM_000704	NP_000695			hydrogen/potassium-exchanging ATPase 4A						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	36308037	36308040	+	IGR	DEL	TTTT	-	-	rs4806210		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36308037_36308040delTTTT								PRODH2 (3836 upstream) : NPHS1 (8234 downstream)																																			---	---	---	---
ZNF260	339324	broad.mit.edu	37	19	37021320	37021321	+	5'Flank	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37021320_37021321delTT	uc002oee.1	-						ZNF260_uc002oef.1_5'Flank	NM_001012756	NP_001012774			zinc finger protein 260						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF529	57711	broad.mit.edu	37	19	37054324	37054325	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37054324_37054325insA	uc002oeh.3	-						ZNF529_uc010xth.1_Intron|ZNF529_uc010xti.1_Intron|ZNF529_uc002oeg.3_Intron	NM_020951	NP_066002			zinc finger protein 529 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	Esophageal squamous(110;0.198)																	---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38685690	38685691	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38685690_38685691insA	uc002ohk.2	+							NM_015073	NP_055888			signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
ACTN4	81	broad.mit.edu	37	19	39218707	39218708	+	Intron	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39218707_39218708delCT	uc002oja.1	+						ACTN4_uc002ojb.1_Intron	NM_004924	NP_004915			actinin, alpha 4						platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	39400054	39400055	+	IGR	INS	-	A	A	rs141351396	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39400054_39400055insA								NFKBIB (521 upstream) : SARS2 (5849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	39982295	39982295	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39982295delA								TIMM50 (767 upstream) : DLL3 (7262 downstream)																																			---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40373032	40373032	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40373032delT	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)															---	---	---	---
C19orf47	126526	broad.mit.edu	37	19	40849703	40849705	+	Intron	DEL	TTT	-	-	rs66512404		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40849703_40849705delTTT	uc002oni.3	-						C19orf47_uc002ong.2_5'Flank|C19orf47_uc002onh.2_Intron	NM_178830	NP_849152			hypothetical protein LOC126526											ovary(1)|skin(1)	2			Lung(22;0.000636)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41030420	41030420	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41030420delA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41055989	41055990	+	Intron	INS	-	A	A	rs75353386		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41055989_41055990insA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc010egy.1_Intron|SPTBN4_uc002ooa.2_Intron	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
LTBP4	8425	broad.mit.edu	37	19	41112522	41112522	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41112522delC	uc002ooh.1	+						LTBP4_uc002oog.1_Intron|LTBP4_uc002ooi.1_Intron	NM_001042544	NP_001036009			latent transforming growth factor beta binding						growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
MIA	8190	broad.mit.edu	37	19	41277266	41277289	+	5'Flank	DEL	TTTTACAGAGTGCTGATTGGTCTG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41277266_41277289delTTTTACAGAGTGCTGATTGGTCTG	uc010xvt.1	+											Homo sapiens rab4b mRNA, complete cds.						cell proliferation	extracellular space	growth factor activity				0			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)	GBM - Glioblastoma multiforme(1328;0.0199)														---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41307557	41307560	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41307557_41307560delTTTT	uc010ehd.2	+						EGLN2_uc002opg.3_Intron|EGLN2_uc002oph.2_Intron|EGLN2_uc002opi.2_Intron	NM_080732	NP_542770			EGL nine (C.elegans) homolog 2						cell redox homeostasis|estrogen receptor signaling pathway|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid 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|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)													---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41449146	41449146	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41449146delT	uc002opo.2	-						CYP2B7P1_uc002opq.2_Intron	NM_000764	NP_000755			cytochrome P450, family 2, subfamily A,							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)															---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41482436	41482436	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41482436delA	uc002opo.2	-							NM_000764	NP_000755			cytochrome P450, family 2, subfamily A,							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)															---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41695878	41695878	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41695878delC	uc010xvw.1	+											SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0																		---	---	---	---
TGFB1	7040	broad.mit.edu	37	19	41844097	41844097	+	Intron	DEL	A	-	-	rs112843512		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41844097delA	uc002oqh.1	-						CYP2F1_uc010xvw.1_Intron	NM_000660	NP_000651			transforming growth factor, beta 1 precursor						active induction of host immune response by virus|ATP biosynthetic process|cell cycle arrest|cell growth|cell-cell junction organization|chondrocyte differentiation|connective tissue replacement involved in inflammatory response wound healing|epidermal growth factor receptor signaling pathway|evasion of host defenses by virus|hemopoietic progenitor cell differentiation|induction of apoptosis|lymph node development|mitotic cell cycle G1/S transition checkpoint|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of cell-cell adhesion|negative regulation of DNA replication|negative regulation of epithelial cell proliferation|negative regulation of fat cell differentiation|negative regulation of macrophage cytokine production|negative regulation of mitotic cell cycle|negative regulation of protein phosphorylation|ossification involved in bone remodeling|pathway-restricted SMAD protein phosphorylation|platelet activation|platelet degranulation|positive regulation of blood vessel endothelial cell migration|positive regulation of bone mineralization|positive regulation of cell division|positive regulation of chemotaxis|positive regulation of collagen biosynthetic process|positive regulation of epithelial to mesenchymal transition|positive regulation of fibroblast migration|positive regulation of interleukin-17 production|positive regulation of isotype switching to IgA isotypes|positive regulation of MAP kinase activity|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of protein dephosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein secretion|positive regulation of SMAD protein import into nucleus|protein export from nucleus|protein import into nucleus, translocation|receptor catabolic process|regulation of DNA binding|regulation of striated muscle tissue development|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|response to estradiol stimulus|response to progesterone stimulus|salivary gland morphogenesis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway|viral infectious cycle	extracellular space|Golgi lumen|nucleus|platelet alpha granule lumen|proteinaceous extracellular matrix	growth factor activity|type II transforming growth factor beta receptor binding				0					Hyaluronidase(DB00070)													---	---	---	---
DMRTC2	63946	broad.mit.edu	37	19	42354148	42354148	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42354148delA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373			DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
DEDD2	162989	broad.mit.edu	37	19	42714553	42714553	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42714553delT	uc002osu.1	-						DEDD2_uc002osv.1_Intron|DEDD2_uc002osw.1_Intron|DEDD2_uc002osx.1_Intron|DEDD2_uc002osy.1_Intron|DEDD2_uc010eid.2_5'Flank	NM_133328	NP_579874			death effector domain-containing  DNA binding						activation of pro-apoptotic gene products|apoptotic nuclear change|cellular homeostasis|induction of apoptosis via death domain receptors|intracellular signal transduction|negative regulation of transcription, DNA-dependent|RNA processing|rRNA catabolic process|transcription, DNA-dependent	nucleolus	DNA binding|receptor signaling complex scaffold activity				0		Prostate(69;0.0704)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43812126	43812127	+	IGR	INS	-	T	T	rs142119498	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43812126_43812127insT								PSG9 (38444 upstream) : PRG1 (41081 downstream)																																			---	---	---	---
ETHE1	23474	broad.mit.edu	37	19	44023693	44023693	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44023693delA	uc002owp.2	-						ETHE1_uc010eiu.1_Intron	NM_014297	NP_055112			ETHE1 protein precursor							mitochondrial matrix|nucleus	hydrolase activity|metal ion binding				0		Prostate(69;0.0153)																---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44272893	44272893	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44272893delT	uc002oxl.2	-						KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241			intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)													---	---	---	---
ZNF221	7638	broad.mit.edu	37	19	44460668	44460669	+	Intron	DEL	TT	-	-	rs142485416		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44460668_44460669delTT	uc002oxx.2	+						ZNF221_uc010ejb.1_Intron	NM_013359	NP_037491			zinc finger protein 221						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Prostate(69;0.0352)																---	---	---	---
ZFP112	7771	broad.mit.edu	37	19	44878047	44878047	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44878047delA	uc010xwz.1	-							NM_013380	NP_037512			zinc finger protein 228 isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
CLPTM1	1209	broad.mit.edu	37	19	45460550	45460553	+	Intron	DEL	TGAC	-	-	rs71912566		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45460550_45460553delTGAC	uc002pai.2	+						CLPTM1_uc010ejv.1_Intron|CLPTM1_uc010xxf.1_Intron|CLPTM1_uc010xxg.1_Intron	NM_001294	NP_001285			cleft lip and palate associated transmembrane						cell differentiation|multicellular organismal development|regulation of T cell differentiation in thymus	external side of plasma membrane|integral to plasma membrane				ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)														---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45759155	45759156	+	Intron	INS	-	AC	AC	rs142373360	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45759155_45759156insAC	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
PTGIR	5739	broad.mit.edu	37	19	47131184	47131184	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47131184delG	uc002pex.2	-							NM_000960	NP_000951			prostaglandin I2 (prostacyclin) receptor (IP)						cell-cell signaling|G-protein signaling, coupled to cyclic nucleotide second messenger|platelet activation	integral to plasma membrane	G-protein coupled receptor activity|guanyl-nucleotide exchange factor activity				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Epoprostenol(DB01240)|Iloprost(DB01088)|Misoprostol(DB00929)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	47326464	47326464	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47326464delA								SLC1A5 (34622 upstream) : SNAR-E (7378 downstream)																																			---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47570462	47570462	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47570462delG	uc002pga.3	-	15	3101	c.3063delC	c.(3061-3063)CCCfs	p.P1021fs	ZC3H4_uc002pgb.1_RNA	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	1021							nucleic acid binding|zinc ion binding			skin(4)|ovary(2)	6		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)														---	---	---	---
MEIS3	56917	broad.mit.edu	37	19	47911730	47911731	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47911730_47911731delTG	uc002pgu.2	-						MEIS3_uc010xyp.1_5'Flank|MEIS3_uc002pgo.2_Intron|MEIS3_uc002pgp.2_Intron|MEIS3_uc002pgq.2_Intron|MEIS3_uc002pgr.2_Intron|MEIS3_uc002pgt.2_Intron|MEIS3_uc002pgv.2_Intron|MEIS3_uc002pgs.2_Intron|MEIS3_uc010eld.2_Intron	NM_001009813	NP_001009813			Meis1, myeloid ecotropic viral integration site							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)														---	---	---	---
TMEM143	55260	broad.mit.edu	37	19	48835272	48835272	+	RNA	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48835272delA	uc002piw.1	-	6		c.2395delT								Homo sapiens cDNA FLJ10922 fis, clone OVARC1000420.							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)														---	---	---	---
BCAT2	587	broad.mit.edu	37	19	49301888	49301888	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49301888delT	uc002pkr.2	-						BCAT2_uc002pkp.2_Intron|BCAT2_uc002pkq.3_Intron|BCAT2_uc002pks.2_Intron|BCAT2_uc002pkt.2_Intron|BCAT2_uc010emh.1_Intron|BCAT2_uc010emi.1_Intron	NM_001190	NP_001181			branched chain aminotransferase 2, mitochondrial							mitochondrial matrix	L-isoleucine transaminase activity|L-leucine transaminase activity|L-valine transaminase activity			ovary(1)	1		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Glutamic Acid(DB00142)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|Pyridoxal Phosphate(DB00114)													---	---	---	---
NUCB1	4924	broad.mit.edu	37	19	49407116	49407119	+	Intron	DEL	TGGA	-	-	rs35337876		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49407116_49407119delTGGA	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)														---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49642228	49642228	+	Intron	DEL	A	-	-	rs142758564		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49642228delA	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron	NM_003660	NP_003651			PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)														---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49644858	49644859	+	Intron	INS	-	GT	GT	rs147872140		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49644858_49644859insGT	uc002pmr.2	+						PPFIA3_uc010yai.1_Intron|PPFIA3_uc010yaj.1_Intron|PPFIA3_uc002pms.2_Intron|PPFIA3_uc002pmt.2_5'Flank	NM_003660	NP_003651			PTPRF interacting protein alpha 3							cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)														---	---	---	---
FCGRT	2217	broad.mit.edu	37	19	50016995	50016996	+	Intron	DEL	CC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50016995_50016996delCC	uc002poe.2	+						FCGRT_uc002pod.2_Intron|FCGRT_uc002pog.2_Intron|FCGRT_uc002pof.1_5'UTR|FCGRT_uc010yax.1_Intron|FCGRT_uc002poh.1_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50047360	50047360	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50047360delA								RCN3 (471 upstream) : NOSIP (11610 downstream)																																			---	---	---	---
IL4I1	259307	broad.mit.edu	37	19	50395879	50395879	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50395879delC	uc002pqt.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron	NM_152899	NP_690863			interleukin 4 induced 1 isoform 1 precursor							lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)														---	---	---	---
FLJ26850	400710	broad.mit.edu	37	19	50567905	50567908	+	Intron	DEL	GAGA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50567905_50567908delGAGA	uc002pro.2	+							NR_027257				Homo sapiens cDNA FLJ26850 fis, clone PRS07964.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	50582261	50582262	+	IGR	INS	-	T	T	rs71306119		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50582261_50582262insT								FLJ26850 (12212 upstream) : SNAR-A4 (38715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	51248196	51248196	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51248196delA								CLEC11A (19217 upstream) : GPR32 (25662 downstream)																																			---	---	---	---
ACPT	93650	broad.mit.edu	37	19	51296789	51296789	+	Intron	DEL	C	-	-	rs71824857		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51296789delC	uc002pta.1	+							NM_033068	NP_149059			testicular acid phosphatase precursor							integral to membrane	acid phosphatase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)														---	---	---	---
ZNF350	59348	broad.mit.edu	37	19	52467692	52467692	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52467692delA	uc002pyd.2	-	5					uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645			zinc finger protein 350						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|transcriptional repressor complex	DNA binding|protein binding|zinc ion binding			breast(1)	1		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)														---	---	---	---
ZNF841	284371	broad.mit.edu	37	19	52597278	52597278	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52597278delA	uc002pyl.1	-						ZNF841_uc010ydh.1_Intron	NM_001136499	NP_001129971			zinc finger protein 841						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	52680321	52680321	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52680321delT								ZNF836 (5425 upstream) : PPP2R1A (12870 downstream)																																			---	---	---	---
ZNF578	147660	broad.mit.edu	37	19	52957864	52957865	+	Intron	INS	-	AAAC	AAAC	rs149047503	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52957864_52957865insAAAC	uc002pzp.3	+						ZNF578_uc002pzm.2_Intron|ZNF578_uc002pzn.2_Intron|ZNF578_uc002pzo.1_Intron|ZNF578_uc010epp.1_Intron	NM_001099694	NP_001093164			zinc finger protein 578						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)														---	---	---	---
ZNF600	162966	broad.mit.edu	37	19	53285776	53285776	+	Intron	DEL	A	-	-	rs112059475		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53285776delA	uc002qab.3	-							NM_198457	NP_940859			zinc finger protein 600						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53551641	53551641	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53551641delA								ZNF702P (54857 upstream) : ZNF160 (18227 downstream)																																			---	---	---	---
ZNF665	79788	broad.mit.edu	37	19	53695099	53695099	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53695099delA	uc010eqm.1	-							NM_024733	NP_079009			zinc finger protein 665						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0196)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54088038	54088038	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54088038delT								ZNF331 (4515 upstream) : LOC284379 (14849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	54518650	54518651	+	IGR	INS	-	TCCTTTC	TCCTTTC	rs72530631		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54518650_54518651insTCCTTTC								CACNG6 (2732 upstream) : VSTM1 (25434 downstream)																																			---	---	---	---
LAIR2	3904	broad.mit.edu	37	19	55008233	55008234	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55008233_55008234insT	uc002qga.1	+						LAIR2_uc002qgb.1_5'Flank					Homo sapiens leukocyte-associated Ig-like receptor-2 (LAIR-2) mRNA, complete cds.							extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	55062827	55062828	+	IGR	INS	-	AT	AT	rs2059666	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55062827_55062828insAT								KIR3DX1 (7632 upstream) : LILRA2 (21654 downstream)																																			---	---	---	---
ZNF628	89887	broad.mit.edu	37	19	55985999	55986000	+	5'Flank	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55985999_55986000insT	uc002qld.2	+							NM_033113	NP_149104			zinc finger protein 628							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)														---	---	---	---
ZNF581	51545	broad.mit.edu	37	19	56153108	56153108	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56153108delG	uc002qln.2	+						ZNF580_uc002qlm.2_Intron|ZNF580_uc002qlo.2_Intron|ZNF580_uc002qlp.2_5'Flank|ZNF580_uc010ygd.1_5'Flank|ZNF581_uc002qlq.2_5'Flank	NM_016535	NP_057619			zinc finger protein 581						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
ZNF787	126208	broad.mit.edu	37	19	56618858	56618875	+	Intron	DEL	GGGAGACACGGGGTCACT	-	-	rs59423271	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56618858_56618875delGGGAGACACGGGGTCACT	uc010eth.1	-						ZNF787_uc002qml.1_Intron	NM_001002836	NP_001002836			zinc finger protein 787						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57003086	57003086	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57003086delA	uc002qnf.2	+						uc002qng.2_Intron					Homo sapiens cDNA clone IMAGE:5753168.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57827584	57827584	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57827584delT								ZNF460 (22148 upstream) : ZNF543 (4293 downstream)																																			---	---	---	---
ZNF773	374928	broad.mit.edu	37	19	58012021	58012022	+	Intron	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58012021_58012022delTG	uc002qox.2	+						ZNF547_uc002qpm.3_Intron|ZNF773_uc002qoy.2_Intron|ZNF773_uc002qoz.2_Intron	NM_198542	NP_940944			zinc finger protein 773						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)														---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	387657	387658	+	5'Flank	INS	-	A	A	rs150244721	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:387657_387658insA	uc002wdp.3	+						RBCK1_uc010zpl.1_5'Flank|RBCK1_uc010zpm.1_5'Flank|RBCK1_uc002wdq.3_5'Flank|RBCK1_uc010fzy.2_5'Flank|RBCK1_uc002wdr.3_5'Flank|RBCK1_uc002wdo.2_5'Flank	NM_031229	NP_112506			RanBP-type and C3HC4-type zinc finger containing						interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	600990	600990	+	IGR	DEL	G	-	-	rs63283561		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:600990delG								TCF15 (10080 upstream) : SRXN1 (26280 downstream)																																			---	---	---	---
ANGPT4	51378	broad.mit.edu	37	20	861231	861231	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:861231delA	uc002wei.2	-						ANGPT4_uc010zpn.1_Intron	NM_015985	NP_057069			angiopoietin 4 precursor						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	1195855	1195855	+	IGR	DEL	A	-	-	rs147329618		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1195855delA								C20orf202 (6939 upstream) : RAD21L1 (10909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	2263397	2263397	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2263397delT								STK35 (134201 upstream) : TGM3 (13216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	2438433	2438433	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2438433delG								TGM6 (25034 upstream) : SNRPB (3848 downstream)																																			---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2929598	2929598	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2929598delA	uc010zqb.1	+						VPS16_uc002whh.2_Intron|PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc010zqd.1_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						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	3298752	3298752	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3298752delT	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5545802	5545802	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5627593	5627593	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5627593delT								GPCPD1 (35921 upstream) : C20orf196 (103450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6592454	6592455	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6592454_6592455delTC								FERMT1 (488263 upstream) : BMP2 (156290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6778825	6778825	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6778825delT								BMP2 (17915 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7557287	7557287	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7557287delA								BMP2 (796377 upstream) : HAO1 (306344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	8081550	8081551	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8081550_8081551delAG								TMX4 (81157 upstream) : PLCB1 (13549 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8189173	8189173	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8189173delT	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9087187	9087188	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9087187_9087188delCA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
C20orf103	24141	broad.mit.edu	37	20	9505719	9505719	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9505719delT	uc002wni.1	+						C20orf103_uc010zrc.1_Intron	NM_012261	NP_036393			chromosome 20 open reading frame 103 precursor							integral to membrane				upper_aerodigestive_tract(1)|lung(1)|breast(1)	3			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	10147298	10147299	+	Intron	INS	-	A	A	rs78609848		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10147298_10147299insA	uc002wnn.1	-											Homo sapiens cDNA FLJ42971 fis, clone BRSTN2018083.																														---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10477316	10477318	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10477316_10477318delAAA	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
JAG1	182	broad.mit.edu	37	20	10630345	10630345	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10630345delA	uc002wnw.2	-						JAG1_uc010gcd.1_Intron	NM_000214	NP_000205			jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	20	11342675	11342675	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11342675delT								JAG1 (687981 upstream) : BTBD3 (528802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12374056	12374056	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12374056delT								BTBD3 (466814 upstream) : SPTLC3 (615571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	13195167	13195168	+	IGR	DEL	CA	-	-	rs72366934		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13195167_13195168delCA								SPTLC3 (47756 upstream) : ISM1 (7250 downstream)																																			---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13410124	13410125	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13410124_13410125delTT	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron	NM_017714	NP_060184			taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14225033	14225034	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14225033_14225034delAA	uc002wou.2	+						MACROD2_uc002wot.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	14508937	14508937	+	Intron	DEL	T	-	-	rs71335971		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14508937delT	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	15677179	15677179	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15677179delG	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)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	16019178	16019180	+	Intron	DEL	TTT	-	-	rs11483793		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16019178_16019180delTTT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16311630	16311630	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16311630delG	uc002wpg.1	-						KIF16B_uc002wpe.1_Intron|KIF16B_uc002wpf.1_Intron|KIF16B_uc010gch.1_Intron	NM_024704	NP_078980			kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	16949848	16949849	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16949848_16949849insT								OTOR (217040 upstream) : PCSK2 (256903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17034254	17034254	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17034254delT								OTOR (301446 upstream) : PCSK2 (172498 downstream)																																			---	---	---	---
SNX5	27131	broad.mit.edu	37	20	17923540	17923540	+	Intron	DEL	A	-	-	rs74179145		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17923540delA	uc002wqc.2	-						SNX5_uc002wqb.2_Intron|SNX5_uc002wqd.2_Intron|SNX5_uc002wqe.2_Intron	NM_014426	NP_055241			sorting nexin 5						cell communication|pinocytosis|protein transport	cytoplasmic vesicle membrane|early endosome membrane|extrinsic to endosome membrane|extrinsic to internal side of plasma membrane|macropinocytic cup|phagocytic cup|ruffle	phosphatidylinositol binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18114638	18114640	+	IGR	DEL	CCA	-	-	rs112350374		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18114638_18114640delCCA								OVOL2 (76117 upstream) : CSRP2BP (3887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	18298780	18298780	+	IGR	DEL	T	-	-	rs3216652		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18298780delT								ZNF133 (1142 upstream) : C20orf12 (65232 downstream)																																			---	---	---	---
C20orf12	55184	broad.mit.edu	37	20	18398730	18398731	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18398730_18398731delAA	uc010zsa.1	-						C20orf12_uc002wqp.3_Intron|C20orf12_uc002wqr.3_Intron|C20orf12_uc002wqs.3_Intron|C20orf12_uc002wqq.3_Intron|C20orf12_uc002wqu.1_Intron|C20orf12_uc010gct.1_Intron	NM_001099407	NP_001092877			hypothetical protein LOC55184							intracellular	zinc ion binding			ovary(1)	1		Myeloproliferative disorder(85;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	18861137	18861137	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18861137delT								C20orf79 (66104 upstream) : SLC24A3 (332153 downstream)																																			---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20284916	20284917	+	Intron	INS	-	TG	TG	rs145089165		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20284916_20284917insTG	uc002wru.2	+						C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20317987	20317990	+	Intron	DEL	TGGG	-	-	rs138008701	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
XRN2	22803	broad.mit.edu	37	20	21357661	21357661	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21357661delA	uc002wsf.1	+						XRN2_uc002wsg.1_Intron|XRN2_uc010zsk.1_Intron	NM_012255	NP_036387			5'-3' exoribonuclease 2						cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	22322244	22322244	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22322244delA								PAX1 (625624 upstream) : LOC284788 (58727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22863441	22863441	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22863441delT								FOXA2 (297340 upstream) : SSTR4 (152616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22960146	22960146	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22960146delT								FOXA2 (394045 upstream) : SSTR4 (55911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24707416	24707417	+	IGR	DEL	GA	-	-	rs2143822		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24707416_24707417delGA								TMEM90B (60249 upstream) : CST7 (222449 downstream)																																			---	---	---	---
LOC284798	284798	broad.mit.edu	37	20	25125146	25125146	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25125146delC	uc010gdg.2	-						LOC284798_uc010gdh.2_Intron|LOC284798_uc010zsx.1_Intron|LOC284798_uc010gdi.2_Intron	NR_027093				Homo sapiens cDNA FLJ38481 fis, clone FEBRA2022956.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25172091	25172092	+	Intron	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25172091_25172092delGA	uc002wui.2	-											Homo sapiens cDNA FLJ35339 fis, clone PROST2015636.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	25216289	25216290	+	IGR	DEL	AA	-	-	rs76865080		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25216289_25216290delAA								ENTPD6 (8929 upstream) : PYGB (12416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25641428	25641429	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25641428_25641429delTT	uc002wuz.2	+											Homo sapiens zinc finger protein 337, mRNA (cDNA clone IMAGE:4826085).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	25743216	25743217	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25743216_25743217delCA								ZNF337 (65747 upstream) : FAM182B (885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25868904	25868905	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25868904_25868905insT								FAM182B (20118 upstream) : LOC100134868 (121530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25910709	25910714	+	IGR	DEL	TTATTC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25910709_25910714delTTATTC								FAM182B (61923 upstream) : LOC100134868 (79721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26146854	26146855	+	IGR	INS	-	TTG	TTG	rs147533599	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26146854_26146855insTTG								C20orf191 (52177 upstream) : MIR663 (41967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26208764	26208765	+	IGR	INS	-	TT	TT	rs139088079		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26208764_26208765insTT								MIR663 (19850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26241161	26241161	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26241161delT								MIR663 (52247 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26254771	26254771	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26254771delA								MIR663 (65857 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29456623	29456624	+	IGR	DEL	AC	-	-	rs3074700		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29456623_29456624delAC								None (None upstream) : FRG1B (155255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29554821	29554822	+	IGR	INS	-	AC	AC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29554821_29554822insAC								None (None upstream) : FRG1B (57057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29588041	29588042	+	IGR	DEL	TG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29588041_29588042delTG								None (None upstream) : FRG1B (23837 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29616935	29616936	+	Intron	INS	-	T	T	rs141973478	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29616935_29616936insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0																		---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29645448	29645449	+	Intron	INS	-	T	T	rs138699737		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29645448_29645449insT	uc010ztl.1	+						FRG1B_uc010ztj.1_Intron|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0																		---	---	---	---
DEFB115	245929	broad.mit.edu	37	20	29844686	29844686	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29844686delT	uc002wvp.1	+							NM_001037730	NP_001032819			beta-defensin 115 precursor						defense response to bacterium	extracellular region				ovary(1)	1			Colorectal(19;0.00445)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30426912	30426913	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30426912_30426913insT								MYLK2 (4412 upstream) : FOXS1 (5190 downstream)																																			---	---	---	---
C20orf203	284805	broad.mit.edu	37	20	31246683	31246683	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31246683delT	uc002wxz.2	-							NR_026959				Homo sapiens cDNA FLJ33706 fis, clone BRAWH2007808.							cytoplasm					0																		---	---	---	---
ITCH	83737	broad.mit.edu	37	20	32954801	32954801	+	Intron	DEL	T	-	-	rs78005172		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32954801delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	33548035	33548035	+	IGR	DEL	T	-	-	rs146671827	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33548035delT								GSS (4434 upstream) : MYH7B (15171 downstream)																																			---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33648581	33648581	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33648581delA	uc002xbk.2	-						TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33743453	33743457	+	Intron	DEL	AAAAA	-	-	rs71196802		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33743453_33743457delAAAAA	uc010zuv.1	-							NM_018217	NP_060687			ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
C20orf152	140894	broad.mit.edu	37	20	34592494	34592494	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34592494delT	uc002xes.1	+						C20orf152_uc002xer.1_Intron|C20orf152_uc010gfp.1_Intron					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34693759	34693759	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34693759delG	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron	NM_012156	NP_036288			erythrocyte membrane protein band 4.1-like 1						cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)																	---	---	---	---
DSN1	79980	broad.mit.edu	37	20	35394950	35394951	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35394950_35394951insG	uc010gfr.2	-						DSN1_uc002xfz.2_Intron|DSN1_uc002xfy.3_Intron|DSN1_uc002xga.2_Intron|DSN1_uc010zvs.1_Intron|DSN1_uc002xgc.2_Intron|DSN1_uc002xgb.2_Intron	NM_001145316	NP_001138788			DSN1, MIND kinetochore complex component,						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			ovary(2)	2		Myeloproliferative disorder(115;0.00874)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	35965250	35965250	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35965250delA								MANBAL (19589 upstream) : SRC (7838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	36038920	36038920	+	IGR	DEL	T	-	-	rs72268950		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36038920delT								SRC (5101 upstream) : BLCAP (106900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	36072107	36072108	+	IGR	INS	-	C	C	rs146134133	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36072107_36072108insC								SRC (38288 upstream) : BLCAP (73712 downstream)																																			---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36498414	36498414	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36498414delA	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	36522208	36522211	+	IGR	DEL	TCCC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36522208_36522211delTCCC								CTNNBL1 (21689 upstream) : VSTM2L (9288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	36522264	36522267	+	IGR	DEL	TCCT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36522264_36522267delTCCT								CTNNBL1 (21745 upstream) : VSTM2L (9232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37275581	37275582	+	IGR	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37275581_37275582delTC								ADIG (58477 upstream) : SLC32A1 (77523 downstream)																																	OREG0025931	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DHX35	60625	broad.mit.edu	37	20	37652159	37652159	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37652159delT	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	38380729	38380729	+	IGR	DEL	G	-	-	rs59914410		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38380729delG								LOC339568 (527338 upstream) : MAFB (933790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39443693	39443694	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39443693_39443694insA								MAFB (125817 upstream) : TOP1 (213768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39472018	39472019	+	IGR	DEL	AG	-	-	rs11467708		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39472018_39472019delAG								MAFB (154142 upstream) : TOP1 (185443 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41049905	41049906	+	Intron	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41049905_41049906delCA	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	41765272	41765273	+	Intron	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41765272_41765273delAC	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)																---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42254145	42254146	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42254145_42254146insA	uc002xkw.2	+						IFT52_uc002xky.2_Intron|IFT52_uc002xkx.2_Intron|IFT52_uc010ggn.2_Intron|IFT52_uc002xkz.2_Intron	NM_016004	NP_057088			intraflagellar transport 52 homolog							intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
MYBL2	4605	broad.mit.edu	37	20	42307515	42307515	+	Intron	DEL	G	-	-	rs61064495		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42307515delG	uc002xlb.1	+						MYBL2_uc010zwj.1_Intron|MYBL2_uc002xla.1_Intron	NM_002466	NP_002457			MYB-related protein B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
JPH2	57158	broad.mit.edu	37	20	42751591	42751591	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42751591delT	uc002xli.1	-							NM_020433	NP_065166			junctophilin 2 isoform 1						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	43481610	43481610	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43481610delT								RIMS4 (42698 upstream) : YWHAB (32734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44357121	44357121	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44357121delA								SPINT4 (2786 upstream) : WFDC3 (45726 downstream)																																			---	---	---	---
ZSWIM3	140831	broad.mit.edu	37	20	44490066	44490066	+	Intron	DEL	A	-	-	rs138333197		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44490066delA	uc002xqd.2	+						ZSWIM3_uc010zxg.1_Intron	NM_080752	NP_542790			zinc finger, SWIM domain containing 3								zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	44614992	44614995	+	IGR	DEL	TTTC	-	-	rs11474641		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44614992_44614995delTTTC								ZNF335 (14159 upstream) : MMP9 (22552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44775635	44775636	+	IGR	DEL	GA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44775635_44775636delGA								CD40 (17251 upstream) : CDH22 (26740 downstream)																																			---	---	---	---
CDH22	64405	broad.mit.edu	37	20	44812743	44812744	+	Intron	DEL	TT	-	-	rs76960056		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44812743_44812744delTT	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)																---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	45062227	45062228	+	5'Flank	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45062227_45062228delTC	uc010zxs.1	-						uc002xry.2_Intron					SubName: Full=ELMO2 protein; SubName: Full=Engulfment and cell motility 2;						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46369387	46369388	+	Intron	INS	-	AAC	AAC	rs150553626	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46369387_46369388insAAC	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron|SULF2_uc010ghv.1_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						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			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47302265	47302265	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47302265delA	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47324165	47324165	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47324165delT	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47876135	47876135	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47876135delT	uc002xui.2	-							NM_021035	NP_066363			zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48512988	48512989	+	IGR	INS	-	GT	GT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48512988_48512989insGT								SLC9A8 (4216 upstream) : SPATA2 (6942 downstream)																																			---	---	---	---
PTPN1	5770	broad.mit.edu	37	20	49162400	49162400	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49162400delA	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818			protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)													---	---	---	---
PTPN1	5770	broad.mit.edu	37	20	49171867	49171868	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49171867_49171868insA	uc002xvl.2	+						PTPN1_uc010zys.1_Intron	NM_002827	NP_002818			protein tyrosine phosphatase, non-receptor type						blood coagulation|interferon-gamma-mediated signaling pathway|negative regulation of insulin receptor signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol|endoplasmic reticulum membrane	protein tyrosine phosphatase activity|zinc ion binding				0		Lung NSC(126;0.163)			Clodronate(DB00720)|Tiludronate(DB01133)													---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49259283	49259284	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49259283_49259284delAA	uc010zyt.1	-						FAM65C_uc010zyu.1_Intron	NM_080829	NP_543019			hypothetical protein LOC140876											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49618661	49618662	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49618661_49618662delAG								MOCS3 (40841 upstream) : KCNG1 (1532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49967742	49967742	+	IGR	DEL	T	-	-	rs11479051		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49967742delT								KCNG1 (328067 upstream) : NFATC2 (40024 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49993633	49993634	+	IGR	INS	-	GCGC	GCGC	rs140915264	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49993633_49993634insGCGC								KCNG1 (353958 upstream) : NFATC2 (14132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50423925	50423926	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50423925_50423926delTT								SALL4 (4877 upstream) : ZFP64 (276625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50426128	50426128	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50426128delA								SALL4 (7080 upstream) : ZFP64 (274423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51112444	51112444	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51112444delA								ZFP64 (303920 upstream) : TSHZ2 (476433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51155211	51155211	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51155211delA								ZFP64 (346687 upstream) : TSHZ2 (433666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51288221	51288221	+	IGR	DEL	T	-	-	rs5841905		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51288221delT								ZFP64 (479697 upstream) : TSHZ2 (300656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51488667	51488668	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51488667_51488668delCA								ZFP64 (680143 upstream) : TSHZ2 (100209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52455204	52455205	+	IGR	DEL	CG	-	-	rs11467800	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52455204_52455205delCG								ZNF217 (244403 upstream) : SUMO1P1 (35837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53275218	53275218	+	IGR	DEL	C	-	-	rs67613189		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53275218delC								DOK5 (7509 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53585757	53585757	+	IGR	DEL	A	-	-	rs11355822		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53585757delA								DOK5 (318048 upstream) : CBLN4 (986740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53820900	53820900	+	IGR	DEL	T	-	-	rs73148585	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53820900delT								DOK5 (553191 upstream) : CBLN4 (751597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54406667	54406668	+	IGR	DEL	AT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54406667_54406668delAT								None (None upstream) : CBLN4 (165829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54879127	54879127	+	IGR	DEL	A	-	-	rs11451247		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54879127delA								MC3R (54256 upstream) : C20orf108 (54856 downstream)																																			---	---	---	---
C20orf108	116151	broad.mit.edu	37	20	54940868	54940868	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54940868delT	uc002xxc.2	+							NM_080821	NP_543011			hypothetical protein LOC116151							integral to membrane					0			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	55139715	55139715	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55139715delA								C20orf107 (28141 upstream) : TFAP2C (64643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55140160	55140161	+	IGR	INS	-	CAAA	CAAA	rs142912798	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55140160_55140161insCAAA								C20orf107 (28586 upstream) : TFAP2C (64197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55177182	55177183	+	IGR	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55177182_55177183insTG								C20orf107 (65608 upstream) : TFAP2C (27175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56604985	56604985	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56604985delT								PMEPA1 (318444 upstream) : C20orf85 (120998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57527362	57527363	+	IGR	DEL	AT	-	-	rs6026614	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57527362_57527363delAT								GNAS (41113 upstream) : TH1L (28948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57840414	57840417	+	IGR	DEL	TTCC	-	-	rs57847155		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57840414_57840417delTTCC								ZNF831 (6249 upstream) : EDN3 (35082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	58068154	58068155	+	IGR	INS	-	A	A	rs113620421		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58068154_58068155insA								EDN3 (167108 upstream) : PHACTR3 (84409 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58294230	58294230	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58294230delT	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_5'Flank|PHACTR3_uc002yax.2_5'Flank	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60004804	60004811	+	Intron	DEL	TAGGTGTG	-	-	rs150433276	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60004804_60004811delTAGGTGTG	uc002ybn.1	+							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	60012634	60012634	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60012634delG	uc002ybn.1	+							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	60347872	60347873	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60347872_60347873delTT	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	60402021	60402022	+	Intron	INS	-	TGTA	TGTA	rs138857247	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60402021_60402022insTGTA	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	60548348	60548349	+	IGR	INS	-	AT	AT	rs144315094	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60548348_60548349insAT								MIR1257 (19630 upstream) : TAF4 (1506 downstream)																																			---	---	---	---
LSM14B	149986	broad.mit.edu	37	20	60709531	60709531	+	3'UTR	DEL	T	-	-	rs67454106		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60709531delT	uc010gjy.1	+	9					LSM14B_uc010zzz.1_3'UTR	NM_144703	NP_653304			LSM14 homolog B						multicellular organismal development|regulation of translation	ribonucleoprotein complex					0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	62749873	62749875	+	IGR	DEL	GGG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62749873_62749875delGGG								NPBWR2 (11689 upstream) : MYT1 (33269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9466976	9466977	+	IGR	INS	-	CAA	CAA			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9466976_9466977insCAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9524847	9524847	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9524847delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9544374	9544374	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9544374delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9652777	9652778	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9652777_9652778insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9674424	9674424	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9674424delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9753235	9753235	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9753235delA	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10148552	10148553	+	IGR	INS	-	TT	TT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10148552_10148553insTT								None (None upstream) : TPTE (758190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10463798	10463798	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10463798delG	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10602441	10602441	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10602441delA								None (None upstream) : TPTE (304302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10832610	10832611	+	IGR	INS	-	TGGAG	TGGAG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10832610_10832611insTGGAG								None (None upstream) : TPTE (74132 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10939548	10939548	+	Intron	DEL	T	-	-	rs113663078		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10939548delT	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	11062747	11062748	+	Intron	INS	-	A	A	rs78264078		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11062747_11062748insA	uc002yit.1	-						BAGE_uc002yiw.1_5'Flank|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)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11075686	11075687	+	Intron	INS	-	TGA	TGA	rs4009958		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11075686_11075687insTGA	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	15202003	15202004	+	IGR	INS	-	A	A	rs77191391		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15202003_15202004insA								POTED (188097 upstream) : C21orf15 (13451 downstream)																																			---	---	---	---
LIPI	149998	broad.mit.edu	37	21	15579916	15579916	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15579916delA	uc002yjm.2	-							NM_198996	NP_945347			lipase, member I						lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16328688	16328688	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16328688delT								SAMSN1 (372965 upstream) : NRIP1 (4868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16748277	16748277	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16748277delC								NRIP1 (311151 upstream) : USP25 (354219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18435890	18435890	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18435890delT								C21orf34 (453796 upstream) : CXADR (449440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18771811	18771811	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18771811delT								C21orf34 (789717 upstream) : CXADR (113519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18787388	18787388	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18787388delG								C21orf34 (805294 upstream) : CXADR (97942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18831510	18831510	+	IGR	DEL	G	-	-	rs71333548		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18831510delG								C21orf34 (849416 upstream) : CXADR (53820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	19038154	19038155	+	IGR	INS	-	TG	TG			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19038154_19038155insTG								BTG3 (52886 upstream) : C21orf91 (111568 downstream)																																			---	---	---	---
CHODL	140578	broad.mit.edu	37	21	19547800	19547801	+	Intron	DEL	CT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19547800_19547801delCT	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron					RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: Precursor;						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20696772	20696772	+	IGR	DEL	A	-	-	rs144394686		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20696772delA								TMPRSS15 (920802 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21410558	21410558	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21410558delT								None (None upstream) : C21orf131 (704356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21680667	21680668	+	IGR	INS	-	AT	AT	rs149287801	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21680667_21680668insAT								None (None upstream) : C21orf131 (434246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21921164	21921164	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21921164delA								None (None upstream) : C21orf131 (193750 downstream)																																			---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22420678	22420678	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22420678delT	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	23782112	23782113	+	IGR	INS	-	CCTC	CCTC	rs146198027	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23782112_23782113insCCTC								NCAM2 (870898 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23997226	23997227	+	IGR	DEL	AG	-	-	rs66561171		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23997226_23997227delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24892665	24892665	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24892665delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25646866	25646866	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25646866delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26867184	26867184	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26867184delA								NCRNA00158 (63171 upstream) : MIR155HG (67273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26995168	26995168	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26995168delA								MRPL39 (15367 upstream) : JAM2 (16421 downstream)																																			---	---	---	---
ATP5J	522	broad.mit.edu	37	21	27105895	27105895	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27105895delA	uc002yls.2	-						GABPA_uc002ylx.3_5'Flank|GABPA_uc002yly.3_5'Flank|ATP5J_uc002ylt.2_Intron|ATP5J_uc002ylu.2_Intron|ATP5J_uc002ylv.2_Intron|ATP5J_uc002ylw.2_Intron	NM_001685	NP_001676			ATP synthase, H+ transporting, mitochondrial F0						ATP catabolic process|respiratory electron transport chain		hydrogen ion transmembrane transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	28149488	28149488	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28149488delT								CYYR1 (203907 upstream) : ADAMTS1 (59120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28720611	28720612	+	IGR	INS	-	G	G	rs145308229		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28720611_28720612insG								ADAMTS5 (381172 upstream) : NCRNA00113 (374086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29184691	29184691	+	IGR	DEL	T	-	-	rs2849681	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29184691delT								NCRNA00113 (61139 upstream) : C21orf94 (200991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29346946	29346946	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29346946delG								NCRNA00113 (223394 upstream) : C21orf94 (38736 downstream)																																			---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30305531	30305532	+	Intron	INS	-	A	A	rs142866680	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30305531_30305532insA	uc002ymr.2	-							NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	30937694	30937694	+	Intron	DEL	T	-	-	rs71744010		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30937694delT	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)													---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31115361	31115361	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31115361delT	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			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)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	31658349	31658349	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31658349delA								KRTAP24-1 (3073 upstream) : KRTAP25-1 (3114 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32915071	32915071	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32915071delG	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	33046837	33046838	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33046837_33046838insA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33074758	33074758	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33074758delA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
HUNK	30811	broad.mit.edu	37	21	33288992	33288993	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33288992_33288993delTT	uc002yph.2	+							NM_014586	NP_055401			hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2																		---	---	---	---
HUNK	30811	broad.mit.edu	37	21	33310085	33310085	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33310085delA	uc002yph.2	+							NM_014586	NP_055401			hormonally upregulated Neu-associated kinase						multicellular organismal development|signal transduction		ATP binding|protein serine/threonine kinase activity			stomach(1)|skin(1)	2																		---	---	---	---
URB1	9875	broad.mit.edu	37	21	33683917	33683918	+	3'UTR	INS	-	G	G	rs145693680	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33683917_33683918insG	uc002ypn.2	-	39					MRAP_uc002ypk.2_Intron|MRAP_uc002ypj.2_Intron|MRAP_uc011ado.1_Intron|MRAP_uc002ypl.2_Intron|uc002ypm.2_5'Flank	NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
GCFC1	94104	broad.mit.edu	37	21	34133212	34133213	+	Intron	DEL	GC	-	-	rs8133271		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34133212_34133213delGC	uc002yqn.2	-						GCFC1_uc002yqo.2_Intron|GCFC1_uc002yqp.2_Intron|GCFC1_uc002yqr.2_Intron	NM_016631	NP_057715			GC-rich sequence DNA-binding factor candidate							cytosol|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	34262452	34262453	+	IGR	INS	-	A	A	rs138031051	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34262452_34262453insA								C21orf62 (76399 upstream) : OLIG2 (135786 downstream)																																			---	---	---	---
IL10RB	3588	broad.mit.edu	37	21	34660708	34660711	+	Intron	DEL	ACAG	-	-	rs67118950		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660708_34660711delACAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619			interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0																		---	---	---	---
IL10RB	3588	broad.mit.edu	37	21	34660710	34660711	+	Intron	DEL	AG	-	-	rs66834406		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34660710_34660711delAG	uc002yrk.1	+						IL10RB_uc002yrl.1_Intron	NM_000628	NP_000619			interleukin 10 receptor, beta precursor						immune response|inflammatory response	interleukin-28 receptor complex	protein binding|receptor activity				0																		---	---	---	---
GART	2618	broad.mit.edu	37	21	34905295	34905295	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34905295delA	uc002yrx.2	-						GART_uc002yrz.2_Intron|GART_uc010gmd.2_Intron|GART_uc002yry.2_Intron|GART_uc002ysa.2_Intron	NM_000819	NP_000810			phosphoribosylglycinamide formyltransferase,						'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)													---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35123412	35123412	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35123412delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35251993	35251993	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35251993delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc010gmn.1_Intron|ITSN1_uc002ytk.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
ATP5O	539	broad.mit.edu	37	21	35280296	35280296	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35280296delA	uc002ytl.2	-						DONSON_uc002ysn.1_Intron	NM_001697	NP_001688			mitochondrial ATP synthase, O subunit precursor						ATP catabolic process|mitochondrial ATP synthesis coupled proton transport|respiratory electron transport chain	mitochondrial proton-transporting ATP synthase complex|plasma membrane|proton-transporting ATP synthase complex, catalytic core F(1)	drug binding|hydrogen ion transporting ATP synthase activity, rotational mechanism			ovary(1)	1																		---	---	---	---
C21orf82	114036	broad.mit.edu	37	21	35554834	35554834	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35554834delT	uc002ytr.3	+						C21orf82_uc002yts.2_Intron	NR_027267				Homo sapiens C21orf82 protein (C21orf82) mRNA, complete cds.												0																		---	---	---	---
RCAN1	1827	broad.mit.edu	37	21	35963761	35963761	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35963761delG	uc002yue.2	-						RCAN1_uc002yuc.2_Intron|RCAN1_uc002yud.2_Intron	NM_004414	NP_004405			calcipressin 1 isoform a						blood circulation|calcium-mediated signaling|central nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
RUNX1	861	broad.mit.edu	37	21	37089568	37089568	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37089568delT	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				---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37578309	37578309	+	Intron	DEL	A	-	-	rs113749030		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37578309delA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37745998	37745998	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37745998delA	uc002yvi.2	+							NM_015358	NP_056173			MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37790316	37790318	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37790316_37790318delTTT								CHAF1B (1192 upstream) : CLDN14 (42602 downstream)																																			---	---	---	---
CLDN14	23562	broad.mit.edu	37	21	37941714	37941715	+	Intron	DEL	AA	-	-	rs76070439		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37941714_37941715delAA	uc002yvo.1	-							NM_001146077	NP_001139549			claudin 14						calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0																		---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38097647	38097647	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38097647delA	uc002yvr.2	+						SIM2_uc002yvq.2_Intron	NM_005069	NP_005060			single-minded homolog 2 long isoform						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38118614	38118614	+	Intron	DEL	A	-	-	rs71873189		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38118614delA	uc002yvr.2	+							NM_005069	NP_005060			single-minded homolog 2 long isoform						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	38664082	38664082	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38664082delA								DSCR3 (24249 upstream) : DYRK1A (75777 downstream)																																			---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39072405	39072405	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39072405delA	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39084999	39084999	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39084999delC	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
ERG	2078	broad.mit.edu	37	21	39839884	39839884	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39839884delG	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	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)																---	---	---	---
ERG	2078	broad.mit.edu	37	21	39860361	39860362	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39860361_39860362insT	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_uc010gnz.2_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40096650	40096651	+	IGR	INS	-	AGATAGAT	AGATAGAT	rs146523294	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40096650_40096651insAGATAGAT								ERG (62946 upstream) : NCRNA00114 (14228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40338048	40338048	+	IGR	DEL	T	-	-	rs67081380		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40338048delT								ETS2 (141172 upstream) : PSMG1 (209342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40432806	40432806	+	IGR	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40432806delC								ETS2 (235930 upstream) : PSMG1 (114584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40485565	40485565	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40485565delT								ETS2 (288689 upstream) : PSMG1 (61825 downstream)																																			---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40645557	40645574	+	Intron	DEL	AGGCTGAGATGGGGGGAC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40645557_40645574delAGGCTGAGATGGGGGGAC	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc010goe.1_Intron|BRWD1_uc010gof.1_Intron|BRWD1_uc010gog.1_Intron|BRWD1_uc010goh.1_Intron|BRWD1_uc010goi.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	40689360	40689360	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40689360delA								BRWD1 (3804 upstream) : HMGN1 (24887 downstream)																																			---	---	---	---
WRB	7485	broad.mit.edu	37	21	40761216	40761216	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40761216delT	uc002yxs.2	+						WRB_uc011aeo.1_Intron|WRB_uc011aep.1_Intron|WRB_uc002yxt.3_Intron|WRB_uc010goj.2_Intron	NM_004627	NP_004618			tryptophan rich basic protein isoform 1							integral to membrane|nucleolus					0		Prostate(19;1.2e-06)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	41061955	41061956	+	IGR	INS	-	CTGT	CTGT	rs72178203		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41061955_41061956insCTGT								B3GALT5 (27140 upstream) : IGSF5 (55378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41110819	41110819	+	IGR	DEL	T	-	-	rs112203012		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41110819delT								B3GALT5 (76004 upstream) : IGSF5 (6515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41306513	41306514	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41306513_41306514insA								PCP4 (5193 upstream) : DSCAM (77829 downstream)																																			---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43283957	43283959	+	Intron	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43283957_43283959delTTT	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
C2CD2	25966	broad.mit.edu	37	21	43375474	43375475	+	5'Flank	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43375474_43375475delGT	uc002yzw.2	-							NM_015500	NP_056315			C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1																		---	---	---	---
TMPRSS3	64699	broad.mit.edu	37	21	43812669	43812670	+	Intron	INS	-	ATGA	ATGA	rs145969335	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43812669_43812670insATGA	uc002zbb.2	-						TMPRSS3_uc002zba.2_5'Flank|TMPRSS3_uc002zbc.2_Intron|TMPRSS3_uc002zbd.2_Intron	NM_024022	NP_076927			transmembrane protease, serine 3 isoform 1						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																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44112366	44112366	+	Intron	DEL	C	-	-	rs11702318	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44112366delC	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																		---	---	---	---
CBS	875	broad.mit.edu	37	21	44476001	44476001	+	Intron	DEL	T	-	-	rs79861734		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476001delT	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_3'UTR	NM_000071	NP_000062			cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	44604372	44604375	+	IGR	DEL	AAAA	-	-	rs142775428		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44604372_44604375delAAAA								CRYAA (11459 upstream) : SIK1 (230023 downstream)																																			---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45469760	45469760	+	Intron	DEL	T	-	-	rs67224636		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45469760delT	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46941727	46941727	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46941727delA	uc002zhl.1	-						SLC19A1_uc010gpy.1_Intron|SLC19A1_uc011aft.1_Intron|SLC19A1_uc002zhm.1_Intron|SLC19A1_uc010gpz.1_Intron	NM_194255	NP_919231			solute carrier family 19 member 1						folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47339729	47339730	+	Intron	DEL	GT	-	-	rs71318018		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47339729_47339730delGT	uc002zhq.1	+						PCBP3_uc010gqb.2_Intron|PCBP3_uc002zhp.1_Intron|PCBP3_uc002zhs.1_Intron|PCBP3_uc002zhr.1_Intron|PCBP3_uc002zht.1_Intron	NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
COL6A1	1291	broad.mit.edu	37	21	47410379	47410423	+	Intron	DEL	AATGGGGCGAGATGGGGAGGGACGGAGTGGACGGCGTGAAGGTGA	-	-	rs72435610	by1000genomes;by1000genomes;by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47410379_47410423delAATGGGGCGAGATGGGGAGGGACGGAGTGGACGGCGTGAAGGTGA	uc002zhu.1	+							NM_001848	NP_001839			collagen, type VI, alpha 1 precursor						axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)													---	---	---	---
C21orf57	54059	broad.mit.edu	37	21	47707040	47707040	+	Intron	DEL	A	-	-	rs71986095		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47707040delA	uc002ziv.2	+						C21orf57_uc002zit.1_Intron|C21orf57_uc002ziu.1_Intron|C21orf57_uc002ziw.2_Intron|C21orf57_uc002zix.2_Intron|C21orf57_uc010gqh.2_Intron|C21orf57_uc002ziy.2_Intron|MCM3AP_uc002zir.1_5'Flank	NM_058181	NP_478061			hypothetical protein LOC54059 isoform 1								metal ion binding|metalloendopeptidase activity				0	Breast(49;0.112)			Colorectal(79;0.236)														---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47754119	47754119	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47754119delA	uc002zji.3	+						PCNT_uc002zjj.2_Intron|PCNT_uc010gqk.1_5'Flank	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	16231996	16231996	+	IGR	DEL	G	-	-	rs3132734		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16231996delG								None (None upstream) : POTEH (24336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17025216	17025216	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17025216delT								OR11H1 (575412 upstream) : CCT8L2 (46432 downstream)																																			---	---	---	---
psiTPTE22	387590	broad.mit.edu	37	22	17112641	17112641	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17112641delA	uc002zls.1	+						psiTPTE22_uc002zlr.2_Intron|psiTPTE22_uc002zlt.2_Intron					Homo sapiens cDNA FLJ10437 fis, clone NT2RP1000581.												0																		---	---	---	---
CECR2	27443	broad.mit.edu	37	22	18031488	18031488	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18031488delA	uc010gqw.1	+						CECR2_uc010gqv.1_Intron|CECR2_uc002zml.2_Intron|CECR2_uc002zmo.2_Intron	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)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19190025	19190026	+	Intron	INS	-	C	C	rs67556687		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19190025_19190026insC	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron|CLTCL1_uc011agt.1_Intron|CLTCL1_uc011agu.1_Intron|CLTCL1_uc010grm.1_Intron|CLTCL1_uc002zpe.2_Intron|CLTCL1_uc002zpd.1_Intron	NM_007098	NP_009029			clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19342593	19342593	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19342593delT	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19372625	19372625	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19372625delC	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
COMT	1312	broad.mit.edu	37	22	19940183	19940183	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19940183delA	uc002zqu.2	+						COMT_uc002zqt.2_Intron|COMT_uc002zqv.2_Intron|COMT_uc002zqw.2_Intron|COMT_uc011ahd.1_Intron|COMT_uc002zqx.2_Intron	NM_000754	NP_000745			catechol-O-methyltransferase isoform MB-COMT						neurotransmitter biosynthetic process|neurotransmitter catabolic process|xenobiotic metabolic process	cytosol|integral to membrane|intracellular membrane-bounded organelle|microsome|plasma membrane|soluble fraction	catechol O-methyltransferase activity|magnesium ion binding|protein binding			ovary(1)	1	Colorectal(54;0.0993)				Carbidopa(DB00190)|Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Folic Acid(DB00158)|L-Valine(DB00161)|Levodopa(DB01235)|Methyldopa(DB00968)|Modafinil(DB00745)|Morphine(DB00295)|S-Adenosylmethionine(DB00118)|Tolcapone(DB00323)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	20149873	20149875	+	IGR	DEL	ACC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20149873_20149875delACC								ZDHHC8 (14344 upstream) : LOC150197 (43980 downstream)																																			---	---	---	---
YPEL1	29799	broad.mit.edu	37	22	22054765	22054766	+	3'UTR	DEL	TT	-	-	rs146591699		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22054765_22054766delTT	uc002zvl.2	-	5					YPEL1_uc002zvm.2_RNA	NM_013313	NP_037445			yippee-like 1							nucleus					0	Colorectal(54;0.105)																	---	---	---	---
MAPK1	5594	broad.mit.edu	37	22	22188230	22188230	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22188230delT	uc002zvn.2	-						MAPK1_uc002zvo.2_Intron|MAPK1_uc010gtk.1_Intron	NM_002745	NP_002736			mitogen-activated protein kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle|epidermal growth factor receptor signaling pathway|ERK1 and ERK2 cascade|induction of apoptosis|innate immune response|insulin receptor signaling pathway|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|Ras protein signal transduction|regulation of sequence-specific DNA binding transcription factor activity|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|transcription, DNA-dependent	cytosol|nucleoplasm	ATP binding|DNA binding|MAP kinase activity|phosphatase binding|RNA polymerase II carboxy-terminal domain kinase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	22225628	22225628	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22225628delA								MAPK1 (3658 upstream) : PPM1F (48165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	22235903	22235903	+	IGR	DEL	A	-	-	rs72330654		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22235903delA								MAPK1 (13933 upstream) : PPM1F (37890 downstream)																																			---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22813122	22813123	+	Intron	INS	-	C	C	rs141641305	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22813122_22813123insC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22832300	22832300	+	Intron	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22832300delC	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23238029	23238030	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23238029_23238030insT	uc011aim.1	+						uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23608269	23608269	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23608269delT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.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								---	---	---	---
C22orf43	51233	broad.mit.edu	37	22	23976575	23976575	+	5'Flank	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23976575delA	uc002zxf.2	-							NM_016449	NP_057533			hypothetical protein LOC51233											skin(1)	1																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26413051	26413054	+	Intron	DEL	CTCC	-	-	rs144669857		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26413051_26413054delCTCC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	26453180	26453180	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26453180delA								MYO18B (26173 upstream) : SEZ6L (112300 downstream)																																			---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26709561	26709570	+	Intron	DEL	CACACACACG	-	-	rs150855077	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26709561_26709570delCACACACACG	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	26720069	26720070	+	Intron	INS	-	AC	AC	rs150705995	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26720069_26720070insAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	26800411	26800412	+	IGR	INS	-	TCTCTC	TCTCTC	rs145783213	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26800411_26800412insTCTCTC								SEZ6L (23977 upstream) : ASPHD2 (24868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	26817784	26817785	+	IGR	INS	-	AC	AC	rs145391910	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26817784_26817785insAC								SEZ6L (41350 upstream) : ASPHD2 (7495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27190978	27190980	+	IGR	DEL	CCT	-	-	rs67091742		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27190978_27190980delCCT								MIAT (76029 upstream) : MN1 (953286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27352841	27352841	+	IGR	DEL	T	-	-	rs66688813		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27352841delT								MIAT (237892 upstream) : MN1 (791425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27361828	27361828	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27361828delA								MIAT (246879 upstream) : MN1 (782438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27761010	27761010	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27761010delT								MIAT (646061 upstream) : MN1 (383256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27797268	27797315	+	IGR	DEL	ATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGA	-	-	rs9680856	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27797268_27797315delATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATGA								MIAT (682319 upstream) : MN1 (346951 downstream)																																			---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28706160	28706163	+	Intron	DEL	ACAA	-	-	rs72207474		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28706160_28706163delACAA	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29395322	29395323	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29395322_29395323insA	uc003aeg.2	+						ZNRF3_uc003aeh.1_Intron	NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29516125	29516126	+	Intron	DEL	AC	-	-	rs57596876		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29516125_29516126delAC	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29529639	29529639	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29529639delT	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29592883	29592884	+	IGR	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29592883_29592884delAA								KREMEN1 (28562 upstream) : EMID1 (9069 downstream)																																			---	---	---	---
RFPL1	5988	broad.mit.edu	37	22	29835329	29835329	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29835329delA	uc003afn.2	+						RFPL1S_uc003afm.1_RNA	NM_021026	NP_066306			ret finger protein-like 1								zinc ion binding				0																		---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30203917	30203917	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30203917delA	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	30437415	30437415	+	IGR	DEL	A	-	-	rs35782551		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30437415delA								MTMR3 (10560 upstream) : HORMAD2 (39038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	30786461	30786461	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30786461delG								RNF215 (3159 upstream) : SEC14L2 (6472 downstream)																																			---	---	---	---
SDC4P	376844	broad.mit.edu	37	22	30880619	30880619	+	5'Flank	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30880619delT	uc003aic.1	-							NR_001580				Homo sapiens syndecan 4 pseudogene mRNA, partial sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	31790738	31790738	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31790738delA								PATZ1 (48489 upstream) : DRG1 (4801 downstream)																																			---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31915260	31915263	+	Intron	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31915260_31915263delTTTT	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	32216099	32216100	+	Intron	DEL	TG	-	-	rs62238924		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32216099_32216100delTG	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_5'Flank|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
BPIL2	254240	broad.mit.edu	37	22	32828101	32828101	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32828101delT	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592			bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2																		---	---	---	---
FBXO7	25793	broad.mit.edu	37	22	32891356	32891357	+	Intron	DEL	TT	-	-	rs11332165		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32891356_32891357delTT	uc003amq.2	+						FBXO7_uc003amr.2_Intron|FBXO7_uc003ams.2_Intron|FBXO7_uc003amt.2_Intron|FBXO7_uc003amu.2_Intron|FBXO7_uc003amv.2_Intron	NM_012179	NP_036311			F-box only protein 7 isoform 1						cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33176966	33176969	+	Intron	DEL	TCCT	-	-	rs68188956		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33176966_33176969delTCCT	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																		---	---	---	---
TIMP3	7078	broad.mit.edu	37	22	33256520	33256520	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33256520delT	uc003anb.2	+	5					SYN3_uc003amx.2_Intron|SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron	NM_000362	NP_000353			tissue inhibitor of metalloproteinase 3						negative regulation of membrane protein ectodomain proteolysis|visual perception		metal ion binding|metalloendopeptidase inhibitor activity|protein binding			lung(1)	1																OREG0003524	type=REGULATORY REGION|Gene=X77690|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
Unknown	0	broad.mit.edu	37	22	33536167	33536167	+	IGR	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33536167delG								SYN3 (81790 upstream) : LARGE (132896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34333677	34333678	+	IGR	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34333677_34333678delGT								LARGE (15093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	34971697	34971697	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34971697delA								LARGE (653113 upstream) : ISX (490432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35406308	35406308	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35406308delA								None (None upstream) : ISX (55821 downstream)																																			---	---	---	---
TOM1	10043	broad.mit.edu	37	22	35739336	35739337	+	Intron	INS	-	CA	CA	rs144221305		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35739336_35739337insCA	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479			target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1																		---	---	---	---
APOL5	80831	broad.mit.edu	37	22	36113785	36113786	+	5'Flank	INS	-	AA	AA	rs71322979		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36113785_36113786insAA	uc003aof.2	+							NM_030642	NP_085145			apolipoprotein L5						lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36236675	36236678	+	Intron	DEL	GTGC	-	-	rs71707277	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36236675_36236678delGTGC	uc003aon.3	-						RBM9_uc003aol.3_5'Flank|RBM9_uc003aoj.3_5'Flank|RBM9_uc003aok.3_5'Flank|RBM9_uc003aoh.3_5'Flank|RBM9_uc003aom.3_5'Flank|RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron|RBM9_uc003aop.3_5'Flank	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36438687	36438688	+	IGR	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36438687_36438688delTT								RBM9 (14102 upstream) : APOL3 (97684 downstream)																																			---	---	---	---
EIF3D	8664	broad.mit.edu	37	22	36907942	36907942	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36907942delT	uc003apq.2	-						EIF3D_uc011amr.1_Intron|EIF3D_uc003apr.2_Intron|EIF3D_uc011ams.1_Intron|EIF3D_uc011amt.1_Intron	NM_003753	NP_003744			eukaryotic translation initiation factor 3							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	36928937	36928939	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36928937_36928939delTTT								EIF3D (3660 upstream) : CACNG2 (31165 downstream)																																			---	---	---	---
IFT27	11020	broad.mit.edu	37	22	37161540	37161540	+	Intron	DEL	A	-	-	rs67738997		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37161540delA	uc003apv.1	-						IFT27_uc003apu.1_Intron|IFT27_uc003apw.1_Intron	NM_006860	NP_006851			RAB, member of RAS oncogene family-like 4						small GTPase mediated signal transduction	intraflagellar transport particle B|microtubule-based flagellum	GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37181646	37181648	+	IGR	DEL	AAA	-	-	rs79821575		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37181646_37181648delAAA								IFT27 (9532 upstream) : PVALB (15098 downstream)																																			---	---	---	---
CSF2RB	1439	broad.mit.edu	37	22	37306764	37306765	+	5'Flank	INS	-	TG	TG	rs142275140	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37306764_37306765insTG	uc003aqa.3	+							NM_000395	NP_000386			colony stimulating factor 2 receptor, beta						respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)													---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37810488	37810488	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37810488delA	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)																	---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37882493	37882494	+	Intron	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37882493_37882494insG	uc003ast.1	-						MFNG_uc003ass.1_5'Flank|MFNG_uc011ani.1_5'Flank|MFNG_uc011anj.1_5'Flank	NM_014550				caspase recruitment domain protein 10						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	37984349	37984351	+	IGR	DEL	TTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37984349_37984351delTTT								LGALS2 (8325 upstream) : GGA1 (20152 downstream)																																			---	---	---	---
LGALS1	3956	broad.mit.edu	37	22	38069361	38069361	+	5'Flank	DEL	C	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38069361delC	uc003atn.2	+							NM_002305	NP_002296			galectin-1						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of apoptosis	cytoplasm|extracellular space|proteinaceous extracellular matrix	galactoside binding|signal transducer activity				0	Melanoma(58;0.0574)																	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38139809	38139812	+	Intron	DEL	TGTG	-	-	rs71324874		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38139809_38139812delTGTG	uc003atr.2	+						TRIOBP_uc003atu.2_Intron	NM_001039141	NP_001034230			TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
LOC646851	646851	broad.mit.edu	37	22	39002182	39002183	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39002182_39002183insT	uc011anx.1	-						LOC646851_uc011anw.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348086;												0																		---	---	---	---
CBY1	25776	broad.mit.edu	37	22	39054135	39054135	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39054135delT	uc003awb.2	+						CBY1_uc011any.1_Intron|CBY1_uc003awc.2_Intron|LOC646851_uc011anw.1_5'Flank|LOC646851_uc011anx.1_5'Flank	NM_001002880	NP_001002880			PKD2 interactor, golgi and endoplasmic reticulum						cardiac muscle cell differentiation|fat cell differentiation|negative regulation of transcription, DNA-dependent|protein localization	nuclear speck|trans-Golgi network	beta-catenin binding|identical protein binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39073254	39073254	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39073254delA	uc003awd.2	-											Homo sapiens PKD2 interactor, golgi and endoplasmic reticulum associated 1, mRNA (cDNA clone IMAGE:4120338).																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	39210453	39210454	+	IGR	DEL	AA	-	-	rs71326731		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39210453_39210454delAA								SUN2 (20292 upstream) : NPTXR (4004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39490153	39490153	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39490153delT								APOBEC3G (6406 upstream) : APOBEC3H (3137 downstream)																																			---	---	---	---
TAB1	10454	broad.mit.edu	37	22	39792788	39792789	+	5'Flank	INS	-	TCTG	TCTG	rs148279910	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39792788_39792789insTCTG	uc003axt.2	+						TAB1_uc003axr.2_Intron|TAB1_uc011aok.1_5'Flank|TAB1_uc003axu.1_5'Flank	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																		---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39905004	39905005	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39905004_39905005delTT	uc003axx.2	+						SMCR7L_uc003axw.2_Intron|SMCR7L_uc010gxz.1_Intron|SMCR7L_uc003axy.2_Intron	NM_019008	NP_061881			hypothetical protein LOC54471							integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)																	---	---	---	---
ENTHD1	150350	broad.mit.edu	37	22	40224723	40224723	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40224723delA	uc003ayg.2	-							NM_152512	NP_689725			ENTH domain containing 1											ovary(2)|skin(1)	3	Melanoma(58;0.0749)																	---	---	---	---
GRAP2	9402	broad.mit.edu	37	22	40320706	40320706	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40320706delA	uc003ayh.1	+						GRAP2_uc003ayi.2_Intron|GRAP2_uc011aom.1_Intron|GRAP2_uc011aon.1_Intron|GRAP2_uc010gya.1_5'Flank|GRAP2_uc011aoo.1_5'Flank|GRAP2_uc011aop.1_5'Flank|GRAP2_uc011aoq.1_5'Flank	NM_004810	NP_004801			GRB2-related adaptor protein 2						cell-cell signaling|Ras protein signal transduction|T cell costimulation|T cell receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41067633	41067633	+	IGR	DEL	T	-	-	rs76572460		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41067633delT								MKL1 (34943 upstream) : MCHR1 (7549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	41155428	41155428	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41155428delT								MCHR1 (76611 upstream) : SLC25A17 (10213 downstream)																																			---	---	---	---
XPNPEP3	63929	broad.mit.edu	37	22	41264850	41264850	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41264850delA	uc003azh.2	+						XPNPEP3_uc011aox.1_Intron|XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_Intron|XPNPEP3_uc010gyh.1_Intron	NM_022098	NP_071381			X-prolyl aminopeptidase (aminopeptidase P) 3,						cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41410470	41410473	+	IGR	DEL	TCTT	-	-	rs71796597		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41410470_41410473delTCTT								RBX1 (41804 upstream) : MIR1281 (78044 downstream)																																			---	---	---	---
EP300	2033	broad.mit.edu	37	22	41522217	41522218	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41522217_41522218insT	uc003azl.3	+							NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41718516	41718516	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41718516delT	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																		---	---	---	---
PPPDE2	27351	broad.mit.edu	37	22	42000737	42000737	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42000737delA	uc003ban.1	-						PPPDE2_uc011apb.1_Intron	NM_015704	NP_056519			PPPDE peptidase domain containing 2												0																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42194060	42194061	+	Intron	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42194060_42194061insC	uc003baz.1	+						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|CCDC134_uc003bbh.1_5'Flank|CCDC134_uc011apg.1_5'Flank|MEI1_uc011apd.1_Intron|MEI1_uc003bbb.1_Intron|MEI1_uc003bbc.1_Intron|MEI1_uc010gym.1_Intron|MEI1_uc003bbd.1_Intron|MEI1_uc010gyn.1_Intron|MEI1_uc003bbe.1_Intron|MEI1_uc003bbf.2_Intron|MEI1_uc003bbg.2_Intron	NM_152513	NP_689726			meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
WBP2NL	164684	broad.mit.edu	37	22	42338949	42338950	+	Intron	INS	-	ACA	ACA	rs150317302	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42338949_42338950insACA	uc011ape.1	+						LOC339674_uc003bba.1_Intron|CENPM_uc003bbm.2_Intron|CENPM_uc003bbn.2_Intron|CENPM_uc003bbo.2_Intron	NM_152613	NP_689826			WBP2 N-terminal like						egg activation|male pronucleus assembly|meiosis	perinuclear theca	WW domain binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42764465	42764466	+	Intron	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42764465_42764466insC	uc003bcm.2	-											Homo sapiens, clone IMAGE:5241654, mRNA.																														---	---	---	---
PACSIN2	11252	broad.mit.edu	37	22	43389179	43389179	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43389179delA	uc003bdg.3	-							NM_007229	NP_009160			protein kinase C and casein kinase substrate in						actin cytoskeleton organization|endocytosis	cytoplasmic membrane-bounded vesicle	transporter activity				0		Glioma(61;0.222)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44531145	44531146	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44531145_44531146delTT	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44618165	44618166	+	IGR	DEL	AG	-	-	rs67236160		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44618165_44618166delAG								PARVG (15131 upstream) : KIAA1644 (21391 downstream)																																			---	---	---	---
C22orf9	23313	broad.mit.edu	37	22	45618568	45618568	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45618568delA	uc003bfx.1	-							NM_001009880	NP_001009880			hypothetical protein LOC23313 isoform b								protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|READ - Rectum adenocarcinoma(1;0.000617)|Colorectal(1;0.0024)														---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45969862	45969863	+	Intron	INS	-	CTC	CTC	rs10654355		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45969862_45969863insCTC	uc003bgj.1	+							NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45990748	45990751	+	Intron	DEL	GGAC	-	-	rs2351086		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45990748_45990751delGGAC	uc003bgj.1	+						FBLN1_uc003bgk.1_5'Flank	NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
LOC400931	400931	broad.mit.edu	37	22	46484518	46484518	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46484518delT	uc003bgr.3	+						LOC400931_uc003bgu.2_Intron|LOC400931_uc003bgt.3_Intron					SubName: Full=FLJ27365 protein, isoform CRA_a; SubName: Full=Novel transcript;												0																		---	---	---	---
PPARA	5465	broad.mit.edu	37	22	46617974	46617975	+	Intron	DEL	AA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46617974_46617975delAA	uc003bgw.1	+						PPARA_uc003bgx.1_Intron|PPARA_uc010hab.1_Intron|PPARA_uc003bhb.1_Intron|PPARA_uc010hac.1_Intron	NM_005036	NP_005027			peroxisome proliferative activated receptor,						fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fatty acid beta-oxidation|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)													---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47066804	47066805	+	Intron	INS	-	T	T	rs150662796	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47066804_47066805insT	uc003bhx.2	+						GRAMD4_uc010had.2_Intron	NM_015124	NP_055939			death-inducing-protein						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)														---	---	---	---
CERK	64781	broad.mit.edu	37	22	47128483	47128484	+	Intron	DEL	TT	-	-	rs72222874		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47128483_47128484delTT	uc003bia.2	-							NM_022766	NP_073603			ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	47918001	47918004	+	IGR	DEL	TTTT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47918001_47918004delTTTT								TBC1D22A (348279 upstream) : FAM19A5 (967284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48017615	48017616	+	Intron	INS	-	T	T	rs149367729	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48017615_48017616insT	uc003bii.2	-											Homo sapiens cDNA FLJ46257 fis, clone TESTI4024240.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48028047	48028047	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48028047delG	uc003bik.1	+						uc003bii.2_5'Flank|uc011ard.1_5'Flank|uc011are.1_5'Flank|uc003bij.2_Intron					Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48028048	48028051	+	Intron	DEL	GAAA	-	-	rs7291054	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48028048_48028051delGAAA	uc003bik.1	+						uc003bii.2_5'Flank|uc011ard.1_5'Flank|uc011are.1_5'Flank|uc003bij.2_Intron					Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48540644	48540644	+	IGR	DEL	C	-	-	rs36032152		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48540644delC								TBC1D22A (970922 upstream) : FAM19A5 (344644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48665322	48665323	+	IGR	DEL	AC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48665322_48665323delAC								None (None upstream) : FAM19A5 (219965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49783444	49783445	+	IGR	INS	-	T	T	rs141113519	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49783444_49783445insT								FAM19A5 (635702 upstream) : C22orf34 (24731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	50111131	50111132	+	IGR	INS	-	ACAG	ACAG	rs76619595		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50111131_50111132insACAG								C22orf34 (59941 upstream) : BRD1 (55806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	510133	510134	+	IGR	INS	-	CATCCATCCATC	CATCCATCCATC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:510133_510134insCATCCATCCATC								PPP2R3B (162506 upstream) : SHOX (74945 downstream)																																			---	---	---	---
SHOX	6473	broad.mit.edu	37	X	614656	614656	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:614656delA	uc004cpi.2	+							NM_006883	NP_006874			short stature homeobox isoform SHOXb						skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor 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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	793314	793314	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:793314delA								SHOX (173169 upstream) : CRLF2 (521573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	815734	815735	+	IGR	INS	-	CTTT	CTTT			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:815734_815735insCTTT								SHOX (195589 upstream) : CRLF2 (499152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1226811	1226812	+	IGR	DEL	CA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1226811_1226812delCA								SHOX (606666 upstream) : CRLF2 (88075 downstream)																																			---	---	---	---
ASMTL	8623	broad.mit.edu	37	X	1535351	1535352	+	Intron	INS	-	AC	AC			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1535351_1535352insAC	uc004cpx.1	-						ASMTL_uc011mhe.1_Intron|ASMTL_uc004cpy.1_Intron|ASMTL_uc011mhf.1_Intron	NM_004192	NP_004183			acetylserotonin O-methyltransferase-like						melatonin biosynthetic process	cytoplasm	acetylserotonin O-methyltransferase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1582064	1582064	+	3'UTR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1582064delT	uc004cpz.2	-	2						NM_178129	NP_835230			G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		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)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1606266	1606266	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1606266delT	uc004cpz.2	-							NM_178129	NP_835230			G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		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)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	X	2000566	2000567	+	IGR	DEL	AG	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2000566_2000567delAG								ASMT (238593 upstream) : DHRSX (136990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2054079	2054079	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2054079delA								ASMT (292106 upstream) : DHRSX (83478 downstream)																																			---	---	---	---
CD99	4267	broad.mit.edu	37	X	2644732	2644734	+	Intron	DEL	GCC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2644732_2644734delGCC	uc004cqm.2	+						CD99_uc010nda.2_Intron|CD99_uc004cqn.2_Intron|CD99_uc004cqo.2_Intron	NM_002414	NP_002405			CD99 antigen isoform a precursor						cell adhesion	cytoplasm|integral to plasma membrane				skin(1)	1																		---	---	---	---
GYG2	8908	broad.mit.edu	37	X	2774786	2774793	+	Intron	DEL	TATCTATG	-	-	rs80318590		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2774786_2774793delTATCTATG	uc004cqs.1	+						GYG2_uc004cqt.1_Intron|GYG2_uc004cqu.1_Intron|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Intron|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909			glycogenin 2 isoform b						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	9379811	9379811	+	5'Flank	DEL	G	-	-	rs149889236		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9379811delG	uc004csm.2	-						uc011mhz.1_5'Flank|uc011mia.1_5'Flank|uc011mib.1_5'Flank|uc004csp.1_5'Flank					DQ597811																														---	---	---	---
PRPS2	5634	broad.mit.edu	37	X	12817561	12817561	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12817561delT	uc004cvb.2	+						PRPS2_uc004cva.2_Intron|PRPS2_uc010nec.2_Intron	NM_002765	NP_002756			phosphoribosyl pyrophosphate synthetase 2						nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0																		---	---	---	---
GEMIN8	54960	broad.mit.edu	37	X	14039512	14039512	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14039512delA	uc004cwb.2	-						GEMIN8_uc004cwc.2_Intron|GEMIN8_uc004cwd.2_Intron	NM_017856	NP_060326			gem (nuclear organelle) associated protein 8						spliceosomal snRNP assembly	Cajal body|cytoplasm|SMN complex|spliceosomal complex	protein binding				0																		---	---	---	---
AP1S2	8905	broad.mit.edu	37	X	15845295	15845295	+	3'UTR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15845295delA	uc004cxi.2	-	5					AP1S2_uc004cxh.2_3'UTR|AP1S2_uc010nex.2_3'UTR	NM_003916	NP_003907			adaptor-related protein complex 1 sigma 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	AP-type membrane coat adaptor complex|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein transporter activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	16302021	16302021	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16302021delA								GRPR (130381 upstream) : CTPS2 (304103 downstream)																																			---	---	---	---
CXorf23	256643	broad.mit.edu	37	X	19953721	19953721	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19953721delA	uc004czp.2	-						CXorf23_uc010nfn.2_Intron|CXorf23_uc011mjg.1_Intron|CXorf23_uc004czo.2_Intron	NM_198279	NP_938020			hypothetical protein LOC256643							mitochondrion				lung(1)|skin(1)	2																		---	---	---	---
RPS6KA3	6197	broad.mit.edu	37	X	20227381	20227381	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20227381delA	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																		---	---	---	---
PRDX4	10549	broad.mit.edu	37	X	23693251	23693251	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23693251delA	uc004dam.2	+							NM_006406	NP_006397			peroxiredoxin 4						cell redox homeostasis|I-kappaB phosphorylation		thioredoxin peroxidase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
KLHL15	80311	broad.mit.edu	37	X	24032723	24032723	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24032723delA	uc004dba.3	-							NM_030624	NP_085127			kelch-like 15											ovary(1)|breast(1)	2																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	32364014	32364014	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32364014delA	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	35971698	35971698	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35971698delT	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845			hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
SYTL5	94122	broad.mit.edu	37	X	37913443	37913443	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37913443delT	uc004ddu.2	+						SYTL5_uc004ddv.2_Intron|SYTL5_uc004ddx.2_Intron	NM_001163335	NP_001156807			synaptotagmin-like 5 isoform 1						intracellular protein transport	membrane	metal ion binding|Rab GTPase binding			skin(1)	1																		---	---	---	---
ATP6AP2	10159	broad.mit.edu	37	X	40459957	40459957	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40459957delA	uc004det.2	+						ATP6AP2_uc010nhc.2_Intron|ATP6AP2_uc011mkl.1_Intron|ATP6AP2_uc011mkm.1_Intron|ATP6AP2_uc011mkn.1_Intron|ATP6AP2_uc004deu.1_Intron	NM_005765	NP_005756			ATPase, H+ transporting, lysosomal accessory						angiotensin maturation|positive regulation of transforming growth factor-beta1 production|regulation of MAPKKK cascade	external side of plasma membrane|integral to membrane	protein binding|receptor activity				0																		---	---	---	---
MED14	9282	broad.mit.edu	37	X	40540221	40540221	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40540221delA	uc004dex.3	-							NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
CCDC22	28952	broad.mit.edu	37	X	49099689	49099689	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49099689delG	uc004dnd.1	+						CCDC22_uc011mna.1_Intron|CCDC22_uc004dnc.1_Intron	NM_014008	NP_054727			coiled-coil domain containing 22											central_nervous_system(1)	1																		---	---	---	---
PPP1R3F	89801	broad.mit.edu	37	X	49139467	49139468	+	Intron	DEL	GT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49139467_49139468delGT	uc004dnh.1	+						PPP1R3F_uc011mnd.1_Intron|PPP1R3F_uc004dni.2_Intron|PPP1R3F_uc004dnj.1_Intron	NM_033215	NP_149992			protein phosphatase 1, regulatory (inhibitor)							integral to membrane				ovary(2)|skin(1)	3	Ovarian(276;0.236)																	---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49777741	49777742	+	Intron	DEL	TC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49777741_49777742delTC	uc004dor.1	+						CLCN5_uc004doq.1_Intron|MIR660_hsa-mir-660|MI0003684_5'Flank|MIR502_hsa-mir-502|MI0003186_5'Flank	NM_001127899	NP_001121371			chloride channel 5 isoform a						excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
DGKK	139189	broad.mit.edu	37	X	50194184	50194185	+	Intron	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50194184_50194185insA	uc010njr.1	-							NM_001013742	NP_001013764			diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)																	---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54330665	54330665	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54330665delA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
ALAS2	212	broad.mit.edu	37	X	55050165	55050165	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55050165delT	uc004dua.3	-						ALAS2_uc004dub.3_Intron|ALAS2_uc004dud.3_Intron	NM_000032	NP_000023			5-aminolevulinate synthase 2 isoform a						cellular iron ion homeostasis|erythrocyte differentiation|heme biosynthetic process|hemoglobin biosynthetic process|oxygen homeostasis|response to hypoxia	mitochondrial inner membrane|mitochondrial matrix	5-aminolevulinate synthase activity|coenzyme binding|glycine binding|protein binding|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(1)	1					Glycine(DB00145)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	61796823	61796823	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61796823delT								None (None upstream) : SPIN4 (770285 downstream)																																			---	---	---	---
PIN4	5303	broad.mit.edu	37	X	71416535	71416535	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71416535delT	uc004eam.2	+						PIN4_uc004eao.1_Intron	NM_006223	NP_006214			protein (peptidyl-prolyl cis/trans isomerase)						protein folding|rRNA processing	cytoplasm|mitochondrial matrix|mitochondrial matrix|nucleolus|nucleolus|preribosome|spindle|spindle	bent DNA binding|DNA binding|double-stranded DNA binding|peptidyl-prolyl cis-trans isomerase activity				0	Renal(35;0.156)																	---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	73971507	73971510	+	Intron	DEL	TCCC	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73971507_73971510delTCCC	uc004eby.2	-							NM_001008537	NP_001008537			hypothetical protein LOC340533						base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	74387595	74387595	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74387595delT								ABCB7 (11463 upstream) : UPRT (106366 downstream)																																			---	---	---	---
ATP7A	538	broad.mit.edu	37	X	77264922	77264923	+	Intron	DEL	TT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77264922_77264923delTT	uc004ecx.3	+						ATP7A_uc004ecw.2_3'UTR	NM_000052	NP_000043			ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	89544585	89544585	+	IGR	DEL	C	-	-	rs3795186	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89544585delC								TGIF2LX (366705 upstream) : None (None downstream)																																			---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107512391	107512391	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108812483delA								NXT2 (24570 upstream) : KCNE1L (54448 downstream)																																			---	---	---	---
ALG13	79868	broad.mit.edu	37	X	110995996	110995996	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110995996delT	uc011msy.1	+						ALG13_uc011msx.1_Intron|ALG13_uc011msz.1_Intron|ALG13_uc011mta.1_Intron|ALG13_uc011mtb.1_Intron					SubName: Full=Asparagine-linked glycosylation 13 homolog (S. cerevisiae);						dolichol-linked oligosaccharide biosynthetic process|lipid glycosylation|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane	carbohydrate binding|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity			lung(1)	1																		---	---	---	---
RPL39	6170	broad.mit.edu	37	X	118920839	118920839	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118920839delA	uc004erx.1	-							NM_001000	NP_000991			ribosomal protein L39						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123780683	123780683	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123780683delA	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																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	124028293	124028293	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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																		---	---	---	---
XPNPEP2	7512	broad.mit.edu	37	X	128871327	128871327	+	5'Flank	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128871327delG	uc004eut.1	+						XPNPEP2_uc011mum.1_5'Flank	NM_003399	NP_003390			X-prolyl aminopeptidase 2, membrane-bound						cellular process|proteolysis	anchored to membrane|plasma membrane	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0																		---	---	---	---
CD40LG	959	broad.mit.edu	37	X	135732733	135732735	+	Intron	DEL	AAA	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135732733_135732735delAAA	uc004faa.2	+						CD40LG_uc010nsd.2_Intron|CD40LG_uc010nse.1_Intron	NM_000074	NP_000065			CD40 ligand						anti-apoptosis|B cell proliferation|inflammatory response|isotype switching|leukocyte cell-cell adhesion|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of interleukin-12 production	extracellular space|integral to plasma membrane|soluble fraction	CD40 receptor binding|cytokine activity|tumor necrosis factor receptor binding			skin(1)	1	Acute lymphoblastic leukemia(192;0.000127)				Atorvastatin(DB01076)									Immune_Deficiency_with_Hyper-IgM				---	---	---	---
Unknown	0	broad.mit.edu	37	X	136065450	136065450	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136065450delT	uc004fai.1	+											Homo sapiens cDNA FLJ31132 fis, clone IMR322000953.																														---	---	---	---
Unknown	0	broad.mit.edu	37	X	141286061	141286061	+	IGR	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141286061delT								MAGEC1 (288879 upstream) : MAGEC2 (4069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	142318848	142318849	+	IGR	DEL	TA	-	-	rs66591288	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:142318848_142318849delTA								SPANXN4 (196783 upstream) : SPANXN3 (277716 downstream)																																			---	---	---	---
HMGB3	3149	broad.mit.edu	37	X	150155930	150155931	+	Intron	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150155930_150155931insT	uc004fep.2	+						HMGB3_uc004feq.2_3'UTR|HMGB3_uc004fer.2_Intron	NM_005342	NP_005333			high-mobility group box 3						DNA recombination|multicellular organismal development	chromosome|nucleus	DNA bending activity|double-stranded DNA binding				0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	153680001	153680002	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153680001_153680002insT								FAM50A (1000 upstream) : PLXNA3 (6621 downstream)																																			---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153689355	153689355	+	Intron	DEL	G	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153689355delG	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)																	---	---	---	---
RBMY3AP	64593	broad.mit.edu	37	Y	9448986	9448986	+	Intron	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9448986delA	uc004fsg.1	-						RBMY3AP_uc010nwq.1_Intron	NR_001573				Homo sapiens RNA binding motif protein, Y-linked, family 3, member A pseudogene (RBMY3AP), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9924245	9924246	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9924245_9924246insG								TTTY22 (273391 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	10070804	10070805	+	IGR	INS	-	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:10070804_10070805insC								TTTY22 (419950 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13433429	13433430	+	IGR	INS	-	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13433429_13433430insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13667423	13667427	+	IGR	DEL	AGTGT	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13667423_13667427delAGTGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	16400165	16400166	+	IGR	INS	-	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:16400165_16400166insA								VCY (301773 upstream) : NLGN4Y (234322 downstream)																																			---	---	---	---
NLGN4Y	22829	broad.mit.edu	37	Y	16644626	16644626	+	Intron	DEL	T	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:16644626delT	uc004ftg.2	+						NLGN4Y_uc004fte.2_Intron|NLGN4Y_uc011nas.1_Intron|NLGN4Y_uc004ftf.2_Intron|NLGN4Y_uc004fth.2_Intron	NM_014893	NP_055708			neuroligin 4, Y-linked isoform 1						brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|integral to plasma membrane|synapse	neurexin binding|receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	23900449	23900450	+	IGR	INS	-	A	A	rs112255364		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:23900449_23900450insA								TTTY13 (143897 upstream) : TTTY6 (71251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	28687199	28687200	+	IGR	INS	-	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28687199_28687200insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	28774180	28774180	+	IGR	DEL	A	-	-			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28774180delA								None (None upstream) : None (None downstream)																																			---	---	---	---
ATAD3B	83858	broad.mit.edu	37	1	1430883	1430883	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1430883A>G	uc001afv.2	+	16	1734	c.1633A>G	c.(1633-1635)AAG>GAG	p.K545E	ATAD3B_uc001afx.2_Missense_Mutation_p.K499E|ATAD3B_uc001afy.2_Missense_Mutation_p.K98E	NM_031921	NP_114127	Q5T9A4	ATD3B_HUMAN	AAA-ATPase  TOB3	545							ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;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;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	5940242	5940242	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5940242C>T	uc001alq.1	-	19	2809	c.2543G>A	c.(2542-2544)CGG>CAG	p.R848Q	NPHP4_uc001als.1_RNA|NPHP4_uc009vlt.1_RNA|NPHP4_uc001alt.1_RNA	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	848					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)														---	---	---	---
TAS1R1	80835	broad.mit.edu	37	1	6637105	6637105	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6637105G>A	uc001ant.2	+	5	1569	c.1569G>A	c.(1567-1569)GGG>GGA	p.G523G	TAS1R1_uc001anu.2_Silent_p.G269G|TAS1R1_uc001anv.2_Silent_p.G269G|TAS1R1_uc001anw.2_Intron|ZBTB48_uc009vmc.1_5'Flank|ZBTB48_uc001anx.2_5'Flank|ZBTB48_uc009vmd.1_5'Flank	NM_138697	NP_619642	Q7RTX1	TS1R1_HUMAN	sweet taste receptor T1r isoform b	523	Extracellular (Potential).				sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
ZBTB48	3104	broad.mit.edu	37	1	6649095	6649095	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6649095G>A	uc009vmc.1	+	11	2013	c.1890G>A	c.(1888-1890)CCG>CCA	p.P630P	ZBTB48_uc001anx.2_Silent_p.P630P|ZBTB48_uc009vmd.1_Silent_p.P630P|ZBTB48_uc001any.1_Silent_p.P268P	NM_005341	NP_005332	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	630						cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KLHL21	9903	broad.mit.edu	37	1	6659418	6659418	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6659418G>A	uc001aoa.2	-	2	1168	c.1116C>T	c.(1114-1116)CGC>CGT	p.R372R	KLHL21_uc001anz.1_Silent_p.R372R|KLHL21_uc009vme.2_Silent_p.R5R	NM_014851	NP_055666	Q9UJP4	KLH21_HUMAN	kelch-like 21	372	Kelch 2.				anaphase|cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|polar microtubule				central_nervous_system(1)	1	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)														---	---	---	---
MTHFR	4524	broad.mit.edu	37	1	11856376	11856376	+	Missense_Mutation	SNP	C	T	T	rs150847674	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11856376C>T	uc001atc.1	-	5	851	c.667G>A	c.(667-669)GAT>AAT	p.D223N	MTHFR_uc001atb.1_Missense_Mutation_p.D246N	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	223					blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				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)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|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)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)													---	---	---	---
MFN2	9927	broad.mit.edu	37	1	12058853	12058853	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12058853T>C	uc001atn.3	+	7	1079	c.626T>C	c.(625-627)CTG>CCG	p.L209P	MFN2_uc009vni.2_Missense_Mutation_p.L209P	NM_014874	NP_055689	O95140	MFN2_HUMAN	mitofusin 2	209	Cytoplasmic (Potential).				blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion	cytosol|integral to membrane|intrinsic to mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)	1	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;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12371978	12371978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12371978G>A	uc001atv.2	+	29	7072	c.6931G>A	c.(6931-6933)GCC>ACC	p.A2311T	VPS13D_uc001atw.2_Missense_Mutation_p.A2311T|VPS13D_uc001atx.2_Missense_Mutation_p.A1499T|VPS13D_uc001aty.1_Missense_Mutation_p.A49T	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	2311					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)														---	---	---	---
AADACL3	126767	broad.mit.edu	37	1	12785289	12785289	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12785289C>T	uc009vnn.1	+	4	612	c.379C>T	c.(379-381)CCA>TCA	p.P127S	AADACL3_uc001aug.1_Missense_Mutation_p.P57S	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	127							hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|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;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRAMEF10	343071	broad.mit.edu	37	1	12954532	12954532	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12954532C>T	uc001auo.2	-	3	824	c.751G>A	c.(751-753)GTC>ATC	p.V251I		NM_001039361	NP_001034450	O60809	PRA10_HUMAN	PRAME family member 10	251											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;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13941356	13941356	+	Intron	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13941356T>G	uc001avd.2	+						PDPN_uc001avc.2_Intron|PDPN_uc009vob.2_Intron|PDPN_uc009voc.2_Intron|PDPN_uc001ave.2_Intron|PDPN_uc001avf.2_Intron	NM_006474	NP_006465			lung type-I cell membrane-associated						cell morphogenesis|lymphangiogenesis|regulation of cell shape	filopodium membrane|integral to plasma membrane|lamellipodium membrane|microvillus membrane|ruffle membrane				ovary(2)	2	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14107072	14107072	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14107072G>A	uc001avi.2	+	8	3638	c.2782G>A	c.(2782-2784)GGT>AGT	p.G928S	PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Missense_Mutation_p.G928S|PRDM2_uc001avj.2_Intron|PRDM2_uc001avk.2_Missense_Mutation_p.G727S|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	928						Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)														---	---	---	---
SLC25A34	284723	broad.mit.edu	37	1	16064618	16064618	+	Missense_Mutation	SNP	C	T	T	rs139368754		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16064618C>T	uc001axb.1	+	3	647	c.475C>T	c.(475-477)CGG>TGG	p.R159W	SLC25A34_uc009vok.1_5'Flank	NM_207348	NP_997231	Q6PIV7	S2534_HUMAN	solute carrier family 25, member 34	159	Solcar 2.				transport	integral to membrane|mitochondrial inner membrane					0		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16256110	16256110	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16256110G>A	uc001axk.1	+	11	3579	c.3375G>A	c.(3373-3375)GAG>GAA	p.E1125E	SPEN_uc010obp.1_Silent_p.E1084E	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1125					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)														---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16892887	16892887	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16892887A>G	uc009vos.1	-						uc001ayw.2_5'Flank	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)														---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17983158	17983158	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17983158G>A	uc001ban.2	+	25	2974	c.2815G>A	c.(2815-2817)GCT>ACT	p.A939T	ARHGEF10L_uc009vpe.1_Missense_Mutation_p.A900T|ARHGEF10L_uc001bao.2_Missense_Mutation_p.A900T|ARHGEF10L_uc001bap.2_Missense_Mutation_p.A895T|ARHGEF10L_uc001baq.2_Missense_Mutation_p.A700T|ARHGEF10L_uc010ocs.1_Missense_Mutation_p.A712T|ARHGEF10L_uc001bar.2_Missense_Mutation_p.A642T|ARHGEF10L_uc009vpf.2_RNA	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	939					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)														---	---	---	---
TAS1R2	80834	broad.mit.edu	37	1	19166209	19166209	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19166209C>T	uc001bba.1	-	6	2405	c.2404G>A	c.(2404-2406)GCC>ACC	p.A802T		NM_152232	NP_689418	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2 precursor	802	Helical; Name=7; (Potential).				detection of chemical stimulus involved in sensory perception of sweet taste	plasma membrane	protein heterodimerization activity|taste receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)													---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19439226	19439226	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19439226C>A	uc001bbi.2	-	78	11597	c.11593G>T	c.(11593-11595)GGC>TGC	p.G3865C	UBR4_uc001bbj.1_3'UTR	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3865					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)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20072102	20072102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20072102G>A	uc001bcn.2	-	10	1042	c.800C>T	c.(799-801)ACG>ATG	p.T267M	TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Missense_Mutation_p.T267M|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Missense_Mutation_p.T267M|TMCO4_uc001bcq.1_Missense_Mutation_p.T267M	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	267						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)														---	---	---	---
HP1BP3	50809	broad.mit.edu	37	1	21091980	21091980	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21091980C>A	uc001bdw.1	-	8	920	c.780G>T	c.(778-780)GAG>GAT	p.E260D	HP1BP3_uc001bdv.1_Missense_Mutation_p.E222D|HP1BP3_uc010odh.1_Missense_Mutation_p.E222D|HP1BP3_uc001bdy.1_Missense_Mutation_p.E260D|HP1BP3_uc001bdz.2_RNA|HP1BP3_uc001bea.2_Missense_Mutation_p.E259D|HP1BP3_uc010odf.1_Translation_Start_Site|HP1BP3_uc010odg.1_Missense_Mutation_p.E108D	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74	260	H15 2.				nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22150185	22150185	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22150185G>A	uc001bfj.2	-	96	12967	c.12927C>T	c.(12925-12927)GTC>GTT	p.V4309V	LDLRAD2_uc001bfg.1_3'UTR|HSPG2_uc001bfi.2_Silent_p.V326V|HSPG2_uc009vqd.2_Silent_p.V4310V	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	4309	Laminin G-like 3.				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	22178102	22178102	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22178102G>A	uc001bfj.2	-	55	7135	c.7095C>T	c.(7093-7095)CCC>CCT	p.P2365P	HSPG2_uc009vqd.2_Silent_p.P2366P	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	2365	Ig-like C2-type 9.				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)													---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22913053	22913053	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22913053C>T	uc001bfx.1	+	4	1029	c.904C>T	c.(904-906)CCA>TCA	p.P302S	EPHA8_uc001bfw.2_Missense_Mutation_p.P302S	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	302	Extracellular (Potential).|Cys-rich.					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23191603	23191603	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23191603C>A	uc009vqj.1	+	5	1346	c.1201C>A	c.(1201-1203)CAC>AAC	p.H401N	EPHB2_uc001bge.2_Missense_Mutation_p.H401N|EPHB2_uc001bgf.2_Missense_Mutation_p.H401N|EPHB2_uc010odu.1_Missense_Mutation_p.H401N|hsa-mir-4253|MI0015860_5'Flank	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	401	Extracellular (Potential).|Fibronectin type-III 1.				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
HTR1D	3352	broad.mit.edu	37	1	23519570	23519570	+	3'UTR	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23519570C>T	uc001bgn.2	-	1						NM_000864	NP_000855			5-hydroxytryptamine (serotonin) receptor 1D						G-protein signaling, coupled to cyclic nucleotide second messenger|intestine smooth muscle contraction|synaptic transmission	integral to plasma membrane	serotonin receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Tegaserod(DB01079)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)													---	---	---	---
IL22RA1	58985	broad.mit.edu	37	1	24447502	24447502	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24447502G>A	uc001biq.1	-	7	1557	c.1518C>T	c.(1516-1518)GGC>GGT	p.G506G	IL22RA1_uc010oeg.1_Silent_p.G438G|IL22RA1_uc009vrb.1_Silent_p.G370G|IL22RA1_uc010oeh.1_3'UTR	NM_021258	NP_067081	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1 precursor	506	Cytoplasmic (Potential).					integral to membrane	interferon receptor activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)														---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	25944365	25944365	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25944365T>C	uc001bkm.2	+	1	407	c.77T>C	c.(76-78)CTC>CCC	p.L26P	MAN1C1_uc009vry.1_5'UTR	NM_020379	NP_065112	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	26	Helical; Signal-anchor for type II membrane protein; (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)														---	---	---	---
STMN1	3925	broad.mit.edu	37	1	26230136	26230136	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26230136C>T	uc001bkz.2	-	3	546	c.182G>A	c.(181-183)CGC>CAC	p.R61H	STMN1_uc010oev.1_Missense_Mutation_p.R61H|STMN1_uc001bla.2_Missense_Mutation_p.R61H|STMN1_uc001blb.2_Missense_Mutation_p.R61H|STMN1_uc001blc.2_Missense_Mutation_p.R61H	NM_203401	NP_981946	P16949	STMN1_HUMAN	stathmin 1 isoform a	61	Potential.				cell differentiation|intracellular signal transduction|microtubule depolymerization|mitotic spindle organization|nervous system development|response to virus	cytoplasm|microtubule	signal transducer activity|tubulin binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PAFAH2	5051	broad.mit.edu	37	1	26303254	26303254	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26303254T>C	uc001bld.3	-	8	857	c.677A>G	c.(676-678)GAC>GGC	p.D226G	PAFAH2_uc001ble.3_Missense_Mutation_p.D226G	NM_000437	NP_000428	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2	226					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding			ovary(2)	2		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
GPATCH3	63906	broad.mit.edu	37	1	27224070	27224070	+	Missense_Mutation	SNP	G	A	A	rs144011521	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27224070G>A	uc001bne.2	-	2	627	c.598C>T	c.(598-600)CGG>TGG	p.R200W	GPATCH3_uc009vsp.1_Missense_Mutation_p.R11W	NM_022078	NP_071361	Q96I76	GPTC3_HUMAN	G patch domain containing 3	200						intracellular	nucleic acid binding				0		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|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)|Epithelial(14;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
SLC9A1	6548	broad.mit.edu	37	1	27480472	27480472	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27480472A>G	uc001bnm.2	-						SLC9A1_uc010ofk.1_Intron|SLC9A1_uc001bnn.2_Intron	NM_003047	NP_003038			solute carrier family 9, isoform A1						regulation of pH	integral to membrane	sodium:hydrogen antiporter activity			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)													---	---	---	---
PPP1R8	5511	broad.mit.edu	37	1	28176658	28176658	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28176658C>T	uc001bov.1	+	7	811	c.757C>T	c.(757-759)CGC>TGC	p.R253C	PPP1R8_uc001bow.1_Missense_Mutation_p.R111C|PPP1R8_uc001box.1_Missense_Mutation_p.R29C|PPP1R8_uc009vtc.1_RNA|PPP1R8_uc009vtd.1_RNA	NM_014110	NP_054829	Q12972	PP1R8_HUMAN	protein phosphatase 1 regulatory inhibitor	253					mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|RNA splicing|transcription, DNA-dependent	cytoplasm|nuclear speck|spliceosomal complex	DNA binding|endonuclease activity|protein binding|protein serine/threonine phosphatase inhibitor activity|ribonuclease E activity|RNA binding				0		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32092444	32092444	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32092444G>T	uc009vtx.2	+	9	1526	c.1141G>T	c.(1141-1143)GGT>TGT	p.G381C	HCRTR1_uc001btb.2_Missense_Mutation_p.G206C|HCRTR1_uc001btc.3_Intron|HCRTR1_uc001btd.2_Missense_Mutation_p.G381C|HCRTR1_uc010ogl.1_Intron	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1	381	Cytoplasmic (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)														---	---	---	---
TSSK3	81629	broad.mit.edu	37	1	32829237	32829237	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32829237C>T	uc001bvf.2	+	2	628	c.187C>T	c.(187-189)CGT>TGT	p.R63C	uc001bve.1_5'Flank	NM_052841	NP_443073	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	63	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.R63G(1)		stomach(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)																---	---	---	---
ZBTB8OS	339487	broad.mit.edu	37	1	33100357	33100357	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33100357C>A	uc001bvp.2	-						ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron	NM_178547	NP_848642			zinc finger and BTB domain containing 8 opposite												0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
PHC2	1912	broad.mit.edu	37	1	33836036	33836036	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33836036G>A	uc001bxg.1	-	4	616	c.562C>T	c.(562-564)CTG>TTG	p.L188L	PHC2_uc001bxh.1_Silent_p.L188L|PHC2_uc009vuh.1_Silent_p.L188L|PHC2_uc001bxi.1_Silent_p.L188L	NM_198040	NP_932157	Q8IXK0	PHC2_HUMAN	polyhomeotic-like 2 isoform a	188					multicellular organismal development	PcG protein complex	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
ZMYM6	9204	broad.mit.edu	37	1	35496158	35496158	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35496158T>C	uc001byh.2	-	2	311	c.83A>G	c.(82-84)GAC>GGC	p.D28G	ZMYM6_uc001byf.1_Missense_Mutation_p.D28G|ZMYM6_uc010oht.1_Intron|ZMYM6_uc009vup.2_Intron|ZMYM6_uc009vuq.1_Missense_Mutation_p.D28G|ZMYM6_uc009vur.1_5'UTR|ZMYM6_uc001byj.2_Missense_Mutation_p.D28G|ZMYM6_uc001byi.2_Missense_Mutation_p.D28G|ZMYM6_uc001byk.2_Missense_Mutation_p.D28G	NM_007167	NP_009098	O95789	ZMYM6_HUMAN	zinc finger protein 258	28					multicellular organismal development	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)																---	---	---	---
MAP7D1	55700	broad.mit.edu	37	1	36638990	36638990	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36638990G>A	uc001bzz.2	+	5	866	c.650G>A	c.(649-651)CGG>CAG	p.R217Q	MAP7D1_uc001caa.2_Missense_Mutation_p.R217Q|MAP7D1_uc001cab.2_Missense_Mutation_p.R217Q|MAP7D1_uc001cac.2_5'UTR	NM_018067	NP_060537	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	217	Potential.					cytoplasm|spindle				ovary(3)|breast(2)	5		Myeloproliferative disorder(586;0.0393)																---	---	---	---
MTF1	4520	broad.mit.edu	37	1	38281018	38281018	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38281018G>A	uc001cce.1	-	11	2193	c.2052C>T	c.(2050-2052)CCC>CCT	p.P684P		NM_005955	NP_005946	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	684						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(1)|pancreas(1)	2	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39747967	39747967	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39747967T>C	uc010ois.1	+	8	836	c.631T>C	c.(631-633)TAC>CAC	p.Y211H	MACF1_uc001cda.1_Missense_Mutation_p.Y119H|MACF1_uc010oit.1_Missense_Mutation_p.Y174H	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	211	Actin-binding.|CH 2.				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)															---	---	---	---
ZNF691	51058	broad.mit.edu	37	1	43317311	43317311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43317311G>A	uc001cih.2	+	2	814	c.763G>A	c.(763-765)GAG>AAG	p.E255K	ZNF691_uc001cig.2_Missense_Mutation_p.E228K|ZNF691_uc009vwm.2_Missense_Mutation_p.E248K	NM_015911	NP_056995	Q5VV52	ZN691_HUMAN	zinc finger protein 691	259	C2H2-type 6.					nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
DPH2	1802	broad.mit.edu	37	1	44435850	44435850	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44435850G>T	uc001ckz.2	+	1	198	c.3G>T	c.(1-3)ATG>ATT	p.M1I	DPH2_uc001cla.2_Missense_Mutation_p.M1I|DPH2_uc010okk.1_5'UTR|DPH2_uc001clb.2_5'UTR	NM_001384	NP_001375	Q9BQC3	DPH2_HUMAN	diphthamide biosynthesis protein 2 isoform a	1					peptidyl-diphthamide biosynthetic process from peptidyl-histidine	cytoplasm				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)																---	---	---	---
PLK3	1263	broad.mit.edu	37	1	45267574	45267574	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45267574C>T	uc001cmn.2	+	5	723	c.623C>T	c.(622-624)GCC>GTC	p.A208V	PLK3_uc001cmo.2_RNA	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	208	Protein kinase.					membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PLK3	1263	broad.mit.edu	37	1	45270181	45270181	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45270181C>T	uc001cmn.2	+						PLK3_uc001cmo.2_Intron	NM_004073	NP_004064			polo-like kinase 3							membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
HECTD3	79654	broad.mit.edu	37	1	45474833	45474833	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45474833C>T	uc009vxk.2	-	7	1153	c.1055G>A	c.(1054-1056)CGC>CAC	p.R352H	HECTD3_uc001cmy.3_5'Flank|HECTD3_uc010olh.1_Missense_Mutation_p.R68H|UROD_uc010oli.1_5'Flank|UROD_uc001cna.1_5'Flank|UROD_uc001cnb.1_5'Flank	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3	352	DOC.				proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4A22	284541	broad.mit.edu	37	1	47610211	47610211	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47610211G>A	uc001cqv.1	+						CYP4A22_uc009vyo.2_Intron|CYP4A22_uc009vyp.2_Intron	NM_001010969	NP_001010969			cytochrome P450, family 4, subfamily A,							endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding			skin(2)|ovary(1)|breast(1)	4																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52891135	52891135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52891135C>T	uc001ctx.2	-	29	4987	c.4753G>A	c.(4753-4755)GCA>ACA	p.A1585T	ZCCHC11_uc001cty.2_Missense_Mutation_p.A1586T|ZCCHC11_uc001ctz.2_Missense_Mutation_p.A1581T	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	1585	Pro-rich.				miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53255711	53255711	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53255711C>A	uc001cuj.2	+	6	1501	c.1306C>A	c.(1306-1308)CGG>AGG	p.R436R	ZYG11B_uc009vzg.2_RNA|ZYG11B_uc010onj.1_Silent_p.R427R	NM_024646	NP_078922	Q9C0D3	ZY11B_HUMAN	zyg-11 homolog B	436							protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	53980295	53980295	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53980295T>C	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55282678	55282678	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55282678G>A	uc001cyb.3	+	9	1121	c.1067G>A	c.(1066-1068)GGC>GAC	p.G356D	C1orf177_uc001cya.3_Missense_Mutation_p.G356D	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2	356											0																		---	---	---	---
C8A	731	broad.mit.edu	37	1	57340695	57340695	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57340695C>T	uc001cyo.2	+	3	377	c.245C>T	c.(244-246)GCC>GTC	p.A82V		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	82	TSP type-1 1.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CYP2J2	1573	broad.mit.edu	37	1	60381679	60381679	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60381679T>C	uc001czq.2	-	2	309	c.304A>G	c.(304-306)ATC>GTC	p.I102V		NM_000775	NP_000766	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J,	102					epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)																	---	---	---	---
CACHD1	57685	broad.mit.edu	37	1	65141222	65141222	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65141222C>A	uc001dbo.1	+	20	2818	c.2713C>A	c.(2713-2715)CGA>AGA	p.R905R	CACHD1_uc001dbp.1_Silent_p.R660R|CACHD1_uc001dbq.1_Silent_p.R660R|CACHD1_uc010opa.1_Silent_p.R149R	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	956	Extracellular (Potential).|Cys-rich.				calcium ion transport	integral to membrane				ovary(2)	2																OREG0013544	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DNAJC6	9829	broad.mit.edu	37	1	65874367	65874367	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65874367T>C	uc001dcd.1	+	17	2528	c.2364T>C	c.(2362-2364)GGT>GGC	p.G788G	DNAJC6_uc010opc.1_Silent_p.G775G|DNAJC6_uc001dce.1_Silent_p.G845G	NM_014787	NP_055602	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	788					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	70504797	70504797	+	Missense_Mutation	SNP	T	C	C	rs139023629		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70504797T>C	uc001dep.2	+	19	3206	c.3176T>C	c.(3175-3177)GTG>GCG	p.V1059A	LRRC7_uc009wbg.2_Missense_Mutation_p.V343A|LRRC7_uc001deq.2_Missense_Mutation_p.V300A	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	1059						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75097397	75097397	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75097397C>T	uc001dgg.2	-	7	1038	c.819G>A	c.(817-819)AAG>AAA	p.K273K	C1orf173_uc001dgi.3_Silent_p.K67K	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	273										ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
DNAJB4	11080	broad.mit.edu	37	1	78478866	78478866	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78478866C>T	uc001dij.2	+	2	502	c.343C>T	c.(343-345)CGA>TGA	p.R115*	DNAJB4_uc010orn.1_Translation_Start_Site	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	115					protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94578618	94578618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94578618C>T	uc001dqh.2	-	2	175	c.71G>A	c.(70-72)CGC>CAC	p.R24H	ABCA4_uc010otn.1_Missense_Mutation_p.R24H	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	24	Helical; (Potential).		R -> H (in STGD1).		phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)														---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99771300	99771300	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99771300C>T	uc001dse.2	+	7	1132	c.1026C>T	c.(1024-1026)GAC>GAT	p.D342D	LPPR4_uc010oue.1_Silent_p.D284D	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	342							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)														---	---	---	---
WDR47	22911	broad.mit.edu	37	1	109538449	109538449	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109538449T>C	uc001dwj.2	-	8	1820	c.1444A>G	c.(1444-1446)AAG>GAG	p.K482E	WDR47_uc001dwl.2_Missense_Mutation_p.K490E|WDR47_uc001dwi.2_Missense_Mutation_p.K483E|WDR47_uc001dwk.2_Missense_Mutation_p.K454E|WDR47_uc010ovf.1_Missense_Mutation_p.K409E	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3	482										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)														---	---	---	---
KCNA3	3738	broad.mit.edu	37	1	111216731	111216731	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111216731C>T	uc001dzv.1	-	1	925	c.701G>A	c.(700-702)CGG>CAG	p.R234Q		NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related	234						voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(4)|pancreas(1)	5		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
C1orf88	128344	broad.mit.edu	37	1	111891167	111891167	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111891167G>T	uc001eaw.2	+	4	368	c.288G>T	c.(286-288)CAG>CAT	p.Q96H	C1orf88_uc001eax.2_Missense_Mutation_p.Q63H|C1orf88_uc009wge.1_Intron|C1orf88_uc001eay.2_Missense_Mutation_p.Q9H	NM_181643	NP_857594	Q8TCI5	CA088_HUMAN	hypothetical protein LOC128344	96										ovary(1)|skin(1)	2		all_cancers(81;3.21e-05)|all_epithelial(167;1.19e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0239)|Colorectal(144;0.0301)|all cancers(265;0.0677)|Epithelial(280;0.0897)|COAD - Colon adenocarcinoma(174;0.116)|LUSC - Lung squamous cell carcinoma(189;0.135)														---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117127667	117127667	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117127667G>A	uc001egr.1	-	9	3153	c.2448C>T	c.(2446-2448)CGC>CGT	p.R816R	IGSF3_uc001egq.1_Silent_p.R836R|IGSF3_uc001egs.1_Silent_p.R489R	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	816	Ig-like C2-type 7.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)														---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145015901	145015901	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145015901G>A	uc001elx.3	-	3	522	c.187C>T	c.(187-189)CCC>TCC	p.P63S	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_Missense_Mutation_p.P63S|PDE4DIP_uc001elo.2_Missense_Mutation_p.P134S|PDE4DIP_uc001emh.2_Missense_Mutation_p.P134S|uc001emj.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	Error:Variant_position_missing_in_Q5VU43_after_alignment					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								---	---	---	---
C1orf56	54964	broad.mit.edu	37	1	151020433	151020433	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151020433G>A	uc001ewn.2	+	1	175	c.110G>A	c.(109-111)AGT>AAT	p.S37N		NM_017860	NP_060330	Q9BUN1	CA056_HUMAN	hypothetical protein LOC54964 precursor	37						extracellular region					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)															---	---	---	---
C1orf56	54964	broad.mit.edu	37	1	151021230	151021230	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151021230G>A	uc001ewn.2	+	1	972	c.907G>A	c.(907-909)GCC>ACC	p.A303T		NM_017860	NP_060330	Q9BUN1	CA056_HUMAN	hypothetical protein LOC54964 precursor	303						extracellular region					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)													OREG0013793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152081442	152081442	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152081442G>A	uc001ezp.2	-	2	4251	c.4251C>T	c.(4249-4251)CGC>CGT	p.R1417R	TCHH_uc009wne.1_Silent_p.R1417R	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1417	23 X 26 AA approximate tandem repeats.				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	152282336	152282336	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152282336T>C	uc001ezu.1	-	3	5062	c.5026A>G	c.(5026-5028)AGT>GGT	p.S1676G		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1676	Ser-rich.|Filaggrin 10.				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				---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152326950	152326950	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152326950T>C	uc001ezw.3	-	3	3385	c.3312A>G	c.(3310-3312)CAA>CAG	p.Q1104Q	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1104	Ser-rich.|Filaggrin 4.						calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
NPR1	4881	broad.mit.edu	37	1	153660672	153660672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153660672C>T	uc001fcs.3	+	15	2813	c.2392C>T	c.(2392-2394)CGC>TGC	p.R798C	NPR1_uc010pdz.1_Missense_Mutation_p.R544C|NPR1_uc010pea.1_Missense_Mutation_p.R276C	NM_000906	NP_000897	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1 precursor	798	Cytoplasmic (Potential).|Protein kinase.				body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation		ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity			ovary(3)|lung(2)|stomach(1)|breast(1)	7	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)													---	---	---	---
KIAA0907	22889	broad.mit.edu	37	1	155896918	155896918	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155896918C>T	uc001fmi.1	-	5	518	c.494G>A	c.(493-495)GGC>GAC	p.G165D	KIAA0907_uc001fmj.1_Missense_Mutation_p.G165D|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_RNA|KIAA0907_uc001fml.1_Missense_Mutation_p.G165D|KIAA0907_uc001fmm.2_Missense_Mutation_p.G165D|SCARNA4_uc001fmn.1_5'Flank|KIAA0907_uc001fmo.2_Missense_Mutation_p.G165D	NM_014949	NP_055764	Q7Z7F0	K0907_HUMAN	hypothetical protein LOC22889	165											0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)															---	---	---	---
RXFP4	339403	broad.mit.edu	37	1	155911718	155911718	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155911718G>A	uc010pgs.1	+	1	239	c.218G>A	c.(217-219)GGC>GAC	p.G73D		NM_181885	NP_871001	Q8TDU9	RL3R2_HUMAN	relaxin 3 receptor 2	73	Cytoplasmic (Potential).					integral to membrane|plasma membrane	angiotensin type II receptor activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156146693	156146693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156146693A>G	uc001fnl.2	+	15	2295	c.2191A>G	c.(2191-2193)AGC>GGC	p.S731G	SEMA4A_uc009wrq.2_Missense_Mutation_p.S731G|SEMA4A_uc001fnm.2_Missense_Mutation_p.S731G|SEMA4A_uc001fnn.2_Missense_Mutation_p.S599G|SEMA4A_uc001fno.2_Missense_Mutation_p.S731G	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	731	Cytoplasmic (Potential).				axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
CCT3	7203	broad.mit.edu	37	1	156288680	156288680	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156288680T>C	uc001fol.1	-	8	958	c.738A>G	c.(736-738)GAA>GAG	p.E246E	CCT3_uc001fom.1_Silent_p.E245E|CCT3_uc001fon.1_Silent_p.E208E|CCT3_uc010phj.1_Silent_p.E200E|CCT3_uc010phk.1_Silent_p.E200E|CCT3_uc010phl.1_Silent_p.E200E	NM_005998	NP_005989	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 isoform a	246					'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156928827	156928827	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156928827C>A	uc001fqo.2	-						ARHGEF11_uc001fqn.2_Intron|ARHGEF11_uc001fqp.1_5'Flank	NM_014784	NP_055599			Rho guanine nucleotide exchange factor (GEF) 11						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)																	---	---	---	---
FCRL1	115350	broad.mit.edu	37	1	157772362	157772362	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157772362T>C	uc001frg.2	-	4	525	c.412A>G	c.(412-414)ATG>GTG	p.M138V	FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Missense_Mutation_p.M138V|FCRL1_uc001fri.2_Missense_Mutation_p.M138V|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	138	Ig-like C2-type 2.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)															---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158061167	158061167	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158061167A>C	uc001frn.3	+	11	1696	c.1292A>C	c.(1291-1293)AAC>ACC	p.N431T	KIRREL_uc010pib.1_Missense_Mutation_p.N331T|KIRREL_uc009wsq.2_Missense_Mutation_p.N267T|KIRREL_uc001fro.3_Missense_Mutation_p.N245T	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	431	Ig-like C2-type 5.|Extracellular (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
CD1B	910	broad.mit.edu	37	1	158300854	158300854	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158300854T>C	uc001frx.2	-	2	170	c.62_splice	c.e2-1	p.A21_splice	CD1B_uc001frw.2_Splice_Site|CD1B_uc010pic.1_Intron	NM_001764	NP_001755			CD1B antigen precursor						antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)																	---	---	---	---
OR10K1	391109	broad.mit.edu	37	1	158435578	158435578	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158435578T>G	uc010pij.1	+	1	227	c.227T>G	c.(226-228)GTC>GGC	p.V76G		NM_001004473	NP_001004473	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K,	76	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
OR10Z1	128368	broad.mit.edu	37	1	158576839	158576839	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158576839T>A	uc010pio.1	+	1	611	c.611T>A	c.(610-612)CTT>CAT	p.L204H		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158617319	158617319	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158617319C>T	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						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)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158626424	158626424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158626424G>A	uc001fst.1	-	20	3027	c.2828C>T	c.(2827-2829)GCC>GTC	p.A943V		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	943	Spectrin 10.				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)																	---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160192546	160192546	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160192546G>T	uc001fvo.2	-	11	1647	c.1335C>A	c.(1333-1335)CCC>CCA	p.P445P	DCAF8_uc001fvn.2_Silent_p.P445P|DCAF8_uc009wth.2_Silent_p.P445P|DCAF8_uc010pjb.1_Silent_p.P445P|DCAF8_uc010pjc.1_Silent_p.P599P	NM_015726	NP_056541	Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	445	WD 6.					CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
ARHGAP30	257106	broad.mit.edu	37	1	161026197	161026197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161026197C>T	uc001fxl.2	-	3	672	c.326G>A	c.(325-327)CGG>CAG	p.R109Q	ARHGAP30_uc001fxk.2_Missense_Mutation_p.R109Q|ARHGAP30_uc001fxm.2_Intron|ARHGAP30_uc009wtx.2_5'UTR|ARHGAP30_uc001fxn.1_5'UTR	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	109	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)															---	---	---	---
PVRL4	81607	broad.mit.edu	37	1	161044096	161044096	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161044096G>A	uc001fxo.2	-	6	1367	c.1068C>T	c.(1066-1068)ATC>ATT	p.I356I	PVRL4_uc010pjy.1_Silent_p.I35I|PVRL4_uc010pjz.1_Silent_p.I90I	NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4 precursor	356	Helical; (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
PVRL4	81607	broad.mit.edu	37	1	161049588	161049588	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161049588C>A	uc001fxo.2	-	2	530	c.231G>T	c.(229-231)CAG>CAT	p.Q77H		NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4 precursor	77	Ig-like V-type 1.|Extracellular (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
USP21	27005	broad.mit.edu	37	1	161130992	161130992	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161130992G>A	uc010pke.1	+	3	939	c.562G>A	c.(562-564)GCC>ACC	p.A188T	USP21_uc010pkc.1_Missense_Mutation_p.A188T|USP21_uc010pkd.1_Missense_Mutation_p.A188T|USP21_uc010pkf.1_Missense_Mutation_p.A188T	NM_001014443	NP_001014443	Q9UK80	UBP21_HUMAN	ubiquitin-specific protease 21	188					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)															---	---	---	---
B4GALT3	8703	broad.mit.edu	37	1	161141819	161141819	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161141819T>C	uc001fyq.1	-	8	1231	c.969A>G	c.(967-969)ACA>ACG	p.T323T	PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_Silent_p.T103T|B4GALT3_uc001fyp.1_RNA|B4GALT3_uc001fyr.1_Silent_p.T323T|B4GALT3_uc001fys.1_Silent_p.T323T	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	323	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
RGS4	5999	broad.mit.edu	37	1	163043361	163043361	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163043361C>A	uc009wuy.2	+	4	838	c.327C>A	c.(325-327)CCC>CCA	p.P109P	RGS4_uc001gcl.3_Silent_p.P206P|RGS4_uc009wuz.2_Intron|RGS4_uc009wva.2_Silent_p.P91P	NM_005613	NP_005604	P49798	RGS4_HUMAN	regulator of G-protein signaling 4 isoform 2	109	RGS.				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
POGK	57645	broad.mit.edu	37	1	166818499	166818499	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166818499A>G	uc001gdt.1	+	5	803	c.683A>G	c.(682-684)GAA>GGA	p.E228G	POGK_uc010ple.1_Missense_Mutation_p.E143G|POGK_uc010plf.1_Missense_Mutation_p.E110G	NM_017542	NP_060012	Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	228					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
F5	2153	broad.mit.edu	37	1	169500040	169500040	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169500040T>C	uc001ggg.1	-	15	5337	c.5192A>G	c.(5191-5193)TAC>TGC	p.Y1731C		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	1731	F5/8 type A 3.|Plastocyanin-like 5.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
SELL	6402	broad.mit.edu	37	1	169676575	169676575	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169676575C>T	uc001ggk.2	-	4	686	c.488G>A	c.(487-489)TGG>TAG	p.W163*	C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Nonsense_Mutation_p.W116*|SELL_uc001ggl.1_Nonsense_Mutation_p.W176*	NM_000655	NP_000646	P14151	LYAM1_HUMAN	selectin L precursor	163	EGF-like.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	integral to plasma membrane	glycosphingolipid binding|heparin binding|protease binding|sugar binding				0	all_hematologic(923;0.208)																	---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173506088	173506088	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173506088G>A	uc001giz.2	-	14	2071	c.1648C>T	c.(1648-1650)CAA>TAA	p.Q550*	SLC9A11_uc009wwe.2_Nonsense_Mutation_p.Q108*|SLC9A11_uc010pmq.1_RNA	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	550					sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175325484	175325484	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175325484C>G	uc001gkp.1	-	14	3170	c.3089G>C	c.(3088-3090)AGT>ACT	p.S1030T	TNR_uc009wwu.1_Missense_Mutation_p.S1030T	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1030	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)																	---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176998870	176998870	+	Silent	SNP	G	A	A	rs138051324		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176998870G>A	uc001glc.2	-	5	1232	c.1020C>T	c.(1018-1020)TCC>TCT	p.S340S	ASTN1_uc001glb.1_Silent_p.S340S|ASTN1_uc001gld.1_Silent_p.S340S|ASTN1_uc009wwx.1_Silent_p.S340S|ASTN1_uc001gle.3_RNA|MIR488_hsa-mir-488|MI0003123_5'Flank	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	340					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177937025	177937025	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177937025C>T	uc001gli.1	-	2	182	c.92G>A	c.(91-93)GGA>GAA	p.G31E	SEC16B_uc001glk.1_5'UTR|SEC16B_uc009wwz.1_5'UTR|SEC16B_uc001glj.1_Missense_Mutation_p.G31E|SEC16B_uc001gll.3_Missense_Mutation_p.G31E	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2	31					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178389670	178389670	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178389670G>T	uc001glr.2	+	3	270	c.145G>T	c.(145-147)GGC>TGC	p.G49C	RASAL2_uc009wxb.2_Missense_Mutation_p.G197C|RASAL2_uc001glq.2_Missense_Mutation_p.G197C	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	49	PH.				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																		---	---	---	---
NPL	80896	broad.mit.edu	37	1	182783988	182783988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182783988C>T	uc009wyb.2	+	7	499	c.359C>T	c.(358-360)ACC>ATC	p.T120I	NPL_uc010pnx.1_Missense_Mutation_p.T101I|NPL_uc010pny.1_RNA|NPL_uc001gpo.1_Missense_Mutation_p.T101I|NPL_uc009wyc.2_Missense_Mutation_p.T120I|NPL_uc001gpp.3_Missense_Mutation_p.T120I|NPL_uc001gpq.1_Missense_Mutation_p.T120I	NM_030769	NP_110396	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase	120					carbohydrate metabolic process	cytoplasm	N-acetylneuraminate lyase activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183177156	183177156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183177156C>T	uc001gqa.2	+	2	534	c.220C>T	c.(220-222)CGG>TGG	p.R74W	LAMC2_uc001gpz.3_Missense_Mutation_p.R74W|LAMC2_uc010poa.1_5'UTR	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	74	Laminin EGF-like 1.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
GLT25D2	23127	broad.mit.edu	37	1	183938581	183938581	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183938581G>A	uc001gqr.2	-	5	1026	c.654C>T	c.(652-654)TAC>TAT	p.Y218Y	GLT25D2_uc010poj.1_Silent_p.Y218Y|GLT25D2_uc001gqs.2_Silent_p.Y98Y	NM_015101	NP_055916	Q8IYK4	GT252_HUMAN	glycosyltransferase 25 domain containing 2	218					lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186305776	186305776	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186305776C>T	uc001grv.2	-	33	4854	c.4557G>A	c.(4555-4557)GTG>GTA	p.V1519V		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1519	Potential.				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								---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196395022	196395022	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196395022G>A	uc001gtd.1	-	11	1141	c.1081C>T	c.(1081-1083)CAA>TAA	p.Q361*	KCNT2_uc009wyt.1_RNA|KCNT2_uc001gte.1_Nonsense_Mutation_p.Q361*|KCNT2_uc001gtf.1_Nonsense_Mutation_p.Q361*|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Nonsense_Mutation_p.Q361*|KCNT2_uc009wyv.1_Nonsense_Mutation_p.Q336*	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	361	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196716354	196716354	+	Missense_Mutation	SNP	C	T	T	rs145347741	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196716354C>T	uc001gtj.3	+	22	3847	c.3607C>T	c.(3607-3609)CGG>TGG	p.R1203W		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	1203	Sushi 20.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CFHR4	10877	broad.mit.edu	37	1	196883716	196883716	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196883716C>T	uc001gto.2	+	4	600	c.531C>T	c.(529-531)TAC>TAT	p.Y177Y	CFHR4_uc009wyy.2_Silent_p.Y423Y|CFHR4_uc001gtp.2_Silent_p.Y424Y	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor	177	Sushi 3.					extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197145714	197145714	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197145714T>C	uc001gtx.1	-	7	1928	c.1859A>G	c.(1858-1860)AAG>AGG	p.K620R	ZBTB41_uc009wyz.1_RNA	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	620	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197586803	197586803	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197586803C>T	uc001guf.3	-	11	1097	c.759G>A	c.(757-759)CTG>CTA	p.L253L	DENND1B_uc010ppe.1_Silent_p.L233L|DENND1B_uc010ppf.1_RNA|DENND1B_uc001gue.3_Silent_p.L223L|DENND1B_uc001gug.3_Silent_p.L52L	NM_144977	NP_659414	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B isoform 2	253	DENN.					clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
LHX9	56956	broad.mit.edu	37	1	197890758	197890758	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197890758G>A	uc001guk.1	+	3	1139	c.702G>A	c.(700-702)GCG>GCA	p.A234A	LHX9_uc001gui.1_Silent_p.A225A|LHX9_uc001guj.1_Silent_p.A240A	NM_020204	NP_064589	Q9NQ69	LHX9_HUMAN	LIM homeobox 9 isoform 1	234					motor axon guidance|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198713337	198713337	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198713337T>C	uc001gur.1	+						PTPRC_uc001gus.1_Intron|PTPRC_uc001gut.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																		---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200017553	200017553	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200017553C>A	uc001gvb.2	+	5	923	c.717C>A	c.(715-717)CCC>CCA	p.P239P	NR5A2_uc001gvc.2_Silent_p.P193P|NR5A2_uc009wzh.2_Silent_p.P199P|NR5A2_uc010pph.1_Silent_p.P167P	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	239					embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)																	---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201687704	201687704	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201687704C>T	uc001gwu.2	+	3	1394	c.1047C>T	c.(1045-1047)GGC>GGT	p.G349G		NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	349					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
PRELP	5549	broad.mit.edu	37	1	203452325	203452325	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203452325C>A	uc001gzs.2	+	2	213	c.13C>A	c.(13-15)CTC>ATC	p.L5I	PRELP_uc001gzt.2_Missense_Mutation_p.L5I	NM_002725	NP_002716	P51888	PRELP_HUMAN	proline arginine-rich end leucine-rich repeat	5					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)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204408163	204408163	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204408163C>T	uc001haw.2	-	24	3895	c.3416G>A	c.(3415-3417)CGT>CAT	p.R1139H	PIK3C2B_uc010pqv.1_Missense_Mutation_p.R1111H	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	1139	PI3K/PI4K.				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)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206821125	206821125	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206821125T>C	uc001hej.2	+	3	750	c.582T>C	c.(580-582)GAT>GAC	p.D194D	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Silent_p.D174D	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	194					erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210856804	210856804	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210856804C>T	uc001hib.2	-	11	2959	c.2789G>A	c.(2788-2790)AGG>AAG	p.R930K	KCNH1_uc001hic.2_Missense_Mutation_p.R903K	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	930	Cytoplasmic (Potential).|CAD (involved in subunit assembly) (By similarity).				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)														---	---	---	---
CNIH3	149111	broad.mit.edu	37	1	224804897	224804897	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224804897G>A	uc001hos.1	+	1	719	c.21G>A	c.(19-21)GCG>GCA	p.A7A		NM_152495	NP_689708	Q8TBE1	CNIH3_HUMAN	cornichon homolog 3	7	Cytoplasmic (Potential).				intracellular signal transduction|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic shaft|postsynaptic membrane					0	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)														---	---	---	---
LBR	3930	broad.mit.edu	37	1	225591108	225591108	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225591108T>C	uc001hoy.2	-	14	1888	c.1745A>G	c.(1744-1746)CAC>CGC	p.H582R	LBR_uc001hoz.2_Missense_Mutation_p.H582R	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	582					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
ACBD3	64746	broad.mit.edu	37	1	226353563	226353563	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226353563C>A	uc001hpy.2	-	2	472	c.425G>T	c.(424-426)AGG>ATG	p.R142M		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	142	ACB.				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)														---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228493068	228493068	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228493068G>A	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	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)																---	---	---	---
TTC13	79573	broad.mit.edu	37	1	231060632	231060632	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231060632A>G	uc001huf.3	-	14	1707	c.1676T>C	c.(1675-1677)TTG>TCG	p.L559S	TTC13_uc009xfi.2_Missense_Mutation_p.L506S|TTC13_uc009xfj.2_RNA|TTC13_uc001hug.3_Missense_Mutation_p.L506S|TTC13_uc009xfk.1_Missense_Mutation_p.L449S	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	559							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)														---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236389790	236389790	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236389790T>C	uc001hxt.2	-	12	1087	c.831A>G	c.(829-831)GGA>GGG	p.G277G		NM_019891	NP_063944	Q86YB8	ERO1B_HUMAN	endoplasmic reticulum oxidoreductin 1-Lbeta	277					electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236760194	236760194	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236760194A>G	uc001hyd.1	-	6	811	c.686T>C	c.(685-687)GTA>GCA	p.V229A		NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	229					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)															---	---	---	---
MTR	4548	broad.mit.edu	37	1	237052583	237052583	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237052583G>T	uc001hyi.3	+	28	3377	c.2954G>T	c.(2953-2955)CGG>CTG	p.R985L	MTR_uc010pxw.1_Missense_Mutation_p.R578L|MTR_uc010pxx.1_Missense_Mutation_p.R934L|MTR_uc010pxy.1_Missense_Mutation_p.R839L	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	985	AdoMet activation.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237777405	237777405	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237777405G>A	uc001hyl.1	+	37	5097	c.4977G>A	c.(4975-4977)CGG>CGA	p.R1659R		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1659	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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	240977013	240977013	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240977013C>A	uc001hyv.2	-	13	1191	c.861G>T	c.(859-861)ACG>ACT	p.T287T	RGS7_uc010pyh.1_Silent_p.T261T|RGS7_uc010pyj.1_Silent_p.T203T|RGS7_uc001hyu.2_Silent_p.T287T|RGS7_uc009xgn.1_Silent_p.T234T|RGS7_uc001hyw.2_Silent_p.T287T|RGS7_uc001hyt.2_Silent_p.T119T	NM_002924	NP_002915	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	287	G protein gamma.				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)															---	---	---	---
EXO1	9156	broad.mit.edu	37	1	242023882	242023882	+	Missense_Mutation	SNP	G	T	T	rs149397534	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242023882G>T	uc001hzh.2	+	9	1360	c.820G>T	c.(820-822)GGG>TGG	p.G274W	EXO1_uc001hzi.2_Missense_Mutation_p.G274W|EXO1_uc001hzj.2_Missense_Mutation_p.G274W|EXO1_uc009xgq.2_Missense_Mutation_p.G274W	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b	274	Interaction with MSH3.				meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)										Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
ZNF669	79862	broad.mit.edu	37	1	247264200	247264200	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247264200C>T	uc001ice.2	-	4	1044	c.871G>A	c.(871-873)GGT>AGT	p.G291S	ZNF669_uc001icf.2_Missense_Mutation_p.G205S	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	291	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)															---	---	---	---
OR11L1	391189	broad.mit.edu	37	1	248004443	248004443	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248004443G>A	uc001idn.1	-	1	756	c.756C>T	c.(754-756)TAC>TAT	p.Y252Y		NM_001001959	NP_001001959	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
TPO	7173	broad.mit.edu	37	2	1497717	1497717	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1497717G>T	uc002qww.2	+	11	2003	c.1912G>T	c.(1912-1914)GGC>TGC	p.G638C	TPO_uc010ewj.2_RNA|TPO_uc002qwu.2_Missense_Mutation_p.G581C|TPO_uc002qwr.2_Missense_Mutation_p.G638C|TPO_uc002qwx.2_Missense_Mutation_p.G581C|TPO_uc010yio.1_Missense_Mutation_p.G465C|TPO_uc010yip.1_Missense_Mutation_p.G638C|TPO_uc002qwy.1_Translation_Start_Site|TPO_uc002qwz.2_RNA	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	638	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)													---	---	---	---
TTC15	51112	broad.mit.edu	37	2	3428446	3428446	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3428446G>T	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114			tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7170255	7170255	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7170255A>G	uc002qys.2	+	8	1100	c.658_splice	c.e8-2	p.D220_splice	RNF144A_uc002qyt.2_Splice_Site_p.D69_splice	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17922967	17922967	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17922967A>G	uc002rco.2	-	4	446	c.150T>C	c.(148-150)AGT>AGC	p.S50S	SMC6_uc010exo.2_Silent_p.S50S|SMC6_uc002rcn.2_Silent_p.S50S|SMC6_uc002rcp.1_Silent_p.S50S|SMC6_uc002rcq.2_Silent_p.S50S|SMC6_uc002rcr.1_Silent_p.S50S	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	50					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)																	---	---	---	---
MSGN1	343930	broad.mit.edu	37	2	17998310	17998310	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17998310C>T	uc010yjt.1	+	1	525	c.525C>T	c.(523-525)ATC>ATT	p.I175I		NM_001105569	NP_001099039	A6NI15	MSGN1_HUMAN	mesogenin 1	175	Helix-loop-helix motif.				cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
NT5C1B	93034	broad.mit.edu	37	2	18764262	18764262	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18764262G>A	uc002rcz.2	-	7	1177	c.1073C>T	c.(1072-1074)GCA>GTA	p.A358V	NT5C1B_uc002rcy.2_Missense_Mutation_p.A358V|NT5C1B_uc010exr.2_Missense_Mutation_p.A300V|NT5C1B_uc010yju.1_Missense_Mutation_p.A298V|NT5C1B_uc002rda.2_Missense_Mutation_p.A298V|NT5C1B_uc010yjv.1_Missense_Mutation_p.A375V|NT5C1B_uc010yjw.1_Missense_Mutation_p.A341V|NT5C1B_uc010exs.2_Missense_Mutation_p.A360V	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	358					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)																---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20138019	20138019	+	Intron	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20138019T>A	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_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)																	---	---	---	---
SDC1	6382	broad.mit.edu	37	2	20403769	20403769	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20403769C>A	uc002rdo.1	-	3	731	c.432G>T	c.(430-432)ACG>ACT	p.T144T	SDC1_uc002rdp.1_Silent_p.T144T|SDC1_uc010exv.2_Silent_p.T144T|SDC1_uc010exw.1_RNA	NM_002997	NP_002988	P18827	SDC1_HUMAN	syndecan 1 precursor	144	Extracellular (Potential).				lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)														---	---	---	---
MFSD2B	388931	broad.mit.edu	37	2	24245392	24245392	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24245392G>T	uc002reo.1	+							NM_001080473	NP_001073942			major facilitator superfamily domain containing						transport	integral to membrane				ovary(2)	2																		---	---	---	---
C2orf44	80304	broad.mit.edu	37	2	24260710	24260710	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24260710T>C	uc002rep.2	-	2	1786	c.1655A>G	c.(1654-1656)AAG>AGG	p.K552R	C2orf44_uc010eya.2_Missense_Mutation_p.K552R	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1	552							protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf16	84226	broad.mit.edu	37	2	27805111	27805111	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27805111T>C	uc002rkz.3	+	1	5723	c.5672T>C	c.(5671-5673)ATG>ACG	p.M1891T	ZNF512_uc010ylv.1_5'Flank|ZNF512_uc010ylw.1_5'Flank|ZNF512_uc002rlb.2_5'Flank|ZNF512_uc010ylx.1_5'Flank|ZNF512_uc002rlc.2_5'Flank|ZNF512_uc002rla.2_5'Flank|ZNF512_uc010yly.1_5'Flank|ZNF512_uc010ylz.1_5'Flank	NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	1891	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.									large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
VIT	5212	broad.mit.edu	37	2	37041497	37041497	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37041497G>T	uc002rpl.2	+	16	2296	c.2075G>T	c.(2074-2076)CGG>CTG	p.R692L	VIT_uc002rpm.2_Missense_Mutation_p.R670L|VIT_uc010ezv.2_Missense_Mutation_p.R648L|VIT_uc010ezw.2_Missense_Mutation_p.R649L	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin	677						proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40657163	40657163	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40657163G>A	uc002rrx.2	-	1	282	c.258C>T	c.(256-258)GTC>GTT	p.V86V	SLC8A1_uc002rry.2_Silent_p.V86V|SLC8A1_uc002rrz.2_Silent_p.V86V|SLC8A1_uc002rsa.2_Silent_p.V86V|SLC8A1_uc002rsd.3_Silent_p.V86V|SLC8A1_uc002rsb.1_Silent_p.V86V|SLC8A1_uc010fan.1_Silent_p.V86V|SLC8A1_uc002rsc.1_Silent_p.V86V	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	86	Helical; (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
PLEKHH2	130271	broad.mit.edu	37	2	43958705	43958705	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43958705C>T	uc010yny.1	+	19	2990	c.2907C>T	c.(2905-2907)TCC>TCT	p.S969S	PLEKHH2_uc002rtf.3_Silent_p.S968S	NM_172069	NP_742066	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H	969	MyTH4.					cytoplasm|cytoskeleton|integral to membrane	binding			skin(2)|central_nervous_system(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
SIX3	6496	broad.mit.edu	37	2	45169750	45169750	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45169750G>A	uc002run.1	+	1	714	c.507G>A	c.(505-507)TGG>TGA	p.W169*		NM_005413	NP_005404	O95343	SIX3_HUMAN	SIX homeobox 3	169					visual perception	nucleus					0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49244619	49244619	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49244619A>G	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54893235	54893235	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54893235G>A	uc002rxu.2	+						SPTBN1_uc010you.1_Intron	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
OTX1	5013	broad.mit.edu	37	2	63281338	63281338	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63281338G>A	uc002scd.2	+						OTX1_uc010ypt.1_Intron	NM_014562	NP_055377			orthodenticle homeobox 1							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(2)	2	Lung NSC(7;0.121)|all_lung(7;0.211)																	---	---	---	---
SERTAD2	9792	broad.mit.edu	37	2	64863063	64863063	+	Nonstop_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64863063A>C	uc002sde.1	-	2	1240	c.943T>G	c.(943-945)TAA>GAA	p.*315E		NM_014755	NP_055570	Q14140	SRTD2_HUMAN	SERTA domain containing 2	315					negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71576203	71576203	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71576203C>A	uc002shx.2	+	2	438	c.119C>A	c.(118-120)CCA>CAA	p.P40Q	ZNF638_uc010fec.2_Missense_Mutation_p.P146Q|ZNF638_uc010yqw.1_Intron|ZNF638_uc002shw.2_Missense_Mutation_p.P40Q|ZNF638_uc002shy.2_Missense_Mutation_p.P40Q|ZNF638_uc002shz.2_Missense_Mutation_p.P40Q|ZNF638_uc002sia.2_Missense_Mutation_p.P40Q|ZNF638_uc002sib.1_Missense_Mutation_p.P40Q	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	40					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71635329	71635329	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71635329T>C	uc002shx.2	+	20	3532	c.3213T>C	c.(3211-3213)GGT>GGC	p.G1071G	ZNF638_uc010yqw.1_Silent_p.G650G|ZNF638_uc002shy.2_Silent_p.G1071G|ZNF638_uc002shz.2_Silent_p.G1071G|ZNF638_uc002sia.2_Silent_p.G1071G|ZNF638_uc002sib.1_Silent_p.G1071G|ZNF638_uc010fed.2_RNA|ZNF638_uc002sic.2_Silent_p.G168G	NM_014497	NP_055312	Q14966	ZN638_HUMAN	zinc finger protein 638	1071					RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
NAT8	9027	broad.mit.edu	37	2	73868171	73868171	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73868171C>G	uc002sji.1	-	2	752	c.585G>C	c.(583-585)AAG>AAC	p.K195N		NM_003960	NP_003951	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8	195	N-acetyltransferase.				gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			ovary(1)	1																		---	---	---	---
TET3	200424	broad.mit.edu	37	2	74327752	74327752	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74327752C>T	uc002skb.3	+	9	3432	c.3432C>T	c.(3430-3432)TAC>TAT	p.Y1144Y		NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3	1144							metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
MOBKL1B	55233	broad.mit.edu	37	2	74386330	74386330	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74386330C>T	uc002skh.3	-	5	655	c.461G>A	c.(460-462)CGT>CAT	p.R154H		NM_018221	NP_060691	Q9H8S9	MOL1B_HUMAN	Mob4B protein	154					hippo signaling cascade		metal ion binding|protein binding				0																		---	---	---	---
CAPG	822	broad.mit.edu	37	2	85628441	85628441	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85628441C>T	uc002spl.1	-	5	613	c.363G>A	c.(361-363)GTG>GTA	p.V121V	CAPG_uc002spm.1_Silent_p.V121V|CAPG_uc010ysq.1_Silent_p.V121V|CAPG_uc010fgi.1_Silent_p.V121V|CAPG_uc010fgj.1_Silent_p.V15V	NM_001747	NP_001738	P40121	CAPG_HUMAN	gelsolin-like capping protein	121					barbed-end actin filament capping|protein complex assembly	F-actin capping protein complex|melanosome|nuclear membrane|nucleolus	actin binding				0																		---	---	---	---
TMEM150A	129303	broad.mit.edu	37	2	85829045	85829045	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85829045G>A	uc002spw.1	-	1	748	c.27C>T	c.(25-27)GTC>GTT	p.V9V	USP39_uc002sqb.2_5'Flank|TMEM150A_uc002spx.1_5'UTR|TMEM150A_uc002spz.1_5'UTR|TMEM150A_uc002sqa.1_5'UTR|TMEM150A_uc002spy.1_Silent_p.V9V	NM_001031738	NP_001026908	Q86TG1	T150A_HUMAN	transmembrane protein 150A isoform 1	9						integral to membrane|plasma membrane					0																		---	---	---	---
SFTPB	6439	broad.mit.edu	37	2	85890528	85890528	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85890528G>A	uc002sqh.2	-	8	949	c.943C>T	c.(943-945)CAG>TAG	p.Q315*	SFTPB_uc002sqi.2_Nonsense_Mutation_p.Q323*|SFTPB_uc002sqj.2_Nonsense_Mutation_p.Q315*|SFTPB_uc010ysw.1_5'Flank	NM_198843	NP_942140	P07988	PSPB_HUMAN	surfactant, pulmonary-associated protein B	315	Saposin B-type 3.				organ morphogenesis|respiratory gaseous exchange|sphingolipid metabolic process	extracellular space|lysosome				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86305040	86305040	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86305040G>A	uc002sqs.2	-	11	1701	c.1322C>T	c.(1321-1323)GCG>GTG	p.A441V		NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	441					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																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86756342	86756342	+	Silent	SNP	G	T	T	rs140980165		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86756342G>T	uc002srj.2	-	3	414	c.285C>A	c.(283-285)CTC>CTA	p.L95L	VPS24_uc002srk.2_Silent_p.L29L|VPS24_uc002srl.2_Intron|VPS24_uc010ytl.1_Silent_p.L124L	NM_016079	NP_057163	Q9Y3E7	CHMP3_HUMAN	vacuolar protein sorting 24 isoform 1	95	Intramolecular interaction with C- terminus.				cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	90121716	90121716	+	Intron	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90121716A>C	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
ZNF514	84874	broad.mit.edu	37	2	95818899	95818899	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95818899A>C	uc002sue.1	-	3	474	c.100T>G	c.(100-102)TTC>GTC	p.F34V	ZNF514_uc002sud.1_Missense_Mutation_p.F107V	NM_032788	NP_116177	Q96K75	ZN514_HUMAN	zinc finger protein 514	34	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PROM2	150696	broad.mit.edu	37	2	95947910	95947910	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95947910C>T	uc002suh.1	+	14	1797	c.1664C>T	c.(1663-1665)GCG>GTG	p.A555V	PROM2_uc002sui.2_Missense_Mutation_p.A555V|PROM2_uc002suj.2_Missense_Mutation_p.A209V|PROM2_uc002suk.2_Missense_Mutation_p.A555V|PROM2_uc002sul.2_Missense_Mutation_p.A81V|PROM2_uc002sum.2_RNA	NM_144707	NP_653308	Q8N271	PROM2_HUMAN	prominin 2 precursor	555	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|cilium membrane|integral to membrane|microvillus membrane				ovary(1)	1																		---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96956091	96956091	+	Silent	SNP	G	A	A	rs138641050		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96956091G>A	uc002svu.2	-	20	2801	c.2715C>T	c.(2713-2715)ATC>ATT	p.I905I	SNRNP200_uc002svw.1_5'Flank	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	905	Helicase C-terminal 1.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding	p.I905I(1)		ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
NEURL3	93082	broad.mit.edu	37	2	97164021	97164021	+	RNA	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97164021G>A	uc010fhx.2	-	6		c.1084C>T			NEURL3_uc002swc.2_RNA					Homo sapiens cDNA FLJ54814 complete cds.												0																		---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98351166	98351166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98351166G>A	uc002syd.1	+	9	1280	c.1073G>A	c.(1072-1074)CGC>CAC	p.R358H	ZAP70_uc010yvf.1_3'UTR|ZAP70_uc002sye.1_Missense_Mutation_p.R248H|ZAP70_uc002syf.1_Missense_Mutation_p.R51H	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	358	Protein kinase.				immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99685473	99685473	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99685473A>G	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron	NM_182911	NP_878915			testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99721883	99721883	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99721883G>A	uc002szg.3	-	7	1026	c.398C>T	c.(397-399)GCA>GTA	p.A133V	TSGA10_uc002szh.3_Missense_Mutation_p.A133V|TSGA10_uc002szi.3_Missense_Mutation_p.A133V|TSGA10_uc010fin.1_Missense_Mutation_p.A133V|TSGA10_uc010yvn.1_Missense_Mutation_p.A133V	NM_182911	NP_878915	Q9BZW7	TSG10_HUMAN	testis specific, 10	133					spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101624428	101624428	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101624428A>G	uc010fiv.2	-	20	3409	c.3278T>C	c.(3277-3279)CTG>CCG	p.L1093P	RPL31_uc010yvu.1_Intron|RPL31_uc010yvv.1_Intron|RPL31_uc010fiu.1_Intron|TBC1D8_uc002tau.3_Missense_Mutation_p.L850P	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	1093					blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
GCC2	9648	broad.mit.edu	37	2	109088197	109088197	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109088197T>C	uc002tec.2	+	6	2566	c.2412T>C	c.(2410-2412)CGT>CGC	p.R804R	GCC2_uc002ted.2_Silent_p.R703R	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	804	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	109111808	109111808	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109111808G>A	uc002tec.2	+	20	4663	c.4509G>A	c.(4507-4509)CCG>CCA	p.P1503P	GCC2_uc002ted.2_Silent_p.P1402P	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2	1503	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																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109380502	109380502	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109380502T>C	uc002tem.3	+	20	3633	c.3507T>C	c.(3505-3507)GGT>GGC	p.G1169G		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	1169					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608394T>C	uc002thi.2	-	14	1856	c.1609A>G	c.(1609-1611)ACT>GCT	p.T537A		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					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																		---	---	---	---
CCDC93	54520	broad.mit.edu	37	2	118764370	118764370	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118764370C>T	uc002tlj.2	-	3	305	c.179G>A	c.(178-180)TGT>TAT	p.C60Y	CCDC93_uc010fld.1_Missense_Mutation_p.C60Y	NM_019044	NP_061917	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	60										large_intestine(1)|ovary(1)	2																		---	---	---	---
SCTR	6344	broad.mit.edu	37	2	120209579	120209579	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120209579C>A	uc002tma.2	-						SCTR_uc002tlz.2_Intron	NM_002980	NP_002971			secretin receptor precursor						digestion|excretion	integral to plasma membrane	secretin receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3					Secretin(DB00021)													---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121747109	121747109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121747109C>T	uc010flp.2	+	13	3649	c.3619C>T	c.(3619-3621)CCC>TCC	p.P1207S	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Missense_Mutation_p.P879S|GLI2_uc002tmu.3_Missense_Mutation_p.P862S	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1207					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
TFCP2L1	29842	broad.mit.edu	37	2	121995399	121995399	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121995399C>A	uc002tmx.2	-	9	981	c.888G>T	c.(886-888)GAG>GAT	p.E296D	TFCP2L1_uc010flr.2_Missense_Mutation_p.E296D	NM_014553	NP_055368	Q9NZI6	TF2L1_HUMAN	LBP-9	296					female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)																	---	---	---	---
TFCP2L1	29842	broad.mit.edu	37	2	122005852	122005852	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122005852T>C	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron	NM_014553	NP_055368			LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)																	---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128334262	128334262	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128334262C>A	uc002top.2	+	8	881	c.828C>A	c.(826-828)TCC>TCA	p.S276S		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	276	Myosin head-like.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136481597	136481597	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136481597G>A	uc002tuo.2	+	26	3405	c.3035G>A	c.(3034-3036)GGC>GAC	p.G1012D	R3HDM1_uc010fni.2_Missense_Mutation_p.G1011D|R3HDM1_uc002tup.2_Missense_Mutation_p.G957D|R3HDM1_uc010zbh.1_Missense_Mutation_p.G760D	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	1012							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
LCT	3938	broad.mit.edu	37	2	136566593	136566593	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136566593G>A	uc002tuu.1	-	8	3335	c.3324C>T	c.(3322-3324)TAC>TAT	p.Y1108Y		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1108	3.|Extracellular (Potential).|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)														---	---	---	---
MCM6	4175	broad.mit.edu	37	2	136614442	136614442	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136614442G>A	uc002tuw.2	-	11	1558	c.1482C>T	c.(1480-1482)AAC>AAT	p.N494N		NM_005915	NP_005906	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	494	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|identical protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.166)	Atorvastatin(DB01076)													---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141130589	141130589	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141130589T>G	uc002tvj.1	-	69	11728	c.10756A>C	c.(10756-10758)AGC>CGC	p.S3586R		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3586	Extracellular (Potential).|LDL-receptor class A 27.				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	141272329	141272329	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141272329G>T	uc002tvj.1	-	51	9134	c.8162C>A	c.(8161-8163)TCT>TAT	p.S2721Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	2721	Extracellular (Potential).|LDL-receptor class A 16.				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)			---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149247765	149247765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149247765C>T	uc002twm.3	+	12	4853	c.3865C>T	c.(3865-3867)CAC>TAC	p.H1289Y	MBD5_uc010zbs.1_Intron|MBD5_uc010fns.2_Missense_Mutation_p.H1289Y|MBD5_uc002two.2_Missense_Mutation_p.H547Y|MBD5_uc002twp.2_Missense_Mutation_p.H339Y	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	1289						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152320331	152320331	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152320331G>T	uc002txm.2	+	30	4427	c.4297G>T	c.(4297-4299)GAT>TAT	p.D1433Y	RIF1_uc002txl.2_Missense_Mutation_p.D1433Y|RIF1_uc002txn.2_Missense_Mutation_p.D1433Y|RIF1_uc002txo.2_Missense_Mutation_p.D1433Y|RIF1_uc002txp.2_RNA	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	1433					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)														---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153471416	153471416	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153471416C>A	uc002tye.2	+	12	1481	c.1114C>A	c.(1114-1116)CTG>ATG	p.L372M		NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2	372	GBD/FH3.				actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
RPRM	56475	broad.mit.edu	37	2	154334842	154334842	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154334842G>A	uc002tyq.1	-	1	481	c.238C>T	c.(238-240)CTG>TTG	p.L80L		NM_019845	NP_062819	Q9NS64	RPRM_HUMAN	reprimo, TP53 dependant G2 arrest mediator	80					cell cycle arrest	cytoplasm|integral to membrane	protein binding				0																		---	---	---	---
GALNT13	114805	broad.mit.edu	37	2	155252628	155252628	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155252628T>C	uc002tyr.3	+	10	1849	c.1282T>C	c.(1282-1284)TAC>CAC	p.Y428H	GALNT13_uc002tyt.3_Missense_Mutation_p.Y428H|GALNT13_uc010foc.1_Missense_Mutation_p.Y247H|GALNT13_uc010fod.2_Missense_Mutation_p.Y181H	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	428	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159922470	159922470	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159922470C>T	uc002uag.2	+	3	322	c.48C>T	c.(46-48)GGC>GGT	p.G16G	TANC1_uc010fol.1_Silent_p.G16G|TANC1_uc010zcm.1_Silent_p.G16G|TANC1_uc010fom.1_Silent_p.G16G	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	16						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166747442	166747442	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166747442C>T	uc002udk.2	-	23	3140	c.3007G>A	c.(3007-3009)GAG>AAG	p.E1003K	TTC21B_uc002udj.1_RNA	NM_024753	NP_079029	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	1003						cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167133718	167133718	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167133718G>A	uc010fpl.2	-	16	2957	c.2616C>T	c.(2614-2616)GTC>GTT	p.V872V	uc002udp.2_RNA	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	883	II.|Helical; Name=S5 of repeat II; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173686691	173686691	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173686691G>A	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc002uhw.3_5'UTR	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)															---	---	---	---
CHRNA1	1134	broad.mit.edu	37	2	175618367	175618367	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175618367G>A	uc002ujd.2	-	7	795	c.717C>T	c.(715-717)CCC>CCT	p.P239P	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Silent_p.P214P|CHRNA1_uc002ujf.3_Silent_p.P214P	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	239	Extracellular.				muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179247806	179247806	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179247806G>A	uc002ulx.2	+	17	2055	c.1677G>A	c.(1675-1677)CTG>CTA	p.L559L	OSBPL6_uc002uly.2_Silent_p.L584L|OSBPL6_uc010zfe.1_Silent_p.L528L|OSBPL6_uc002ulz.2_Silent_p.L523L|OSBPL6_uc002uma.2_Silent_p.L563L	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	559					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179588653	179588653	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179588653C>A	uc010zfg.1	-	70	17825	c.17601G>T	c.(17599-17601)ATG>ATT	p.M5867I	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.M2528I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6794							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	179645895	179645895	+	Missense_Mutation	SNP	C	T	T	rs149883066		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179645895C>T	uc010zfg.1	-	21	3700	c.3476G>A	c.(3475-3477)CGC>CAC	p.R1159H	TTN_uc010zfh.1_Missense_Mutation_p.R1113H|TTN_uc010zfi.1_Missense_Mutation_p.R1113H|TTN_uc010zfj.1_Missense_Mutation_p.R1113H|TTN_uc002unb.2_Missense_Mutation_p.R1159H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1159							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)															---	---	---	---
WDR75	84128	broad.mit.edu	37	2	190320086	190320086	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190320086A>G	uc002uql.1	+	5	474	c.414A>G	c.(412-414)TCA>TCG	p.S138S	WDR75_uc002uqm.1_Silent_p.S74S|WDR75_uc002uqn.1_5'UTR|WDR75_uc002uqo.1_5'Flank	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	138						nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)															---	---	---	---
WDR75	84128	broad.mit.edu	37	2	190329974	190329974	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190329974C>T	uc002uql.1	+	12	1343	c.1283C>T	c.(1282-1284)ACA>ATA	p.T428I	WDR75_uc002uqm.1_Missense_Mutation_p.T364I|WDR75_uc002uqn.1_Missense_Mutation_p.T206I|WDR75_uc002uqo.1_Missense_Mutation_p.T206I	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	428						nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)															---	---	---	---
NAB1	4664	broad.mit.edu	37	2	191524622	191524622	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191524622T>C	uc002usb.2	+	4	1292	c.720T>C	c.(718-720)GAT>GAC	p.D240D	NAB1_uc010fsc.2_Silent_p.D240D|NAB1_uc010fsd.2_Silent_p.D240D|NAB1_uc002usc.2_Silent_p.D240D|NAB1_uc010zgh.1_Silent_p.D240D	NM_005966	NP_005957	Q13506	NAB1_HUMAN	NGFI-A binding protein 1	240	NCD2.				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)															---	---	---	---
SF3B1	23451	broad.mit.edu	37	2	198262811	198262811	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198262811C>A	uc002uue.2	-	22	3212	c.3164G>T	c.(3163-3165)TGG>TTG	p.W1055L		NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1	1055	HEAT 9.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
BZW1	9689	broad.mit.edu	37	2	201681849	201681849	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201681849T>G	uc010zhg.1	+	6	571	c.519T>G	c.(517-519)GGT>GGG	p.G173G	BZW1_uc002uwc.2_Silent_p.G141G|BZW1_uc010zhh.1_Silent_p.G141G	NM_014670	NP_055485	Q7L1Q6	BZW1_HUMAN	basic leucine zipper and W2 domains 1	141					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	protein binding				0																		---	---	---	---
CASP8	841	broad.mit.edu	37	2	202123107	202123107	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202123107T>C	uc002uxr.1	+						CASP8_uc010ftc.1_Intron|CASP8_uc002uxo.1_Intron|CASP8_uc002uxp.1_Intron|CASP8_uc002uxq.1_Intron|CASP8_uc002uxs.1_Splice_Site|CASP8_uc002uxt.1_Splice_Site_p.D51_splice|CASP8_uc002uxu.1_Splice_Site|CASP8_uc010ftd.1_Intron|CASP8_uc002uxv.1_Intron|CASP8_uc002uxw.1_5'Flank	NM_033355	NP_203519			caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5															HNSCC(4;0.00038)	OREG0015144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WDR12	55759	broad.mit.edu	37	2	203745590	203745590	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203745590C>T	uc002uzl.2	-	13	2015	c.1265G>A	c.(1264-1266)GGG>GAG	p.G422E	WDR12_uc010ftt.2_3'UTR	NM_018256	NP_060726	Q9GZL7	WDR12_HUMAN	WD repeat domain 12 protein	422	Sufficient for nucleolar localization.|WD 7.				cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0																		---	---	---	---
PIKFYVE	200576	broad.mit.edu	37	2	209198113	209198113	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209198113T>C	uc002vcz.2	+	24	4196	c.4038T>C	c.(4036-4038)TAT>TAC	p.Y1346Y	PIKFYVE_uc002vcy.1_Silent_p.Y1290Y	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1346					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																		---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210560646	210560646	+	Missense_Mutation	SNP	G	A	A	rs142649637	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210560646G>A	uc002vde.1	+	7	4000	c.3752G>A	c.(3751-3753)CGC>CAC	p.R1251H	MAP2_uc002vdc.1_Missense_Mutation_p.R1251H|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Missense_Mutation_p.R1247H	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	1251					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)													---	---	---	---
UNC80	285175	broad.mit.edu	37	2	210658554	210658554	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210658554T>G	uc010zjc.1	+	7	989	c.909T>G	c.(907-909)ACT>ACG	p.T303T	UNC80_uc002vdj.1_Silent_p.T303T	NM_032504	NP_115893	Q8N2C7	UNC80_HUMAN	chromosome 2 open reading frame 21 isoform 1	303						integral to membrane					0																		---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212251610	212251610	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212251610T>C	uc002veg.1	-	27	3547	c.3449A>G	c.(3448-3450)TAC>TGC	p.Y1150C	ERBB4_uc002veh.1_Missense_Mutation_p.Y1134C|ERBB4_uc010zji.1_Missense_Mutation_p.Y1140C|ERBB4_uc010zjj.1_Missense_Mutation_p.Y1124C	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	1150	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)			---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215823125	215823125	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215823125G>A	uc002vew.2	-	41	6213	c.5993C>T	c.(5992-5994)TCT>TTT	p.S1998F	ABCA12_uc002vev.2_Missense_Mutation_p.S1680F|ABCA12_uc010zjn.1_Missense_Mutation_p.S925F	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1998	Helical; (Potential).				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216236932	216236932	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216236932C>A	uc002vfa.2	-	40	6680	c.6414G>T	c.(6412-6414)GGG>GGT	p.G2138G	FN1_uc002vfb.2_Silent_p.G1957G|FN1_uc002vfc.2_Silent_p.G1932G|FN1_uc002vfd.2_Silent_p.G2113G|FN1_uc002vfe.2_Silent_p.G2047G|FN1_uc002vff.2_Silent_p.G2022G|FN1_uc002vfg.2_Silent_p.G1957G|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Silent_p.G2138G|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Silent_p.G332G|FN1_uc010zjp.1_Silent_p.G675G|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Intron|FN1_uc010fvb.1_Intron|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Silent_p.G229G	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	2047	Connecting strand 3 (CS-3) (V region).				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)													---	---	---	---
FN1	2335	broad.mit.edu	37	2	216249629	216249629	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216249629A>G	uc002vfa.2	-	29	4949	c.4683T>C	c.(4681-4683)GCT>GCC	p.A1561A	FN1_uc002vfb.2_Silent_p.A1470A|FN1_uc002vfc.2_Silent_p.A1470A|FN1_uc002vfd.2_Silent_p.A1561A|FN1_uc002vfe.2_Silent_p.A1470A|FN1_uc002vff.2_Silent_p.A1470A|FN1_uc002vfg.2_Silent_p.A1470A|FN1_uc002vfh.2_Silent_p.A1470A|FN1_uc002vfi.2_Silent_p.A1561A|FN1_uc002vfj.2_Silent_p.A1561A|FN1_uc002vez.2_5'UTR|FN1_uc010zjp.1_Silent_p.A188A|FN1_uc010fvc.1_5'Flank|FN1_uc010fvd.1_5'Flank	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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)													---	---	---	---
TMEM169	92691	broad.mit.edu	37	2	216960851	216960851	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216960851C>T	uc010zjr.1	+	3	491	c.165C>T	c.(163-165)TAC>TAT	p.Y55Y	TMEM169_uc010zjs.1_Silent_p.Y55Y|TMEM169_uc002vfw.2_Silent_p.Y55Y|TMEM169_uc002vfv.3_Silent_p.Y55Y	NM_001142310	NP_001135782	Q96HH4	TM169_HUMAN	transmembrane protein 169	55	Extracellular (Potential).					integral to membrane				ovary(1)	1		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
XRCC5	7520	broad.mit.edu	37	2	216992311	216992311	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216992311T>A	uc002vfy.2	+	8	991	c.851T>A	c.(850-852)CTA>CAA	p.L284Q	XRCC5_uc002vfz.2_Missense_Mutation_p.L170Q	NM_021141	NP_066964	P13010	XRCC5_HUMAN	ATP-dependent DNA helicase II	284	Ku.				double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)									Direct_reversal_of_damage|NHEJ					---	---	---	---
NHEJ1	79840	broad.mit.edu	37	2	219941148	219941148	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219941148C>T	uc002vjp.3	-	8	1001	c.855G>A	c.(853-855)CAG>CAA	p.Q285Q	NHEJ1_uc002vjq.3_RNA	NM_024782	NP_079058	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	285					B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			lung(1)	1		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)									Direct_reversal_of_damage|NHEJ					---	---	---	---
TMEM198	130612	broad.mit.edu	37	2	220414482	220414482	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220414482T>C	uc002vme.2	+	6	1574	c.989T>C	c.(988-990)CTG>CCG	p.L330P	TMEM198_uc002vmf.2_Missense_Mutation_p.L330P|hsa-mir-3132|MI0014152_5'Flank	NM_001005209	NP_001005209	Q66K66	TM198_HUMAN	transmembrane protein 198	330						integral to membrane				ovary(1)	1		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)														---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223066632	223066632	+	3'UTR	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223066632G>A	uc010fwo.2	-	8					PAX3_uc002vmt.1_Intron|PAX3_uc002vmy.1_Intron|PAX3_uc002vmv.1_Intron|PAX3_uc002vmw.1_Intron|PAX3_uc002vmx.1_Intron	NM_181457	NP_852122			paired box 3 isoform PAX3						apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)				T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223086050	223086050	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223086050C>T	uc010fwo.2	-	6	1215	c.849G>A	c.(847-849)CTG>CTA	p.L283L	PAX3_uc002vmt.1_Silent_p.L283L|PAX3_uc002vmy.1_Silent_p.L282L|PAX3_uc002vmv.1_Silent_p.L283L|PAX3_uc002vmw.1_Silent_p.L283L|PAX3_uc002vmx.1_Silent_p.L283L	NM_181457	NP_852122	P23760	PAX3_HUMAN	paired box 3 isoform PAX3	283					apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)				T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230672446	230672446	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230672446C>A	uc002vpw.1	-	16	2439	c.2330G>T	c.(2329-2331)AGG>ATG	p.R777M	TRIP12_uc002vpx.1_Missense_Mutation_p.R825M|TRIP12_uc002vpy.1_Missense_Mutation_p.R480M|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Missense_Mutation_p.R783M	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	777	WWE.				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)														---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232156155	232156155	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232156155C>T	uc002vrq.3	+	18	1828	c.1716C>T	c.(1714-1716)TCC>TCT	p.S572S	ARMC9_uc002vrp.3_Silent_p.S572S|ARMC9_uc002vrr.1_RNA	NM_025139	NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	572							binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
MIR1244	100302285	broad.mit.edu	37	2	232578108	232578108	+	RNA	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232578108A>G	hsa-mir-1244-1|MI0006379	+			c.85A>G			PTMA_uc002vsb.3_3'UTR|PTMA_uc002vsc.3_3'UTR|PTMA_uc010zmf.1_RNA																	0																		---	---	---	---
ECEL1	9427	broad.mit.edu	37	2	233348873	233348873	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233348873C>T	uc002vsv.2	-	7	1450	c.1245G>A	c.(1243-1245)CCG>CCA	p.P415P	ECEL1_uc010fya.1_Silent_p.P415P|ECEL1_uc010fyb.1_Silent_p.P122P	NM_004826	NP_004817	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	415	Lumenal (Potential).				neuropeptide signaling pathway|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity	p.P415L(1)		central_nervous_system(2)	2		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)														---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236817445	236817445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236817445G>A	uc002vvs.2	+	11	1814	c.1219G>A	c.(1219-1221)GGG>AGG	p.G407R	AGAP1_uc002vvt.2_Missense_Mutation_p.G407R	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	407	PH.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
CXCR7	57007	broad.mit.edu	37	2	237489221	237489221	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237489221C>T	uc010fyq.2	+	3	343	c.113C>T	c.(112-114)CCC>CTC	p.P38L	CXCR7_uc002vwd.2_Missense_Mutation_p.P38L	NM_020311	NP_064707	P25106	CXCR7_HUMAN	chemokine orphan receptor 1	38	Extracellular (Potential).				interspecies interaction between organisms	integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3		Breast(86;0.000182)|Renal(207;0.00339)|all_hematologic(139;0.0048)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|all_lung(227;0.147)|all_neural(83;0.223)		Epithelial(121;8.35e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.09e-11)|Kidney(56;1.11e-07)|KIRC - Kidney renal clear cell carcinoma(57;3.03e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000176)|Lung(119;0.00468)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.118)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238262045	238262045	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238262045C>T	uc002vwl.2	-	25	6914	c.6629G>A	c.(6628-6630)GGC>GAC	p.G2210D	COL6A3_uc002vwo.2_Missense_Mutation_p.G2004D|COL6A3_uc010znj.1_Missense_Mutation_p.G1603D|COL6A3_uc002vwp.1_Missense_Mutation_p.G31D	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2210	Triple-helical region.|Collagen-like 3.				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)														---	---	---	---
LRRFIP1	9208	broad.mit.edu	37	2	238668757	238668757	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238668757C>T	uc002vxe.2	+	10	1090	c.798C>T	c.(796-798)TCC>TCT	p.S266S	LRRFIP1_uc002vxc.2_Silent_p.S456S|LRRFIP1_uc010znm.1_Silent_p.S210S|LRRFIP1_uc002vxd.2_Silent_p.S242S|LRRFIP1_uc002vxf.2_Silent_p.S210S	NM_001137552	NP_001131024	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting	266					negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|cytoskeleton|nucleus	DNA binding|double-stranded RNA binding|protein binding			breast(3)	3		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239162026	239162026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239162026C>T	uc002vyc.2	-	19	2875	c.2638G>A	c.(2638-2640)GCT>ACT	p.A880T	PER2_uc010znv.1_Missense_Mutation_p.A880T	NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	880	Pro-rich.				circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
MYEOV2	150678	broad.mit.edu	37	2	241066248	241066248	+	Missense_Mutation	SNP	G	A	A	rs137993079		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241066248G>A	uc002vyu.1	-	5	491	c.491C>T	c.(490-492)CCG>CTG	p.P164L		NM_138336	NP_612209	Q8WXC6	MYOV2_HUMAN	hypothetical protein LOC150678 isoform 1	Error:Variant_position_missing_in_Q8WXC6_after_alignment											0		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)														---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9034632	9034632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9034632G>A	uc003brf.1	-	20	3192	c.2516C>T	c.(2515-2517)ACG>ATG	p.T839M	SRGAP3_uc003brg.1_Missense_Mutation_p.T815M	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	839					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
SETD5	55209	broad.mit.edu	37	3	9483295	9483295	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9483295A>G	uc003brt.2	+	9	1264	c.829A>G	c.(829-831)ACT>GCT	p.T277A	SETD5_uc003brs.1_Missense_Mutation_p.T258A|SETD5_uc003bru.2_Missense_Mutation_p.T179A|SETD5_uc003brv.2_Missense_Mutation_p.T166A|SETD5_uc010hck.2_5'Flank|SETD5_uc003brw.1_5'Flank|SETD5_uc003brx.2_5'Flank	NM_001080517	NP_001073986	Q9C0A6	SETD5_HUMAN	SET domain containing 5	277	SET.									ovary(2)	2	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)														---	---	---	---
SLC6A1	6529	broad.mit.edu	37	3	11064133	11064133	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11064133G>T	uc010hdq.2	+	7	1104	c.693G>T	c.(691-693)AAG>AAT	p.K231N		NM_003042	NP_003033	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter	231					neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)|skin(1)	2		Ovarian(110;0.0392)		OV - Ovarian serous cystadenocarcinoma(96;0.00099)	Cocaine(DB00907)|Tiagabine(DB00906)													---	---	---	---
C3orf31	132001	broad.mit.edu	37	3	11885643	11885643	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11885643C>T	uc003bwh.2	-	2	420	c.178G>A	c.(178-180)GCA>ACA	p.A60T	C3orf31_uc003bwj.2_Missense_Mutation_p.A60T|C3orf31_uc003bwi.2_RNA|C3orf31_uc011auo.1_Missense_Mutation_p.A60T|C3orf31_uc011aup.1_RNA|C3orf31_uc010hdy.1_RNA	NM_138807	NP_620162	Q96BW9	MMP37_HUMAN	MMP37-like protein, mitochondrial precursor	60					protein import into mitochondrial matrix	extrinsic to mitochondrial inner membrane					0																		---	---	---	---
CAND2	23066	broad.mit.edu	37	3	12875478	12875478	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12875478C>T	uc003bxk.2	+	15	3757	c.3708C>T	c.(3706-3708)AGC>AGT	p.S1236S	CAND2_uc003bxj.2_Silent_p.S1119S	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	TBP-interacting protein isoform 1	1236	HEAT 26.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4																		---	---	---	---
C3orf19	51244	broad.mit.edu	37	3	14711585	14711585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14711585G>A	uc003byw.2	+	10	1188	c.1097G>A	c.(1096-1098)CGC>CAC	p.R366H	C3orf19_uc010hej.2_Missense_Mutation_p.R195H	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	366											0																		---	---	---	---
ZFYVE20	64145	broad.mit.edu	37	3	15137471	15137471	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15137471G>A	uc003bzm.1	-						ZFYVE20_uc010hek.1_Intron|ZFYVE20_uc011avn.1_Intron	NM_022340	NP_071735			FYVE-finger-containing Rab5 effector protein						blood coagulation|endosome transport|protein transport	early endosome membrane|plasma membrane	protein binding|zinc ion binding			skin(2)	2																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15749455	15749455	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15749455G>A	uc003caj.1	-	14	1576	c.1433C>T	c.(1432-1434)GCA>GTA	p.A478V	ANKRD28_uc003cai.1_Missense_Mutation_p.A324V|ANKRD28_uc011avz.1_Missense_Mutation_p.A324V|ANKRD28_uc003cak.1_RNA|ANKRD28_uc011awa.1_RNA|ANKRD28_uc003cal.1_Missense_Mutation_p.A508V|ANKRD28_uc003cam.2_Missense_Mutation_p.A511V	NM_015199	NP_056014	O15084	ANR28_HUMAN	ankyrin repeat domain 28	478	ANK 14.					nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19492689	19492689	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19492689A>G	uc003cbk.1	+	10	1813	c.1618A>G	c.(1618-1620)ATG>GTG	p.M540V	KCNH8_uc011awe.1_3'UTR|KCNH8_uc010hex.1_Missense_Mutation_p.M1V|KCNH8_uc011awf.1_3'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	540	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
NR1D2	9975	broad.mit.edu	37	3	24004097	24004097	+	Splice_Site	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24004097G>A	uc003ccs.2	+	5	1465	c.1146_splice	c.e5+1	p.L382_splice	NR1D2_uc010hfd.2_Splice_Site|NR1D2_uc011awk.1_Splice_Site_p.L307_splice	NM_005126	NP_005117			nuclear receptor subfamily 1, group D, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			urinary_tract(1)|kidney(1)|skin(1)	3																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37368531	37368531	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37368531T>C	uc003cgv.2	+	14	5458	c.5154T>C	c.(5152-5154)TAT>TAC	p.Y1718Y	GOLGA4_uc010hgr.1_Silent_p.Y1279Y|GOLGA4_uc003cgw.2_Silent_p.Y1740Y|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Silent_p.Y1599Y	NM_002078	NP_002069	Q13439	GOGA4_HUMAN	golgi autoantigen, golgin subfamily a, 4	1718	Potential.|Glu-rich.				Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
XYLB	9942	broad.mit.edu	37	3	38438615	38438615	+	Missense_Mutation	SNP	C	T	T	rs2234625		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38438615C>T	uc003cic.2	+	17	1512	c.1403C>T	c.(1402-1404)TCG>TTG	p.S468L	XYLB_uc011ayp.1_Missense_Mutation_p.S331L|XYLB_uc003cid.1_Missense_Mutation_p.S390L	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase	468					D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)														---	---	---	---
TGM4	7047	broad.mit.edu	37	3	44943299	44943299	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44943299G>T	uc003coc.3	+	8	920	c.847G>T	c.(847-849)GGC>TGC	p.G283C		NM_003241	NP_003232	P49221	TGM4_HUMAN	transglutaminase 4 (prostate)	283					peptide cross-linking|protein polyamination		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)													---	---	---	---
LIMD1	8994	broad.mit.edu	37	3	45637492	45637492	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45637492G>A	uc003coq.2	+	1	1170	c.1121G>A	c.(1120-1122)TGC>TAC	p.C374Y		NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	374					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)														---	---	---	---
CCR9	10803	broad.mit.edu	37	3	45943150	45943150	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45943150C>A	uc003coz.1	+	3	1027	c.870C>A	c.(868-870)GCC>GCA	p.A290A	LZTFL1_uc003coy.1_Intron|LZTFL1_uc011bak.1_Intron|CCR9_uc010hiv.1_Silent_p.A278A|CCR9_uc003cpa.1_Silent_p.A278A	NM_031200	NP_112477	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9 isoform A	290	Extracellular (Potential).				cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane				ovary(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)														---	---	---	---
FYCO1	79443	broad.mit.edu	37	3	46009351	46009351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46009351C>T	uc003cpb.3	-	8	1681	c.1475G>A	c.(1474-1476)CGG>CAG	p.R492Q	FYCO1_uc011bal.1_Missense_Mutation_p.R492Q	NM_024513	NP_078789	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	492	Potential.				transport	integral to membrane	metal ion binding|protein binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)														---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48699642	48699642	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48699642G>A	uc003cul.2	-	1	707	c.426C>T	c.(424-426)TGC>TGT	p.C142C	CELSR3_uc003cuf.1_Silent_p.C212C	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	142	Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
QARS	5859	broad.mit.edu	37	3	49139862	49139862	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49139862T>C	uc003cvx.2	-	6	565	c.560A>G	c.(559-561)AAG>AGG	p.K187R	QARS_uc011bcd.1_Missense_Mutation_p.K42R|QARS_uc003cvy.2_Missense_Mutation_p.K42R|QARS_uc011bce.1_Missense_Mutation_p.K176R|QARS_uc011bcf.1_Missense_Mutation_p.K187R	NM_005051	NP_005042	P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	187					glutaminyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|glutamine-tRNA ligase activity|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)													---	---	---	---
CCDC71	64925	broad.mit.edu	37	3	49200881	49200881	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49200881T>C	uc003cwg.3	-	2	899	c.761A>G	c.(760-762)CAC>CGC	p.H254R		NM_022903	NP_075054	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	254										ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49688509	49688509	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49688509G>A	uc003cxe.3	+	4	2097	c.1983G>A	c.(1981-1983)GCG>GCA	p.A661A		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	661					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)														---	---	---	---
GMPPB	29925	broad.mit.edu	37	3	49759801	49759801	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49759801G>A	uc003cxk.1	-						AMIGO3_uc003cxj.2_5'Flank|GMPPB_uc003cxl.1_Intron	NM_021971	NP_068806			GDP-mannose pyrophosphorylase B isoform 2						dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity				0				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
MON1A	84315	broad.mit.edu	37	3	49947986	49947986	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49947986C>T	uc003cxz.2	-	4	1362	c.1236G>A	c.(1234-1236)GCG>GCA	p.A412A	MON1A_uc003cya.2_Silent_p.A250A|MON1A_uc003cyb.2_Silent_p.A250A	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	315							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
NISCH	11188	broad.mit.edu	37	3	52521801	52521801	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52521801C>T	uc011beg.1	+	17	2365	c.2293C>T	c.(2293-2295)CAT>TAT	p.H765Y	NISCH_uc003ded.3_Missense_Mutation_p.H765Y|NISCH_uc003dee.3_Missense_Mutation_p.H254Y|NISCH_uc003deg.1_RNA	NM_007184	NP_009115	Q9Y2I1	NISCH_HUMAN	nischarin	765	Interaction with LIMK (By similarity).|Interaction with ITGA5 (By similarity).|Interaction with PAK1 (By similarity).				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)														---	---	---	---
NT5DC2	64943	broad.mit.edu	37	3	52559266	52559266	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52559266G>A	uc003deo.2	-	11	1478	c.1054C>T	c.(1054-1056)CGC>TGC	p.R352C	NT5DC2_uc003dem.2_Missense_Mutation_p.R222C|NT5DC2_uc003den.2_Missense_Mutation_p.R389C|NT5DC2_uc010hmi.2_Missense_Mutation_p.R364C|NT5DC2_uc010hmj.2_Missense_Mutation_p.R168C	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	352							hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52595943	52595943	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52595943G>T	uc003des.2	-	25	4140	c.4128C>A	c.(4126-4128)GGC>GGA	p.G1376G	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Silent_p.G1376G|PBRM1_uc003der.2_Silent_p.G1344G|PBRM1_uc003det.2_Silent_p.G1391G|PBRM1_uc003deu.2_Silent_p.G1391G|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Silent_p.G1376G|PBRM1_uc010hmk.1_Silent_p.G1351G|PBRM1_uc003dey.2_Silent_p.G1324G|PBRM1_uc003dez.1_Silent_p.G1375G	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1376					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
RFT1	91869	broad.mit.edu	37	3	53156573	53156573	+	Silent	SNP	G	T	T	rs146536827		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53156573G>T	uc003dgj.2	-	4	327	c.273C>A	c.(271-273)CCC>CCA	p.P91P	RFT1_uc003dgk.2_Silent_p.P52P	NM_052859	NP_443091	Q96AA3	RFT1_HUMAN	RFT1 homolog	91	Helical; (Potential).				carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)														---	---	---	---
IL17RB	55540	broad.mit.edu	37	3	53899191	53899191	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53899191C>T	uc003dha.2	+	11	1404	c.1365C>T	c.(1363-1365)GAC>GAT	p.D455D		NM_018725	NP_061195	Q9NRM6	I17RB_HUMAN	interleukin 17B receptor precursor	455	SEFIR.|Cytoplasmic (Potential).			Missing (in Ref. 2; AA sequence).	defense response|regulation of cell growth	extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)|pancreas(1)	3				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)														---	---	---	---
LRTM1	57408	broad.mit.edu	37	3	54952709	54952709	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54952709T>A	uc003dhl.2	-	3	949	c.815A>T	c.(814-816)GAG>GTG	p.E272V	CACNA2D3_uc003dhf.2_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_020678	NP_065729	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	272	Extracellular (Potential).					integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)														---	---	---	---
FAM107A	11170	broad.mit.edu	37	3	58555555	58555555	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58555555G>A	uc003dkm.2	-	3	592	c.33C>T	c.(31-33)GAC>GAT	p.D11D	FAM107A_uc003dko.2_Silent_p.D42D|FAM107A_uc003dkn.2_Silent_p.D11D|FAM107A_uc010hnm.2_Silent_p.D39D|FAM107A_uc003dkp.1_Silent_p.D11D	NM_007177	NP_009108	O95990	F107A_HUMAN	downregulated in renal cell carcinoma	11					regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66467669	66467669	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66467669G>A	uc003dmx.2	-	4	401	c.387C>T	c.(385-387)AGC>AGT	p.S129S	LRIG1_uc010hnz.2_5'UTR|LRIG1_uc010hoa.2_Silent_p.S129S	NM_015541	NP_056356	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like	129	Extracellular (Potential).|LRR 3.					integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)														---	---	---	---
KBTBD8	84541	broad.mit.edu	37	3	67053771	67053771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67053771C>T	uc003dmy.2	+	3	433	c.380C>T	c.(379-381)GCT>GTT	p.A127V	KBTBD8_uc011bfv.1_Intron	NM_032505	NP_115894	Q8NFY9	KBTB8_HUMAN	T-cell activation kelch repeat protein	127										ovary(2)|large_intestine(1)|breast(1)	4		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)														---	---	---	---
GXYLT2	727936	broad.mit.edu	37	3	72971426	72971426	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72971426A>G	uc003dpg.2	+	3	540	c.540A>G	c.(538-540)GGA>GGG	p.G180G		NM_001080393	NP_001073862	A0PJZ3	GXLT2_HUMAN	glycosyltransferase 8 domain containing 4	180	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74420384	74420384	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74420384C>T	uc003dpm.1	-	5	701	c.621G>A	c.(619-621)GTG>GTA	p.V207V		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	207	Ig-like C2-type 2.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)														---	---	---	---
VGLL3	389136	broad.mit.edu	37	3	87027811	87027811	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87027811G>T	uc003dqn.2	-	2	632	c.268C>A	c.(268-270)CTT>ATT	p.L90I		NM_016206	NP_057290	A8MV65	VGLL3_HUMAN	colon carcinoma related protein	90					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)														---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89499360	89499360	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89499360C>T	uc003dqy.2	+	15	2755	c.2530C>T	c.(2530-2532)CCA>TCA	p.P844S	EPHA3_uc010hon.1_RNA	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	844	Cytoplasmic (Potential).|Protein kinase.					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)			---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	100949961	100949961	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100949961G>A	uc003duq.1	-	16	3465	c.3262C>T	c.(3262-3264)CGA>TGA	p.R1088*	IMPG2_uc011bhe.1_Nonsense_Mutation_p.R951*|IMPG2_uc010hpj.1_Intron	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1088	Extracellular (Potential).|EGF-like 2.|Hyaluronan-binding motif involved in chondroitin sulfate C-binding (By similarity).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108183492	108183492	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108183492G>A	uc003dxa.1	-	16	1841	c.1784C>T	c.(1783-1785)GCA>GTA	p.A595V		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	595	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113092397	113092397	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113092397A>G	uc003eae.1	-	18	2351	c.2305T>C	c.(2305-2307)TAT>CAT	p.Y769H		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	769										central_nervous_system(1)	1																		---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113285337	113285337	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113285337G>A	uc003eak.2	+	2	944	c.293G>A	c.(292-294)CGC>CAC	p.R98H	SIDT1_uc011bif.1_RNA|SIDT1_uc003eaj.1_Missense_Mutation_p.R98H|SIDT1_uc011big.1_5'UTR	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor	98	Extracellular (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113378994	113378994	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113378994T>G	uc003eam.2	-	7	1946	c.1535A>C	c.(1534-1536)CAG>CCG	p.Q512P	KIAA2018_uc003eal.2_Missense_Mutation_p.Q456P	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	512					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3																		---	---	---	---
KIAA1407	57577	broad.mit.edu	37	3	113697052	113697052	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113697052C>T	uc003eax.2	-	16	2734	c.2587G>A	c.(2587-2589)GCA>ACA	p.A863T	KIAA1407_uc011bin.1_RNA	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577	863										ovary(2)	2																		---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	121132132	121132132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121132132C>T	uc003eec.3	+	25	3288	c.3148C>T	c.(3148-3150)CGG>TGG	p.R1050W	STXBP5L_uc011bji.1_Missense_Mutation_p.R1026W	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	1050	WD 14.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
CD86	942	broad.mit.edu	37	3	121825268	121825268	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825268T>C	uc003eet.2	+	4	740	c.624T>C	c.(622-624)CCT>CCC	p.P208P	CD86_uc011bjo.1_Silent_p.P126P|CD86_uc011bjp.1_Silent_p.P96P|CD86_uc003eeu.2_Silent_p.P202P	NM_175862	NP_787058	P42081	CD86_HUMAN	CD86 antigen isoform 1	208	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)													---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	124951370	124951370	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124951370G>A	uc003ehx.3	-	9	2686	c.2200C>T	c.(2200-2202)CGT>TGT	p.R734C	SLC12A8_uc003ehw.3_Intron|ZNF148_uc003ehz.3_Missense_Mutation_p.R734C|ZNF148_uc010hsa.2_Missense_Mutation_p.R734C|ZNF148_uc003eia.3_Missense_Mutation_p.R734C|ZNF148_uc003ehy.2_Missense_Mutation_p.R71C	NM_021964	NP_068799	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	734					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																		---	---	---	---
TXNRD3IT1	645840	broad.mit.edu	37	3	126291169	126291169	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126291169C>A	uc003ejc.2	-	3	697	c.218G>T	c.(217-219)AGG>ATG	p.R73M		NM_001039783	NP_001034872	Q6F5E7	TR3N_HUMAN	thioredoxin reductase 3 intronic transcript 1	73											0																		---	---	---	---
TPRA1	131601	broad.mit.edu	37	3	127292459	127292459	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127292459C>A	uc003ejl.2	-	10	1318	c.1027G>T	c.(1027-1029)GGG>TGG	p.G343W	TPRA1_uc003ejm.2_RNA|TPRA1_uc003ejo.2_Missense_Mutation_p.G343W|TPRA1_uc010hsk.2_Missense_Mutation_p.R288L|TPRA1_uc003ejn.2_Missense_Mutation_p.G343W	NM_016372	NP_057456	Q86W33	TPRA1_HUMAN	G protein-coupled receptor 175 isoform 1	343					aging|lipid metabolic process	integral to membrane	G-protein coupled receptor activity				0																		---	---	---	---
MGLL	11343	broad.mit.edu	37	3	127454620	127454620	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127454620G>A	uc003ejx.2	-						MGLL_uc003ejw.2_Intron|MGLL_uc011bko.1_Intron|MGLL_uc010hsp.1_Intron|MGLL_uc003ejv.2_Silent_p.L28L	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																		---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128621403	128621403	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128621403T>C	uc003ela.3	+	9	1092	c.890T>C	c.(889-891)ATG>ACG	p.M297T	ACAD9_uc010hsw.1_Missense_Mutation_p.M174T|ACAD9_uc011bks.1_Missense_Mutation_p.M174T|ACAD9_uc003elb.2_Missense_Mutation_p.M174T|ACAD9_uc003elc.1_Missense_Mutation_p.M115T|ACAD9_uc003eld.1_RNA|ACAD9_uc003ele.2_5'Flank	NM_014049	NP_054768	Q9H845	ACAD9_HUMAN	acyl-Coenzyme A dehydrogenase family, member 9	297						mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
NPHP3	27031	broad.mit.edu	37	3	132403635	132403635	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132403635T>C	uc003epe.1	-	24	3410	c.3333A>G	c.(3331-3333)ACA>ACG	p.T1111T	NPHP3_uc003eoz.1_5'UTR|NPHP3_uc003epd.1_Silent_p.T353T	NM_153240	NP_694972	Q7Z494	NPHP3_HUMAN	nephrocystin 3	1111	TPR 7.				maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1																		---	---	---	---
CEP63	80254	broad.mit.edu	37	3	134278244	134278244	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134278244G>A	uc003eqo.1	+	15	2375	c.1926G>A	c.(1924-1926)ATG>ATA	p.M642I	CEP63_uc003eql.1_Intron|CEP63_uc003eqm.2_Intron|CEP63_uc003eqn.1_Intron	NM_025180	NP_079456	Q96MT8	CEP63_HUMAN	centrosomal protein 63 isoform a	642					cell division|DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitosis|signal transduction in response to DNA damage|spindle assembly	centrosome|cytosol|spindle pole	protein binding			ovary(1)	1																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138456740	138456740	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138456740G>T	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																		---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141161920	141161920	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141161920A>C	uc003etw.2	+	8	1672	c.690A>C	c.(688-690)GAA>GAC	p.E230D	ZBTB38_uc010hun.2_Missense_Mutation_p.E227D|ZBTB38_uc010huo.2_Missense_Mutation_p.E230D|ZBTB38_uc003ety.2_Missense_Mutation_p.E230D|ZBTB38_uc010hup.2_Missense_Mutation_p.E231D	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	230					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143292918	143292918	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143292918T>C	uc003evn.2	-							NM_173653	NP_775924			solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3																		---	---	---	---
FAM194A	131831	broad.mit.edu	37	3	150416589	150416589	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150416589T>C	uc003eyg.2	-	3	599	c.542A>G	c.(541-543)AAA>AGA	p.K181R	FAM194A_uc003eyh.2_Missense_Mutation_p.K35R	NM_152394	NP_689607	Q7L0X2	F194A_HUMAN	hypothetical protein LOC131831	181										skin(2)|ovary(1)	3																		---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157920896	157920896	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157920896G>A	uc003fbt.2	+	4	467	c.356G>A	c.(355-357)CGT>CAT	p.R119H	RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Missense_Mutation_p.R119H|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	119	Arg/Ser-rich.				nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167246886	167246886	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167246886A>C	uc003fev.1	-	10	1610	c.1304T>G	c.(1303-1305)CTT>CGT	p.L435R	WDR49_uc003feu.1_Missense_Mutation_p.L260R|WDR49_uc011bpd.1_Missense_Mutation_p.L499R|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	435	WD 7.									large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
GOLIM4	27333	broad.mit.edu	37	3	167750557	167750557	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167750557A>G	uc003ffe.2	-	9	1271	c.927T>C	c.(925-927)CAT>CAC	p.H309H	GOLIM4_uc011bpe.1_Silent_p.H309H|GOLIM4_uc011bpf.1_Silent_p.H281H|GOLIM4_uc011bpg.1_Silent_p.H281H	NM_014498	NP_055313	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	309	Lumenal (Potential).				transport	cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus				breast(4)|skin(1)	5																		---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174814591	174814591	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174814591G>A	uc003fit.2	+	2	142	c.55G>A	c.(55-57)GCC>ACC	p.A19T	NAALADL2_uc003fiu.1_Missense_Mutation_p.A12T	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	19	Cytoplasmic (Potential).				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)														---	---	---	---
TBL1XR1	79718	broad.mit.edu	37	3	176756101	176756101	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176756101C>T	uc003fiw.3	-	11	1307	c.1047G>A	c.(1045-1047)ACG>ACA	p.T349T	TBL1XR1_uc003fix.3_Silent_p.T349T|TBL1XR1_uc011bpz.1_Silent_p.T21T	NM_024665	NP_078941	Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	349	WD 5.				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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183471920	183471920	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183471920C>A	uc003fly.2	+	11	1352	c.1157C>A	c.(1156-1158)CCA>CAA	p.P386Q		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	386					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
EIF2B5	8893	broad.mit.edu	37	3	183859721	183859721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183859721G>A	uc003fmp.2	+	8	1529	c.1165G>A	c.(1165-1167)GTG>ATG	p.V389M	EIF2B5_uc003fmq.2_Missense_Mutation_p.V110M|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	389					astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
ADIPOQ	9370	broad.mit.edu	37	3	186572260	186572260	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186572260A>G	uc003fra.2	+	3	586	c.502A>G	c.(502-504)ATG>GTG	p.M168V	ADIPOQ_uc010hyy.2_Missense_Mutation_p.M168V	NM_004797	NP_004788	Q15848	ADIPO_HUMAN	adiponectin precursor	168	C1q.				brown fat cell differentiation|cellular response to drug|cellular response to insulin stimulus|detection of oxidative stress|fatty acid beta-oxidation|generation of precursor metabolites and energy|glucose homeostasis|glucose metabolic process|low-density lipoprotein particle clearance|negative regulation of blood pressure|negative regulation of DNA biosynthetic process|negative regulation of ERK1 and ERK2 cascade|negative regulation of eukaryotic cell surface binding|negative regulation of fat cell differentiation|negative regulation of gluconeogenesis|negative regulation of granulocyte differentiation|negative regulation of heterotypic cell-cell adhesion|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of intracellular protein transport|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|negative regulation of macrophage differentiation|negative regulation of MAP kinase activity|negative regulation of phagocytosis|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein autophosphorylation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|negative regulation of synaptic transmission|negative regulation of transcription, DNA-dependent|negative regulation of tumor necrosis factor production|negative regulation of tumor necrosis factor-mediated signaling pathway|positive regulation of cAMP-dependent protein kinase activity|positive regulation of cholesterol efflux|positive regulation of fatty acid metabolic process|positive regulation of glucose import|positive regulation of glycogen (starch) synthase activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of metanephric glomerular visceral epithelial cell development|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myeloid cell apoptosis|positive regulation of protein kinase A signaling cascade|positive regulation of renal albumin absorption|protein homooligomerization|protein localization in plasma membrane|response to glucose stimulus|response to tumor necrosis factor	collagen|endoplasmic reticulum|extracellular space	cytokine activity|eukaryotic cell surface binding|hormone activity|protein homodimerization activity			ovary(1)	1	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)														---	---	---	---
LPP	4026	broad.mit.edu	37	3	188327061	188327061	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188327061A>G	uc003frs.1	+	6	788	c.542A>G	c.(541-543)AAA>AGA	p.K181R	LPP_uc011bsg.1_Missense_Mutation_p.K181R|LPP_uc011bsi.1_Missense_Mutation_p.K181R|LPP_uc003frt.2_Missense_Mutation_p.K181R|LPP_uc011bsj.1_Missense_Mutation_p.K18R	NM_005578	NP_005569	Q93052	LPP_HUMAN	LIM domain containing preferred translocation	181	Pro-rich.				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								---	---	---	---
IL1RAP	3556	broad.mit.edu	37	3	190366420	190366420	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190366420C>T	uc003fsm.1	+	12	1845	c.1639C>T	c.(1639-1641)CCA>TCA	p.P547S	IL1RAP_uc010hzg.1_Missense_Mutation_p.P547S|IL1RAP_uc003fsn.1_RNA|IL1RAP_uc003fso.1_Missense_Mutation_p.P547S|IL1RAP_uc003fsp.1_RNA|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173	Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein isoform	547	Cytoplasmic (Potential).|TIR.				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)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193160315	193160315	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193160315G>A	uc003ftd.2	-	19	2291	c.2183C>T	c.(2182-2184)GCC>GTC	p.A728V	ATP13A4_uc003fte.1_Missense_Mutation_p.A728V|ATP13A4_uc011bsr.1_Missense_Mutation_p.A199V|ATP13A4_uc010hzi.2_RNA	NM_032279	NP_115655	Q4VNC1	AT134_HUMAN	ATPase type 13A4	728	Extracellular (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
GP5	2814	broad.mit.edu	37	3	194118478	194118478	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194118478C>T	uc003ftv.1	-	2	565	c.534G>A	c.(532-534)TCG>TCA	p.S178S		NM_004488	NP_004479	P40197	GPV_HUMAN	glycoprotein V (platelet) precursor	178	Extracellular (Potential).|LRR 5.				blood coagulation, intrinsic pathway|cell adhesion|platelet activation	integral to plasma membrane				skin(2)|breast(1)	3	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)														---	---	---	---
PAK2	5062	broad.mit.edu	37	3	196554107	196554107	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196554107A>G	uc003fwy.3	+	14	1713	c.1391A>G	c.(1390-1392)CAG>CGG	p.Q464R		NM_002577	NP_002568	Q13177	PAK2_HUMAN	p21-activated kinase 2	464	Protein kinase.				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)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	843764	843764	+	Silent	SNP	C	T	T	rs146290503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:843764C>T	uc003gbm.3	-	27	3949	c.3750G>A	c.(3748-3750)ACG>ACA	p.T1250T	GAK_uc003gbn.3_Silent_p.T1171T|GAK_uc003gbk.3_Silent_p.T47T|GAK_uc010ibi.2_Silent_p.T475T|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Silent_p.T1103T	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	1250	J.				cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1373950	1373950	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1373950C>T	uc003gde.3	+	11	2131	c.1684C>T	c.(1684-1686)CCT>TCT	p.P562S	KIAA1530_uc010ibv.2_Missense_Mutation_p.P113S	NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	562											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2951844	2951844	+	Missense_Mutation	SNP	C	A	A	rs145122268		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2951844C>A	uc003ggj.1	-	8	1171	c.1099G>T	c.(1099-1101)GGG>TGG	p.G367W	C4orf10_uc003ggh.2_Intron|C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_Missense_Mutation_p.G113W|NOP14_uc003ggk.3_Missense_Mutation_p.G367W|NOP14_uc003ggl.2_Missense_Mutation_p.G367W	NM_003703	NP_003694	P78316	NOP14_HUMAN	probable nucleolar complex protein 14	367					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
HTT	3064	broad.mit.edu	37	4	3224185	3224185	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3224185G>A	uc011bvq.1	+	55	7592	c.7447G>A	c.(7447-7449)GTG>ATG	p.V2483M		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	2481					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5469805	5469805	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5469805C>T	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871			serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5567005	5567005	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5567005C>A	uc003gij.2	-	21	3693	c.3639G>T	c.(3637-3639)TGG>TGT	p.W1213C	EVC2_uc011bwb.1_Missense_Mutation_p.W653C|EVC2_uc003gik.2_Missense_Mutation_p.W1133C	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	1213						integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
WFS1	7466	broad.mit.edu	37	4	6303640	6303640	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6303640C>T	uc003giy.2	+	8	2284	c.2118C>T	c.(2116-2118)TAC>TAT	p.Y706Y	WFS1_uc003gix.2_Silent_p.Y706Y|WFS1_uc003giz.2_Silent_p.Y524Y	NM_001145853	NP_001139325	O76024	WFS1_HUMAN	wolframin	706					endoplasmic reticulum calcium ion homeostasis|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|glucose homeostasis|kidney development|negative regulation of neuron apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|polyubiquitinated misfolded protein transport|positive regulation of calcium ion transport|positive regulation of growth|positive regulation of protein ubiquitination|positive regulation of proteolysis|protein stabilization|renal water homeostasis|sensory perception of sound|visual perception	dendrite|integral to endoplasmic reticulum membrane	activating transcription factor binding|ATPase binding|transporter activity|ubiquitin protein ligase binding			central_nervous_system(2)	2				Colorectal(103;0.0512)														---	---	---	---
MIR95	407052	broad.mit.edu	37	4	8007067	8007067	+	RNA	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8007067G>A	hsa-mir-95|MI0000097	-			c.42G>A			ABLIM2_uc003gkk.2_Intron|ABLIM2_uc003gkl.2_Intron|ABLIM2_uc003gkj.3_Intron|ABLIM2_uc003gko.2_Intron|ABLIM2_uc003gkm.3_Intron|ABLIM2_uc003gkp.2_Intron|ABLIM2_uc003gkq.2_Intron|ABLIM2_uc003gkr.2_Intron																	0																		---	---	---	---
DRD5	1816	broad.mit.edu	37	4	9783925	9783925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9783925C>T	uc003gmb.3	+	1	668	c.272C>T	c.(271-273)GCG>GTG	p.A91V		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	91	Helical; Name=2; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)													---	---	---	---
ZNF518B	85460	broad.mit.edu	37	4	10446426	10446426	+	Silent	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10446426A>C	uc003gmn.2	-	3	2014	c.1527T>G	c.(1525-1527)GCT>GCG	p.A509A		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	509					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
BOD1L	259282	broad.mit.edu	37	4	13604645	13604645	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13604645C>A	uc003gmz.1	-	10	3996	c.3879G>T	c.(3877-3879)AGG>AGT	p.R1293S	BOD1L_uc010idr.1_Missense_Mutation_p.R630S	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division	1293							DNA binding			ovary(5)|breast(1)	6																		---	---	---	---
CPEB2	132864	broad.mit.edu	37	4	15009022	15009022	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15009022C>T	uc003gni.1	+	2	532	c.445C>T	c.(445-447)CGT>TGT	p.R149C	CPEB2_uc003gnj.1_Missense_Mutation_p.R149C|CPEB2_uc003gnk.1_Missense_Mutation_p.R149C|CPEB2_uc003gnl.1_Missense_Mutation_p.R149C|CPEB2_uc003gnm.1_Missense_Mutation_p.R149C|CPEB2_uc003gnn.1_Missense_Mutation_p.R149C	NM_182485	NP_872291	Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding	149					regulation of translation	cytoplasm	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
DCAF16	54876	broad.mit.edu	37	4	17805438	17805438	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17805438T>C	uc003gpn.2	-	3	1388	c.327A>G	c.(325-327)CCA>CCG	p.P109P	DCAF16_uc003gpo.2_RNA	NM_017741	NP_060211	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	109						CUL4 RING ubiquitin ligase complex				ovary(1)	1																		---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27010595	27010595	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27010595A>C	uc003gsh.3	+	11	1961	c.1745A>C	c.(1744-1746)GAC>GCC	p.D582A	STIM2_uc003gsg.3_Missense_Mutation_p.D574A|STIM2_uc010iex.2_Missense_Mutation_p.D574A|STIM2_uc010iey.2_Missense_Mutation_p.D198A	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	487	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39254779	39254779	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39254779G>C	uc003gtv.2	+	25	2897	c.2743G>C	c.(2743-2745)GTT>CTT	p.V915L	WDR19_uc011byi.1_Missense_Mutation_p.V755L|WDR19_uc003gtw.1_Missense_Mutation_p.V512L	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	915	TPR 4.				cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39929681	39929681	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39929681T>G	uc003guv.3	-	3	782	c.242A>C	c.(241-243)AAC>ACC	p.N81T	PDS5A_uc010ifo.2_Missense_Mutation_p.N41T|PDS5A_uc003guw.3_Missense_Mutation_p.N81T	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	81					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	40827943	40827943	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40827943C>T	uc003gvl.2	-	15	2404	c.1774G>A	c.(1774-1776)GTG>ATG	p.V592M	APBB2_uc010ifu.2_Missense_Mutation_p.V164M|APBB2_uc003gvm.2_Missense_Mutation_p.V570M|APBB2_uc003gvn.2_Missense_Mutation_p.V593M|APBB2_uc003gvk.2_Missense_Mutation_p.V44M	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	592	PID 2.				cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	40832595	40832595	+	Splice_Site	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40832595C>A	uc003gvl.2	-	13	2157	c.1527_splice	c.e13-1	p.R509_splice	APBB2_uc010ifu.2_Splice_Site_p.R81_splice|APBB2_uc003gvm.2_Splice_Site_p.R488_splice|APBB2_uc003gvn.2_Splice_Site_p.R510_splice|APBB2_uc003gvk.2_Splice_Site	NM_173075	NP_775098			amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
GUF1	60558	broad.mit.edu	37	4	44699460	44699460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44699460G>A	uc003gww.3	+	16	2078	c.1871G>A	c.(1870-1872)TGT>TAT	p.C624Y	GUF1_uc011bza.1_Missense_Mutation_p.C31Y	NM_021927	NP_068746	Q8N442	GUF1_HUMAN	GUF1 GTPase homolog	624					translation	mitochondrial inner membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48559087	48559087	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48559087G>A	uc003gyh.1	-	35	4779	c.4174C>T	c.(4174-4176)CTT>TTT	p.L1392F	FRYL_uc003gyk.2_Missense_Mutation_p.L1392F|FRYL_uc003gyg.1_Missense_Mutation_p.L88F|FRYL_uc003gyi.1_Missense_Mutation_p.L281F	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1392					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
KDR	3791	broad.mit.edu	37	4	55958789	55958789	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55958789G>A	uc003has.2	-	22	3366	c.3064C>T	c.(3064-3066)CGA>TGA	p.R1022*	KDR_uc003hat.1_Nonsense_Mutation_p.R1022*	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	1022	Protein kinase.|Cytoplasmic (Potential).				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)			---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57244433	57244433	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57244433G>A	uc003hbn.2	-	4	702	c.549C>T	c.(547-549)CAC>CAT	p.H183H	AASDH_uc010ihb.2_5'UTR|AASDH_uc011caa.1_Silent_p.H30H|AASDH_uc003hbo.2_Silent_p.H83H|AASDH_uc011cab.1_Intron|AASDH_uc010ihc.2_Silent_p.H183H|AASDH_uc003hbp.2_Silent_p.H183H	NM_181806	NP_861522	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	183					fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)																---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69195805	69195805	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69195805C>A	uc003hdx.2	-	9	1617	c.1264G>T	c.(1264-1266)GGA>TGA	p.G422*	YTHDC1_uc003hdy.2_Nonsense_Mutation_p.G404*	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	422	YTH.									upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
ENAM	10117	broad.mit.edu	37	4	71508780	71508780	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71508780C>T	uc011caw.1	+	9	1918	c.1637C>T	c.(1636-1638)GCT>GTT	p.A546V		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	546					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)															---	---	---	---
ENAM	10117	broad.mit.edu	37	4	71509090	71509090	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71509090C>T	uc011caw.1	+	9	2228	c.1947C>T	c.(1945-1947)GTC>GTT	p.V649V		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	649					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)															---	---	---	---
ENAM	10117	broad.mit.edu	37	4	71509960	71509960	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71509960G>T	uc011caw.1	+	9	3098	c.2817G>T	c.(2815-2817)AGG>AGT	p.R939S		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	939					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)															---	---	---	---
G3BP2	9908	broad.mit.edu	37	4	76587173	76587173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76587173G>A	uc003hir.2	-	2	202	c.37C>T	c.(37-39)CGG>TGG	p.R13W	G3BP2_uc003his.2_Missense_Mutation_p.R13W|G3BP2_uc003hit.2_Missense_Mutation_p.R13W	NM_012297	NP_036429	Q9UN86	G3BP2_HUMAN	Ras-GTPase activating protein SH3 domain-binding	13	NTF2.				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)															---	---	---	---
SCARB2	950	broad.mit.edu	37	4	77095334	77095334	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77095334C>A	uc003hju.1	-	7	1296	c.957G>T	c.(955-957)CTG>CTT	p.L319L	SCARB2_uc011cbu.1_Silent_p.L176L	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	319	Lumenal (Potential).				cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)															---	---	---	---
SCARB2	950	broad.mit.edu	37	4	77095377	77095377	+	Missense_Mutation	SNP	G	A	A	rs148588727	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77095377G>A	uc003hju.1	-	7	1253	c.914C>T	c.(913-915)ACG>ATG	p.T305M	SCARB2_uc011cbu.1_Missense_Mutation_p.T162M	NM_005506	NP_005497	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	305	Lumenal (Potential).				cell adhesion|protein targeting to lysosome	integral to plasma membrane|lysosomal lumen|lysosomal membrane|membrane fraction	enzyme binding|receptor activity				0			Lung(101;0.196)															---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77283437	77283437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77283437C>T	uc003hkb.3	-	12	2015	c.1862G>A	c.(1861-1863)CGG>CAG	p.R621Q		NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	621	Potential.									skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
ANKRD56	345079	broad.mit.edu	37	4	77816758	77816758	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77816758T>G	uc003hki.2	-	1	2245	c.2245A>C	c.(2245-2247)AGC>CGC	p.S749R		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	749											0																		---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85645698	85645698	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85645698T>C	uc003hpd.2	-	46	7730	c.7322A>G	c.(7321-7323)TAC>TGC	p.Y2441C	WDFY3_uc003hpe.1_Missense_Mutation_p.Y52C	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2441						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)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87680177	87680177	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87680177T>C	uc003hpz.2	+	23	3984	c.3504T>C	c.(3502-3504)CCT>CCC	p.P1168P	PTPN13_uc003hpy.2_Silent_p.P1168P|PTPN13_uc003hqa.2_Silent_p.P1149P|PTPN13_uc003hqb.2_Silent_p.P977P	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	1168	PDZ 1.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88104415	88104415	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88104415T>C	uc011cdb.1	-	4	1277	c.892A>G	c.(892-894)AGC>GGC	p.S298G	KLHL8_uc003hql.1_Missense_Mutation_p.S298G|KLHL8_uc003hqm.1_Missense_Mutation_p.S222G|KLHL8_uc003hqn.1_Missense_Mutation_p.S115G|KLHL8_uc010ikj.1_Intron	NM_020803	NP_065854	Q9P2G9	KLHL8_HUMAN	kelch-like 8	298											0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
IBSP	3381	broad.mit.edu	37	4	88732603	88732603	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88732603C>T	uc003hqx.3	+	7	593	c.495C>T	c.(493-495)AGC>AGT	p.S165S		NM_004967	NP_004958	P21815	SIAL_HUMAN	integrin-binding sialoprotein precursor	165	Asp/Glu-rich (acidic).				biomineral tissue development|cell adhesion|ossification						0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)														---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94159650	94159650	+	Intron	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94159650A>C	uc011cdt.1	+						GRID2_uc011cdu.1_Intron|GRID2_uc010ikz.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)													---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99407915	99407915	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99407915G>A	uc003hub.2	-	3	603	c.253C>T	c.(253-255)CGG>TGG	p.R85W	TSPAN5_uc011cdz.1_Missense_Mutation_p.R14W	NM_005723	NP_005714	P62079	TSN5_HUMAN	transmembrane 4 superfamily member 9	85	Cytoplasmic (Potential).					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99823101	99823101	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99823101T>C	uc003hue.2	-	2	1574	c.51A>G	c.(49-51)ACA>ACG	p.T17T	EIF4E_uc011cea.1_Silent_p.T37T|EIF4E_uc011ceb.1_Silent_p.T17T|EIF4E_uc011cec.1_Silent_p.T17T	NM_001968	NP_001959	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	17					G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			lung(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)														---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100530094	100530094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100530094G>A	uc003hvc.3	+	13	1985	c.1729G>A	c.(1729-1731)GCC>ACC	p.A577T	MTTP_uc011cej.1_Missense_Mutation_p.A604T	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	577	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
CYP2U1	113612	broad.mit.edu	37	4	108870669	108870669	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108870669G>A	uc003hyp.2	+	4	1535	c.1452G>A	c.(1450-1452)GGG>GGA	p.G484G	CYP2U1_uc011cfi.1_Silent_p.G275G	NM_183075	NP_898898	Q7Z449	CP2U1_HUMAN	cytochrome P450, family 2, subfamily U,	484					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000128)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109765696	109765696	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109765696G>T	uc003hze.1	-	29	2139	c.1608C>A	c.(1606-1608)CCC>CCA	p.P536P	COL25A1_uc003hzg.2_Silent_p.P536P|COL25A1_uc003hzd.2_RNA|COL25A1_uc003hzf.2_Silent_p.P294P	NM_198721	NP_942014	Q9BXS0	COPA1_HUMAN	collagen, type XXV, alpha 1 isoform 1	536	Extracellular (Potential).					collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
CFI	3426	broad.mit.edu	37	4	110673647	110673647	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110673647A>T	uc003hzr.3	-	8	1125	c.917T>A	c.(916-918)ATT>AAT	p.I306N	CFI_uc003hzq.2_Missense_Mutation_p.I103N|CFI_uc011cft.1_Missense_Mutation_p.I314N|CFI_uc003hzs.3_Missense_Mutation_p.I299N	NM_000204	NP_000195	P05156	CFAI_HUMAN	complement factor I preproprotein	306					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)														---	---	---	---
PITX2	5308	broad.mit.edu	37	4	111539779	111539779	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111539779G>A	uc003iad.2	-	5	1038	c.456C>T	c.(454-456)TGC>TGT	p.C152C	PITX2_uc003iac.2_Silent_p.C159C|PITX2_uc003iae.2_Silent_p.C106C|PITX2_uc010iml.2_Silent_p.C23C|PITX2_uc003iaf.2_Silent_p.C152C	NM_153426	NP_700475	Q99697	PITX2_HUMAN	paired-like homeodomain transcription factor 2	152					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)														---	---	---	---
UGT8	7368	broad.mit.edu	37	4	115597196	115597196	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115597196C>A	uc003ibs.2	+	6	1900	c.1378C>A	c.(1378-1380)CTA>ATA	p.L460I	UGT8_uc003ibt.2_Missense_Mutation_p.L460I|UGT8_uc011cge.1_RNA	NM_001128174	NP_001121646	Q16880	CGT_HUMAN	UDP-galactose-ceramide galactosyltransferase 8	460					central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)														---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126328260	126328260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126328260G>A	uc003ifj.3	+	3	5533	c.5533G>A	c.(5533-5535)GTG>ATG	p.V1845M	FAT4_uc011cgp.1_Missense_Mutation_p.V143M	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1845	Cadherin 18.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126411935	126411935	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126411935G>T	uc003ifj.3	+	17	13958	c.13958G>T	c.(13957-13959)AGG>ATG	p.R4653M	FAT4_uc011cgp.1_Missense_Mutation_p.R2894M|FAT4_uc003ifi.1_Missense_Mutation_p.R2130M	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4653	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128739575	128739575	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128739575G>T	uc003ifm.2	+	13	1927	c.1674G>T	c.(1672-1674)AAG>AAT	p.K558N	HSPA4L_uc010iny.1_Missense_Mutation_p.K517N|HSPA4L_uc011cgr.1_Missense_Mutation_p.K525N	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	558					protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143159169	143159169	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143159169A>G	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)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146807029	146807029	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146807029G>A	uc003ikn.2	-	4	1596	c.1548C>T	c.(1546-1548)GGC>GGT	p.G516G	ZNF827_uc003ikm.2_Silent_p.G516G|ZNF827_uc010iox.2_Silent_p.G166G	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	516					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149002580	149002580	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149002580G>A	uc003ilj.3	-	9	3204	c.2870C>T	c.(2869-2871)CCC>CTC	p.P957L	NR3C2_uc003ilk.3_Missense_Mutation_p.P840L|NR3C2_uc010iph.2_RNA	NM_000901	NP_000892	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	957	Steroid-binding.			P->A: Slightly reduces aldosterone binding and transcription transactivation.	regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151023845	151023845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151023845C>T	uc003ilm.3	+	2	737	c.637C>T	c.(637-639)CGG>TGG	p.R213W	DCLK2_uc003iln.3_Missense_Mutation_p.R213W|DCLK2_uc003ilo.3_Missense_Mutation_p.R213W|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	213	Doublecortin 2.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151114360	151114360	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151114360A>G	uc003ilm.3	+	3	927	c.827A>G	c.(826-828)TAT>TGT	p.Y276C	DCLK2_uc003iln.3_Missense_Mutation_p.Y276C|DCLK2_uc003ilo.3_Missense_Mutation_p.Y276C|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	276	Doublecortin 2.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153247366	153247366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153247366C>T	uc003ims.2	-	10	1585	c.1436G>A	c.(1435-1437)CGA>CAA	p.R479Q	FBXW7_uc011cii.1_Missense_Mutation_p.R479Q|FBXW7_uc003imt.2_Missense_Mutation_p.R479Q|FBXW7_uc011cih.1_Missense_Mutation_p.R303Q|FBXW7_uc003imq.2_Missense_Mutation_p.R399Q|FBXW7_uc003imr.2_Missense_Mutation_p.R361Q	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	479	WD 3.				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding	p.R479Q(31)|p.R479L(7)|p.R479G(3)|p.R399Q(2)|p.R240L(1)|p.R399L(1)		haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
FHDC1	85462	broad.mit.edu	37	4	153897541	153897541	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153897541C>T	uc003inf.2	+	11	3173	c.3098C>T	c.(3097-3099)CCG>CTG	p.P1033L		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	1033					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)																	---	---	---	---
GRIA2	2891	broad.mit.edu	37	4	158224864	158224864	+	Silent	SNP	C	A	A	rs138262729		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158224864C>A	uc003ipm.3	+	3	849	c.390C>A	c.(388-390)CCC>CCA	p.P130P	GRIA2_uc011cit.1_Silent_p.P83P|GRIA2_uc003ipl.3_Silent_p.P130P|GRIA2_uc003ipk.3_Silent_p.P83P|GRIA2_uc010iqh.1_RNA	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	130	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)													---	---	---	---
PPID	5481	broad.mit.edu	37	4	159630906	159630906	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159630906A>G	uc003iqc.2	-	10	1207	c.1095T>C	c.(1093-1095)TAT>TAC	p.Y365Y		NM_005038	NP_005029	Q08752	PPID_HUMAN	peptidylprolyl isomerase D	365					protein folding	cytoplasm|intermediate filament cytoskeleton	cyclosporin A binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160253767	160253767	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160253767G>A	uc003iqg.3	+	11	1880	c.1570G>A	c.(1570-1572)GCC>ACC	p.A524T		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	524					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)														---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162307355	162307355	+	Silent	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162307355A>T	uc003iqh.2	-	16	2524	c.2088T>A	c.(2086-2088)ACT>ACA	p.T696T	FSTL5_uc003iqi.2_Silent_p.T695T|FSTL5_uc010iqv.2_Silent_p.T686T|uc010iqu.1_RNA	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	696						extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166795234	166795234	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166795234C>A	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
MFAP3L	9848	broad.mit.edu	37	4	170926737	170926737	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170926737C>T	uc003isp.3	-	2	470	c.292G>A	c.(292-294)GGA>AGA	p.G98R	MFAP3L_uc003isn.3_5'Flank	NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform	98	Extracellular (Potential).|Ig-like C2-type.					integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)														---	---	---	---
AADAT	51166	broad.mit.edu	37	4	171008379	171008379	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171008379C>A	uc003isr.2	-	3	599	c.257G>T	c.(256-258)TGG>TTG	p.W86L	AADAT_uc003iss.2_Missense_Mutation_p.W86L|AADAT_uc003ist.2_Missense_Mutation_p.W90L	NM_016228	NP_057312	Q8N5Z0	AADAT_HUMAN	kynurenine aminotransferase II	86					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)													---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186545449	186545449	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186545449G>A	uc003iyl.2	-	13	1980	c.1122C>T	c.(1120-1122)ACC>ACT	p.T374T	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Silent_p.T474T|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Silent_p.T278T|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Silent_p.T488T|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	374						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187524858	187524858	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187524858C>A	uc003izf.2	-	19	11010	c.10822G>T	c.(10822-10824)GGG>TGG	p.G3608W		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	3608	Extracellular (Potential).|Cadherin 33.				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)			---	---	---	---
ZFP42	132625	broad.mit.edu	37	4	188924151	188924151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188924151G>A	uc003izg.1	+	3	435	c.190G>A	c.(190-192)GGA>AGA	p.G64R	ZFP42_uc003izh.1_Missense_Mutation_p.G64R|ZFP42_uc003izi.1_Missense_Mutation_p.G64R	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	64					female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)														---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7626360	7626360	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7626360G>A	uc003jdz.1	+	4	718	c.651G>A	c.(649-651)CAG>CAA	p.Q217Q		NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	217	Cytoplasmic (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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
FASTKD3	79072	broad.mit.edu	37	5	7867164	7867164	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7867164C>A	uc003jeb.2	-	2	1170	c.1033G>T	c.(1033-1035)GGG>TGG	p.G345W	FASTKD3_uc011cmp.1_Missense_Mutation_p.G47W|FASTKD3_uc003jec.2_Intron|MTRR_uc010itn.1_5'Flank|MTRR_uc003jee.3_5'Flank|MTRR_uc003jed.2_5'Flank|MTRR_uc003jef.3_5'Flank|MTRR_uc003jeg.3_5'Flank|MTRR_uc010ito.2_5'Flank	NM_024091	NP_076996	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	345					apoptosis|cellular respiration	mitochondrion	ATP binding|protein kinase activity			ovary(2)|breast(1)|pancreas(1)	4																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11364843	11364843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11364843G>A	uc003jfa.1	-	8	1482	c.1337C>T	c.(1336-1338)CCG>CTG	p.P446L	CTNND2_uc010itt.2_Missense_Mutation_p.P355L|CTNND2_uc011cmy.1_Missense_Mutation_p.P109L|CTNND2_uc011cmz.1_Missense_Mutation_p.P13L|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.P13L	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	446					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14504649	14504649	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14504649C>T	uc003jff.2	+	55	8565	c.8559C>T	c.(8557-8559)GTC>GTT	p.V2853V	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2853	Protein kinase.				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)																	---	---	---	---
ZNF622	90441	broad.mit.edu	37	5	16465635	16465635	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16465635A>G	uc003jfq.2	-	1	260	c.140T>C	c.(139-141)TTC>TCC	p.F47S		NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622	47						cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PRDM9	56979	broad.mit.edu	37	5	23527891	23527891	+	3'UTR	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23527891T>C	uc003jgo.2	+	11						NM_020227	NP_064612			PR domain containing 9						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6															HNSCC(3;0.000094)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24537611	24537611	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24537611C>A	uc003jgr.1	-	3	736	c.404G>T	c.(403-405)AGA>ATA	p.R135I	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	135	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35025913	35025913	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35025913G>T	uc003jjf.2	-	9	997	c.918C>A	c.(916-918)GCC>GCA	p.A306A	AGXT2_uc003jje.1_5'UTR|AGXT2_uc011com.1_Silent_p.A306A	NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor	306					glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
CCDC152	100129792	broad.mit.edu	37	5	42801362	42801362	+	3'UTR	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42801362C>T	uc003jmx.3	+	9					CCDC152_uc011cpr.1_3'UTR|SEPP1_uc011cps.1_RNA|SEPP1_uc011cpt.1_RNA|SEPP1_uc011cpu.1_RNA|SEPP1_uc011cpv.1_RNA|SEPP1_uc003jna.2_RNA	NM_001134848	NP_001128320			coiled-coil domain containing 152												0																		---	---	---	---
C5orf34	375444	broad.mit.edu	37	5	43488034	43488034	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43488034A>C	uc003jnz.1	-	13	2014	c.1697T>G	c.(1696-1698)CTT>CGT	p.L566R		NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444	566										breast(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45262407	45262407	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262407C>T	uc003jok.2	-	8	2314	c.2289G>A	c.(2287-2289)CCG>CCA	p.P763P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	763	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
ISL1	3670	broad.mit.edu	37	5	50685764	50685764	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50685764A>G	uc003jor.2	+	4	1311	c.763A>G	c.(763-765)ACT>GCT	p.T255A		NM_002202	NP_002193	P61371	ISL1_HUMAN	islet-1	255	Gln-rich.				generation of precursor metabolites and energy|multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3		Lung NSC(810;0.000845)|Breast(144;0.0411)																---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55407543	55407543	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55407543G>A	uc003jqu.2	-	10	1184	c.1032C>T	c.(1030-1032)AAC>AAT	p.N344N	ANKRD55_uc003jqt.2_Silent_p.N56N	NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	343										skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)																---	---	---	---
GPBP1	65056	broad.mit.edu	37	5	56546862	56546862	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56546862A>G	uc003jrh.3	+	10	2328	c.1054A>G	c.(1054-1056)ATT>GTT	p.I352V	GPBP1_uc010iwg.2_Missense_Mutation_p.I372V|GPBP1_uc003jri.3_Missense_Mutation_p.I181V|GPBP1_uc003jrj.3_Missense_Mutation_p.I344V|GPBP1_uc003jrk.3_Missense_Mutation_p.I359V|GPBP1_uc003jrl.3_RNA	NM_022913	NP_075064	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 1	352					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)														---	---	---	---
ACTBL2	345651	broad.mit.edu	37	5	56778014	56778014	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56778014T>C	uc003jrm.2	-	1	623	c.521A>G	c.(520-522)CAT>CGT	p.H174R		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	174						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)														---	---	---	---
ACTBL2	345651	broad.mit.edu	37	5	56778343	56778343	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56778343G>A	uc003jrm.2	-	1	294	c.192C>T	c.(190-192)GGC>GGT	p.G64G		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	64						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)														---	---	---	---
RNF180	285671	broad.mit.edu	37	5	63509571	63509571	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63509571C>T	uc003jti.2	+	4	528	c.418C>T	c.(418-420)CAT>TAT	p.H140Y	RNF180_uc003jth.3_Missense_Mutation_p.H140Y|RNF180_uc010iws.2_Intron	NM_001113561	NP_001107033	Q86T96	RN180_HUMAN	ring finger protein 180 isoform 1	140	Cytoplasmic (Potential).					integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)														---	---	---	---
TRIM23	373	broad.mit.edu	37	5	64887740	64887740	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64887740A>G	uc003jty.2	-	11	1667	c.1581T>C	c.(1579-1581)ACT>ACC	p.T527T	TRIM23_uc003jtw.2_Silent_p.T527T|TRIM23_uc003jtx.2_Silent_p.T527T	NM_001656	NP_001647	P36406	TRI23_HUMAN	ADP-ribosylation factor domain protein 1 isoform	527	ARF-like.				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)														---	---	---	---
CD180	4064	broad.mit.edu	37	5	66479437	66479437	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66479437G>T	uc003juy.2	-	3	1382	c.1234C>A	c.(1234-1236)CAG>AAG	p.Q412K		NM_005582	NP_005573	Q99467	CD180_HUMAN	CD180 molecule precursor	412	LRR 13.|Extracellular (Potential).				inflammatory response|innate immune response	integral to membrane|plasma membrane	receptor activity			ovary(1)	1		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)														---	---	---	---
ENC1	8507	broad.mit.edu	37	5	73930887	73930887	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73930887G>T	uc003kdc.3	-	2	2555	c.1424C>A	c.(1423-1425)CCG>CAG	p.P475Q	ENC1_uc011css.1_Missense_Mutation_p.P402Q	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	475	Kelch 4.				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	75597266	75597266	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75597266T>A	uc003kei.1	+	12	2030	c.1896T>A	c.(1894-1896)AGT>AGA	p.S632R		NM_014979	NP_055794	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	632	Extracellular (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)														---	---	---	---
ARSB	411	broad.mit.edu	37	5	78077720	78077720	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78077720C>T	uc003kfq.2	-	7	2577	c.1291G>A	c.(1291-1293)GCT>ACT	p.A431T		NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor	431					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)														---	---	---	---
MTX3	345778	broad.mit.edu	37	5	79279521	79279521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79279521G>A	uc010jag.2	-	9	952	c.925C>T	c.(925-927)CGG>TGG	p.R309W	MTX3_uc010jah.2_3'UTR|MTX3_uc003kge.3_Missense_Mutation_p.R248W	NM_001010891	NP_001010891	Q5HYI7	MTX3_HUMAN	metaxin 3	309					protein targeting to mitochondrion	mitochondrial outer membrane					0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79837534	79837534	+	Silent	SNP	C	T	T	rs138264758	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79837534C>T	uc003kgv.1	+	6	857	c.714C>T	c.(712-714)TCC>TCT	p.S238S	FAM151B_uc010jal.1_RNA	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555	238											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)														---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80521544	80521544	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80521544G>A	uc003kha.1	+	27	3669	c.3669G>A	c.(3667-3669)ACG>ACA	p.T1223T	RNU5E_uc011cto.1_Intron|RASGRF2_uc011ctn.1_RNA	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	1223	Ras-GEF.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
CKMT2	1160	broad.mit.edu	37	5	80550855	80550855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80550855G>A	uc003khc.3	+	6	733	c.491G>A	c.(490-492)CGG>CAG	p.R164Q	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Missense_Mutation_p.R164Q|CKMT2_uc003khd.3_Missense_Mutation_p.R164Q|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	164	Phosphagen kinase C-terminal.|ATP.				creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)													---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80724431	80724431	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80724431A>T	uc003kho.2	-	16	1240	c.1029T>A	c.(1027-1029)AAT>AAA	p.N343K	RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Missense_Mutation_p.N228K|SSBP2_uc003khn.2_Missense_Mutation_p.N217K|SSBP2_uc003khp.2_Missense_Mutation_p.N351K|SSBP2_uc011ctp.1_Missense_Mutation_p.N323K|SSBP2_uc011ctq.1_Missense_Mutation_p.N321K|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2	343					regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87502851	87502851	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87502851T>C	uc003kjc.2	-	6	718	c.593A>G	c.(592-594)GAA>GGA	p.E198G	TMEM161B_uc011cty.1_Missense_Mutation_p.E187G|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctz.1_Missense_Mutation_p.E65G|TMEM161B_uc011ctx.1_Missense_Mutation_p.E16G	NM_153354	NP_699185	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	198						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)														---	---	---	---
ANKRD32	84250	broad.mit.edu	37	5	94030563	94030563	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94030563C>T	uc003kkr.3	+	21	2803	c.2723C>T	c.(2722-2724)GCT>GTT	p.A908V	ANKRD32_uc003kks.2_Missense_Mutation_p.A272V	NM_032290	NP_115666	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	908										ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)														---	---	---	---
ST8SIA4	7903	broad.mit.edu	37	5	100191911	100191911	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100191911T>G	uc003knk.2	-	4	1021	c.693A>C	c.(691-693)AAA>AAC	p.K231N		NM_005668	NP_005659	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide	231	Lumenal (Potential).				axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)														---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112862461	112862461	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112862461T>C	uc003kqn.2	+	4	837	c.654T>C	c.(652-654)ACT>ACC	p.T218T	YTHDC2_uc010jce.1_Silent_p.T218T|YTHDC2_uc010jcf.1_Intron	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	218	Helicase ATP-binding.|ATP (By similarity).						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118728940	118728940	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118728940G>T	uc003ksh.2	+	3	1149	c.461G>T	c.(460-462)CGG>CTG	p.R154L	TNFAIP8_uc003ksf.1_3'UTR|TNFAIP8_uc003ksg.2_Missense_Mutation_p.R144L|TNFAIP8_uc011cwf.1_Missense_Mutation_p.R148L|TNFAIP8_uc003ksi.2_Missense_Mutation_p.R154L	NM_014350	NP_055165	O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	154					anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
LMNB1	4001	broad.mit.edu	37	5	126168436	126168436	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126168436G>A	uc003kud.1	+	10	2030	c.1662G>A	c.(1660-1662)GAG>GAA	p.E554E	LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_Silent_p.E344E	NM_005573	NP_005564	P20700	LMNB1_HUMAN	lamin B1	554	Glu-rich (highly acidic; could be involved in chromatin binding).|Tail.				cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)														---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127599223	127599223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127599223C>T	uc003kuu.2	-	63	8525	c.8086G>A	c.(8086-8088)GTG>ATG	p.V2696M		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2696	EGF-like 47; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
SLC27A6	28965	broad.mit.edu	37	5	128365383	128365383	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128365383C>T	uc003kuy.2	+	10	2062	c.1666C>T	c.(1666-1668)CGA>TGA	p.R556*	SLC27A6_uc003kuz.2_Nonsense_Mutation_p.R556*	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	556					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)														---	---	---	---
ACSL6	23305	broad.mit.edu	37	5	131326646	131326646	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131326646T>C	uc010jdo.1	-	3	293	c.210A>G	c.(208-210)GCA>GCG	p.A70A	ACSL6_uc003kvv.1_RNA|ACSL6_uc003kvx.1_Silent_p.A95A|ACSL6_uc003kvy.1_Silent_p.A95A|ACSL6_uc003kwb.2_Silent_p.A60A|ACSL6_uc003kvz.1_Silent_p.A35A|ACSL6_uc003kwa.1_Silent_p.A81A|ACSL6_uc003kwc.1_Silent_p.A35A|ACSL6_uc003kwd.1_Silent_p.A70A|ACSL6_uc010jdn.1_Silent_p.A70A	NM_015256	NP_056071	Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	70	Cytoplasmic (Potential).				fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
SLC22A4	6583	broad.mit.edu	37	5	131647935	131647935	+	Missense_Mutation	SNP	G	A	A	rs11568509	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131647935G>A	uc003kwq.2	+	2	640	c.475G>A	c.(475-477)GTG>ATG	p.V159M	SLC22A4_uc010jdq.1_RNA|uc003kwr.3_RNA	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	solute carrier family 22 member 4	159	Helical; Name=2; (Potential).				body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity				0		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)													---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131926968	131926968	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131926968T>C	uc003kxi.2	+	10	1892	c.1505T>C	c.(1504-1506)ATG>ACG	p.M502T	RAD50_uc003kxh.2_Missense_Mutation_p.M363T	NM_005732	NP_005723	Q92878	RAD50_HUMAN	RAD50 homolog isoform 1	502	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					---	---	---	---
PCBD2	84105	broad.mit.edu	37	5	134246093	134246093	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134246093A>G	uc010jdz.2	+	2	173	c.153A>G	c.(151-153)GGA>GGG	p.G51G	PCBD2_uc011cxw.1_Silent_p.G51G	NM_032151	NP_115527	Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase 2	51					positive regulation of transcription, DNA-dependent|tetrahydrobiopterin biosynthetic process		4-alpha-hydroxytetrahydrobiopterin dehydratase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
EGR1	1958	broad.mit.edu	37	5	137802513	137802513	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137802513C>A	uc003ldb.1	+	2	645	c.375C>A	c.(373-375)ACC>ACA	p.T125T	EGR1_uc011cyu.1_Silent_p.T125T	NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	125					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|interleukin-1-mediated signaling pathway|positive regulation of glomerular metanephric mesangial cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of protein sumoylation|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytoplasm|nucleus	histone acetyltransferase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
DNAJC18	202052	broad.mit.edu	37	5	138758500	138758500	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138758500A>G	uc003len.2	-	6	681	c.676T>C	c.(676-678)TAT>CAT	p.Y226H	DNAJC18_uc010jff.2_Missense_Mutation_p.Y164H	NM_152686	NP_689899	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	226					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)|kidney(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139260458	139260458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139260458C>T	uc003lex.1	-	3	1199	c.974G>A	c.(973-975)CGG>CAG	p.R325Q	NRG2_uc003lev.1_Missense_Mutation_p.R325Q|NRG2_uc003lew.1_Missense_Mutation_p.R325Q|NRG2_uc003ley.1_Missense_Mutation_p.R325Q	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	325	Ig-like C2-type.|Extracellular (Potential).				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140167635	140167635	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167635C>T	uc003lhb.2	+	1	1760	c.1760C>T	c.(1759-1761)GCG>GTG	p.A587V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lgz.2_Missense_Mutation_p.A587V	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	587	Extracellular (Potential).				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)															---	---	---	---
PCDHA2	56146	broad.mit.edu	37	5	140176220	140176220	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176220C>T	uc003lhd.2	+	1	1777	c.1671C>T	c.(1669-1671)GAC>GAT	p.D557D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.D557D|PCDHA2_uc011czy.1_Silent_p.D557D	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	557	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA8	56140	broad.mit.edu	37	5	140222221	140222221	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140222221G>A	uc003lhs.2	+	1	1315	c.1315G>A	c.(1315-1317)GCC>ACC	p.A439T	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_uc003lhr.1_Missense_Mutation_p.A439T	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	439	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA12	56137	broad.mit.edu	37	5	140256301	140256301	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140256301G>A	uc003lic.2	+	1	1371	c.1244G>A	c.(1243-1245)CGC>CAC	p.R415H	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_uc011daf.1_Missense_Mutation_p.R415H	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	415	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB2	56133	broad.mit.edu	37	5	140474624	140474624	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140474624G>A	uc003lil.2	+	1	388	c.250G>A	c.(250-252)GGG>AGG	p.G84R	PCDHB2_uc003lim.1_Intron	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	84	Extracellular (Potential).|Cadherin 1.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB7	56129	broad.mit.edu	37	5	140554636	140554636	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140554636C>T	uc003lit.2	+	1	2394	c.2220C>T	c.(2218-2220)ACC>ACT	p.T740T	PCDHB8_uc011dai.1_5'Flank	NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	740	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140558582	140558582	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140558582A>G	uc011dai.1	+	1	1153	c.967A>G	c.(967-969)AGA>GGA	p.R323G	PCDHB16_uc003liv.2_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	323	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB14	56122	broad.mit.edu	37	5	140604658	140604658	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140604658C>T	uc003ljb.2	+	1	1581	c.1581C>T	c.(1579-1581)TTC>TTT	p.F527F	PCDHB14_uc011dal.1_Silent_p.F374F	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	527	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA1	56114	broad.mit.edu	37	5	140711018	140711018	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140711018C>A	uc003lji.1	+	1	767	c.767C>A	c.(766-768)CCG>CAG	p.P256Q	PCDHGA1_uc011dan.1_Missense_Mutation_p.P256Q	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	256	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140753898	140753898	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140753898G>A	uc003ljy.1	+	1	248	c.248G>A	c.(247-249)AGC>AAC	p.S83N	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_uc011dau.1_Missense_Mutation_p.S83N	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	83	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB6	56100	broad.mit.edu	37	5	140789013	140789013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140789013C>T	uc003lkj.1	+	1	1244	c.1244C>T	c.(1243-1245)ACA>ATA	p.T415I	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_uc003lki.1_Missense_Mutation_p.T415I	NM_018926	NP_061749	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6 isoform 1	415	Extracellular (Potential).|Cadherin 4.				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)															---	---	---	---
PCDHGB7	56099	broad.mit.edu	37	5	140799786	140799786	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140799786T>C	uc003lkn.1	+	1	2505	c.2360T>C	c.(2359-2361)CTA>CCA	p.L787P	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_uc003lkm.2_Missense_Mutation_p.L787P|PCDHGA11_uc003lko.1_5'Flank|PCDHGA11_uc003lkp.1_5'Flank|PCDHGA11_uc003lkq.1_5'Flank	NM_018927	NP_061750	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7 isoform 1	787	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140955848	140955848	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140955848A>G	uc003llb.3	-	14	1551	c.1410T>C	c.(1408-1410)GAT>GAC	p.D470D	DIAPH1_uc003llc.3_Silent_p.D461D|DIAPH1_uc010jgc.1_5'Flank	NM_005219	NP_005210	O60610	DIAP1_HUMAN	diaphanous 1 isoform 1	470	Potential.				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)															---	---	---	---
ARAP3	64411	broad.mit.edu	37	5	141051554	141051554	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141051554G>T	uc003llm.2	-						ARAP3_uc011dbe.1_Intron|ARAP3_uc003lln.2_Intron	NM_022481	NP_071926			ArfGAP with RhoGAP domain, ankyrin repeat and PH						cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7																		---	---	---	---
KCTD16	57528	broad.mit.edu	37	5	143586874	143586874	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143586874C>A	uc003lnm.1	+	3	1226	c.597C>A	c.(595-597)TCC>TCA	p.S199S	KCTD16_uc003lnn.1_Silent_p.S199S	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain	199						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
PLAC8L1	153770	broad.mit.edu	37	5	145483816	145483816	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145483816A>G	uc003lnv.2	-	1	131	c.59T>C	c.(58-60)ATA>ACA	p.I20T	PLAC8L1_uc011dbp.1_RNA	NM_001029869	NP_001025040	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	20											0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147473990	147473990	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147473990G>A	uc003lox.2	+	9	813	c.740G>A	c.(739-741)CGT>CAT	p.R247H	SPINK5_uc010jgq.1_RNA|SPINK5_uc010jgs.1_Missense_Mutation_p.R219H|SPINK5_uc010jgr.2_Missense_Mutation_p.R228H|SPINK5_uc003low.2_Missense_Mutation_p.R247H|SPINK5_uc003loy.2_Missense_Mutation_p.R247H	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform	247	Kazal-like 4.				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)															---	---	---	---
SPINK14	408187	broad.mit.edu	37	5	147554938	147554938	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147554938T>C	uc003loz.1	+	4	271	c.271T>C	c.(271-273)TTT>CTT	p.F91L		NM_001001325	NP_001001325	Q6IE38	ISK14_HUMAN	Kazal type serine protease inhibitor 5-like 2	91	Kazal-like.					extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147928374	147928374	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147928374C>T	uc003lpn.2	-	4	374	c.210G>A	c.(208-210)TCG>TCA	p.S70S	HTR4_uc010jgu.1_RNA|HTR4_uc003lpi.1_Silent_p.S70S|HTR4_uc003lpj.1_Silent_p.S70S|HTR4_uc003lpk.2_Silent_p.S70S|HTR4_uc011dby.1_Silent_p.S70S|HTR4_uc003lpl.2_Silent_p.S70S|HTR4_uc003lpm.2_Silent_p.S70S|HTR4_uc010jgv.2_RNA|HTR4_uc003lpo.1_Silent_p.S70S	NM_000870	NP_000861	Q13639	5HT4R_HUMAN	serotonin 5-HT4 receptor isoform b	70	Helical; Name=2; (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148392271	148392271	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148392271A>G	uc003lpu.2	-	13	3232	c.3080T>C	c.(3079-3081)ATC>ACC	p.I1027T	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Missense_Mutation_p.I671T|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_Missense_Mutation_p.I574T|SH3TC2_uc010jgx.2_Missense_Mutation_p.I1020T	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1027	TPR 4.						binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148406142	148406142	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148406142T>C	uc003lpu.2	-	12	3198	c.3046A>G	c.(3046-3048)ACC>GCC	p.T1016A	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Missense_Mutation_p.T660A|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_Missense_Mutation_p.T563A|SH3TC2_uc010jgx.2_Missense_Mutation_p.T1009A|SH3TC2_uc003lpv.1_3'UTR|SH3TC2_uc011dbz.1_3'UTR	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1016	TPR 4.						binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SH3TC2	79628	broad.mit.edu	37	5	148407408	148407408	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148407408G>A	uc003lpu.2	-	11	2039	c.1887C>T	c.(1885-1887)AGC>AGT	p.S629S	SH3TC2_uc003lpp.1_RNA|SH3TC2_uc010jgw.2_Silent_p.S273S|SH3TC2_uc003lps.2_RNA|SH3TC2_uc003lpt.2_Silent_p.S176S|SH3TC2_uc010jgx.2_Silent_p.S622S|SH3TC2_uc003lpv.1_Silent_p.S176S|SH3TC2_uc011dbz.1_Silent_p.S514S	NM_024577	NP_078853	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	629							binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150924599	150924599	+	Missense_Mutation	SNP	C	T	T	rs145039507		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150924599C>T	uc003lue.3	-	9	6102	c.6089G>A	c.(6088-6090)CGG>CAG	p.R2030Q	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2030	Extracellular (Potential).|Cadherin 17.				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)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150930358	150930358	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150930358A>G	uc003lue.3	-	7	4384	c.4371T>C	c.(4369-4371)GTT>GTC	p.V1457V	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1457	Extracellular (Potential).|Cadherin 13.				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)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150945341	150945341	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150945341A>G	uc003lue.3	-	1	3165	c.3152T>C	c.(3151-3153)GTG>GCG	p.V1051A	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Missense_Mutation_p.V1051A	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	1051	Cadherin 9.|Extracellular (Potential).				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)															---	---	---	---
NMUR2	56923	broad.mit.edu	37	5	151784474	151784474	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151784474G>A	uc003luv.2	-	1	367	c.201C>T	c.(199-201)TGC>TGT	p.C67C		NM_020167	NP_064552	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	67	Helical; Name=1; (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|arachidonic acid secretion|calcium ion transport|central nervous system development|elevation of cytosolic calcium ion concentration|regulation of smooth muscle contraction	integral to membrane|plasma membrane	GTP binding|intracellular calcium activated chloride channel activity|neuromedin U receptor activity			ovary(3)|skin(2)|lung(1)|breast(1)|pancreas(1)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)															---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156915267	156915267	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156915267A>G	uc003lwz.2	-						ADAM19_uc003lww.1_Intron|ADAM19_uc003lwy.2_Intron|ADAM19_uc011ddr.1_Intron	NM_033274	NP_150377			ADAM metallopeptidase domain 19 preproprotein						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158621757	158621757	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158621757G>T	uc003lxp.2	-	3	573	c.260C>A	c.(259-261)GCT>GAT	p.A87D	RNF145_uc011ddy.1_Missense_Mutation_p.A101D|RNF145_uc003lxo.1_Missense_Mutation_p.A115D|RNF145_uc011ddz.1_Missense_Mutation_p.A104D|RNF145_uc010jiq.1_Missense_Mutation_p.A117D|RNF145_uc011dea.1_Missense_Mutation_p.A103D	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145	87	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
CCNJL	79616	broad.mit.edu	37	5	159738871	159738871	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159738871G>A	uc003lyb.1	-	2	312	c.60C>T	c.(58-60)CGC>CGT	p.R20R	CCNJL_uc011dee.1_Silent_p.R20R|CCNJL_uc003lyc.1_Intron|CCNJL_uc011def.1_Silent_p.R20R	NM_024565	NP_078841	Q8IV13	CCNJL_HUMAN	cyclin J-like	20	Cyclin N-terminal.					nucleus					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
MAT2B	27430	broad.mit.edu	37	5	162943622	162943622	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162943622A>G	uc003lzk.2	+	5	733	c.625A>G	c.(625-627)AAG>GAG	p.K209E	MAT2B_uc003lzj.2_Missense_Mutation_p.K198E|MAT2B_uc003lzl.1_Missense_Mutation_p.K209E|MAT2B_uc003lzm.2_5'Flank	NM_013283	NP_037415	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta isoform	209					extracellular polysaccharide biosynthetic process|methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol|methionine adenosyltransferase complex|nucleus	dTDP-4-dehydrorhamnose reductase activity|methionine adenosyltransferase regulator activity|protein binding			upper_aerodigestive_tract(1)	1	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)													---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167673855	167673855	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167673855C>A	uc010jjd.2	+	27	5884	c.5884C>A	c.(5884-5886)CGG>AGG	p.R1962R	ODZ2_uc003lzr.3_Silent_p.R1732R|ODZ2_uc003lzt.3_Silent_p.R1335R|ODZ2_uc010jje.2_Silent_p.R1226R	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169484581	169484581	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169484581C>A	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|DOCK2_uc003mah.2_Missense_Mutation_p.Q16K	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
MSX2	4488	broad.mit.edu	37	5	174156184	174156184	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174156184C>T	uc003mcy.2	+	2	490	c.402C>T	c.(400-402)TGC>TGT	p.C134C		NM_002449	NP_002440	P35548	MSX2_HUMAN	msh homeobox 2	134					cranial suture morphogenesis|negative regulation of transcription, DNA-dependent|osteoblast differentiation	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
FGFR4	2264	broad.mit.edu	37	5	176522590	176522590	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176522590C>T	uc003mfl.2	+	13	1854	c.1687C>T	c.(1687-1689)CGG>TGG	p.R563W	FGFR4_uc003mfm.2_Missense_Mutation_p.R563W|FGFR4_uc011dfu.1_Missense_Mutation_p.R495W|FGFR4_uc003mfo.2_Missense_Mutation_p.R523W	NM_002011	NP_002002	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4 isoform 1	563	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	176942974	176942974	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176942974C>A	uc003mho.2	-	5	411	c.390G>T	c.(388-390)AAG>AAT	p.K130N	DDX41_uc003mhm.2_5'Flank|DDX41_uc003mhn.2_Translation_Start_Site|DDX41_uc003mhp.2_Translation_Start_Site|DDX41_uc003mhq.1_Translation_Start_Site	NM_016222	NP_057306	Q9UJV9	DDX41_HUMAN	DEAD-box protein abstrakt	130					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-4256-01A-01D-1126-08	TCGA-BR-4256-11A-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)														---	---	---	---
ZNF454	285676	broad.mit.edu	37	5	178392951	178392951	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178392951A>G	uc003mjo.1	+	5	1817	c.1546A>G	c.(1546-1548)AGA>GGA	p.R516G	ZNF454_uc010jkz.1_Missense_Mutation_p.R516G	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	516	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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;0.234)														---	---	---	---
C5orf45	51149	broad.mit.edu	37	5	179271187	179271187	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179271187C>T	uc003mla.2	-	4	300	c.256G>A	c.(256-258)GTG>ATG	p.V86M	C5orf45_uc003mky.2_Missense_Mutation_p.V83M|C5orf45_uc011dgt.1_Missense_Mutation_p.V86M|C5orf45_uc011dgu.1_Intron|C5orf45_uc003mlc.2_Intron|C5orf45_uc003mlb.2_Translation_Start_Site	NM_016175	NP_057259	Q6NTE8	CE045_HUMAN	hypothetical protein LOC51149 isoform 1	86											0																		---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179290918	179290918	+	Missense_Mutation	SNP	C	T	T	rs113335971	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179290918C>T	uc003mlh.2	-	22	3320	c.3283G>A	c.(3283-3285)GCA>ACA	p.A1095T	TBC1D9B_uc003mli.2_Missense_Mutation_p.A1078T|TBC1D9B_uc003mlj.2_Missense_Mutation_p.A1077T|TBC1D9B_uc003mlf.2_Missense_Mutation_p.A169T|TBC1D9B_uc003mlg.2_Missense_Mutation_p.A254T|TBC1D9B_uc011dgv.1_Missense_Mutation_p.A254T	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	1095						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)															---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7226757	7226757	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7226757G>A	uc003mxc.2	+	9	1155	c.765G>A	c.(763-765)GCG>GCA	p.A255A	RREB1_uc003mxb.2_Silent_p.A255A|RREB1_uc010jnx.2_Silent_p.A255A	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	255	C2H2-type 5.				multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
RNF182	221687	broad.mit.edu	37	6	13977897	13977897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13977897C>T	uc003nbe.2	+	3	965	c.547C>T	c.(547-549)CGG>TGG	p.R183W	RNF182_uc003nbf.2_Missense_Mutation_p.R183W|RNF182_uc003nbg.2_Missense_Mutation_p.R183W	NM_152737	NP_689950	Q8N6D2	RN182_HUMAN	ring finger protein 182	183						cytoplasm|integral to membrane|intracellular membrane-bounded organelle	protein binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Breast(50;0.00405)|Ovarian(93;0.0964)	all_hematologic(90;0.135)	Epithelial(50;0.195)															---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16306697	16306697	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16306697T>C	uc003nbt.2	-	9	3282	c.2311A>G	c.(2311-2313)AAG>GAG	p.K771E	ATXN1_uc010jpi.2_Missense_Mutation_p.K771E|ATXN1_uc010jpj.1_RNA	NM_000332	NP_000323	P54253	ATX1_HUMAN	ataxin 1	771	Interaction with USP7.				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)																---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17826310	17826310	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17826310C>T	uc003ncg.3	-	15	1683	c.1578G>A	c.(1576-1578)TGG>TGA	p.W526*	KIF13A_uc003ncf.2_Nonsense_Mutation_p.W526*|KIF13A_uc003nch.3_Nonsense_Mutation_p.W526*|KIF13A_uc003nci.3_Nonsense_Mutation_p.W526*|KIF13A_uc003ncj.2_Nonsense_Mutation_p.W202*	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	526					cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
NHLRC1	378884	broad.mit.edu	37	6	18122083	18122083	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18122083C>T	uc003ncl.1	-	1	769	c.755G>A	c.(754-756)CGG>CAG	p.R252Q		NM_198586	NP_940988	Q6VVB1	NHLC1_HUMAN	NHL repeat containing 1	252	NHL 4.				proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	endoplasmic reticulum|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0	Ovarian(93;0.016)|Breast(50;0.0245)	all_hematologic(90;0.165)	all cancers(50;0.0451)|Epithelial(50;0.0493)															---	---	---	---
GPLD1	2822	broad.mit.edu	37	6	24460553	24460553	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24460553T>C	uc003ned.1	-	12	1073	c.962A>G	c.(961-963)AAC>AGC	p.N321S	GPLD1_uc010jpr.1_Missense_Mutation_p.N158S|GPLD1_uc010jps.1_Missense_Mutation_p.N321S	NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific	321						extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3																		---	---	---	---
SLC17A2	10246	broad.mit.edu	37	6	25914895	25914895	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25914895A>T	uc011dkb.1	-	10	1298	c.1215T>A	c.(1213-1215)TAT>TAA	p.Y405*	SLC17A2_uc011dkc.1_Missense_Mutation_p.M356K|SLC17A2_uc003nfl.2_Missense_Mutation_p.M356K			O00624	NPT3_HUMAN	SubName: Full=Solute carrier family 17 (Sodium phosphate), member 2, isoform CRA_b; SubName: Full=Putative uncharacterized protein SLC17A2;	405					phosphate metabolic process	integral to plasma membrane|membrane fraction	sodium:phosphate symporter activity			ovary(1)	1																		---	---	---	---
ZNF165	7718	broad.mit.edu	37	6	28053645	28053645	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28053645A>C	uc003nkg.2	+	3	1471	c.387A>C	c.(385-387)AGA>AGC	p.R129S	ZNF165_uc003nkh.2_Missense_Mutation_p.R129S|ZNF165_uc003nki.3_Missense_Mutation_p.R129S	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	129					viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GABBR1	2550	broad.mit.edu	37	6	29589896	29589896	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29589896G>A	uc003nmt.3	-	9	1386	c.1050C>T	c.(1048-1050)CCC>CCT	p.P350P	GABBR1_uc003nmp.3_Silent_p.P233P|GABBR1_uc003nms.3_Silent_p.P233P|GABBR1_uc003nmu.3_Silent_p.P288P|GABBR1_uc011dlr.1_Silent_p.P173P|GABBR1_uc011dls.1_Silent_p.P350P	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	350	Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity	p.P350L(1)		ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)													---	---	---	---
MRPS18B	28973	broad.mit.edu	37	6	30592649	30592649	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30592649T>C	uc003nqo.2	+						MRPS18B_uc011dml.1_Intron|MRPS18B_uc010jsd.1_Intron|C6orf134_uc003nqr.3_5'Flank|C6orf134_uc003rdc.2_5'Flank|C6orf134_uc003nqs.3_5'Flank|C6orf134_uc003rdd.2_5'Flank|C6orf134_uc003nqu.2_5'Flank|C6orf134_uc003nqt.2_5'Flank|C6orf134_uc011dmm.1_5'Flank|C6orf134_uc003nqv.2_5'Flank	NM_014046	NP_054765			mitochondrial ribosomal protein S18B precursor						translation	mitochondrial small ribosomal subunit	protein binding|structural constituent of ribosome			ovary(1)	1																		---	---	---	---
VARS2	57176	broad.mit.edu	37	6	30888205	30888205	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30888205C>A	uc003nsc.1	+	13	2021	c.1389C>A	c.(1387-1389)CCC>CCA	p.P463P	VARS2_uc011dmx.1_Silent_p.P463P|VARS2_uc011dmy.1_Silent_p.P323P|VARS2_uc011dmz.1_Silent_p.P493P|VARS2_uc011dna.1_Silent_p.P461P|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_5'UTR|VARS2_uc010jsg.1_5'UTR|VARS2_uc010jsh.1_5'Flank	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	463					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
MCCD1	401250	broad.mit.edu	37	6	31496971	31496971	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31496971C>T	uc003ntp.1	+							NM_001011700	NP_001011700			mitochondrial coiled-coil domain 1 precursor							mitochondrion					0																		---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31602535	31602535	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31602535T>C	uc003nvb.3	+	21	5190	c.4941T>C	c.(4939-4941)AGT>AGC	p.S1647S	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Silent_p.S1647S	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1647	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
BAT3	7917	broad.mit.edu	37	6	31616485	31616485	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31616485C>A	uc003nvg.3	-	6	835	c.521G>T	c.(520-522)AGG>ATG	p.R174M	BAT3_uc003nvf.3_Missense_Mutation_p.R174M|BAT3_uc003nvh.3_Missense_Mutation_p.R174M|BAT3_uc003nvi.3_Missense_Mutation_p.R174M|BAT3_uc011dnw.1_Missense_Mutation_p.R174M|BAT3_uc011dnx.1_Missense_Mutation_p.R174M|BAT3_uc003nvj.1_Missense_Mutation_p.R174M	NM_004639	NP_004630	P46379	BAG6_HUMAN	HLA-B associated transcript-3 isoform a	174					apoptosis in response to endoplasmic reticulum stress|brain development|cell differentiation|chromatin modification|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|embryo development|internal peptidyl-lysine acetylation|kidney development|lung development|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|protein stabilization|spermatogenesis|synaptonemal complex assembly|tail-anchored membrane protein insertion into ER membrane|transport|ubiquitin-dependent protein catabolic process	BAT3 complex|nucleus	polyubiquitin binding|proteasome binding|ribosome binding				0																		---	---	---	---
CLIC1	1192	broad.mit.edu	37	6	31701700	31701700	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31701700T>C	uc003nwr.2	-	3	452	c.188A>G	c.(187-189)CAG>CGG	p.Q63R	CLIC1_uc003rje.2_Missense_Mutation_p.Q63R	NM_001288	NP_001279	O00299	CLIC1_HUMAN	chloride intracellular channel 1	63	Required for insertion into the membrane.			Q -> E (in Ref. 1; AAC25675 and 3; AAD26137).	signal transduction	brush border|chloride channel complex|cytoplasm|membrane fraction|nuclear membrane|plasma membrane|soluble fraction	protein binding|voltage-gated chloride channel activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
HLA-DMA	3108	broad.mit.edu	37	6	32917066	32917066	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32917066G>A	uc003ocm.2	-	4	849	c.763C>T	c.(763-765)CGG>TGG	p.R255W		NM_006120	NP_006111	Q31604	Q31604_HUMAN	major histocompatibility complex, class II, DM	255						integral to membrane|MHC class II protein complex					0																		---	---	---	---
HLA-DOA	3111	broad.mit.edu	37	6	32977255	32977255	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32977255G>A	uc003ocr.2	-	1	135	c.59C>T	c.(58-60)CCG>CTG	p.P20L	HLA-DOA_uc010juj.2_5'UTR|HLA-DOA_uc010jui.2_Missense_Mutation_p.P20L	NM_002119	NP_002110	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO	20					antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0																		---	---	---	---
HLA-DPB1	3115	broad.mit.edu	37	6	33048483	33048483	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33048483C>T	uc003ocu.1	+	2	194	c.135C>T	c.(133-135)TAC>TAT	p.Y45Y	HLA-DPA1_uc003oct.1_5'UTR|HLA-DPB1_uc011dqn.1_RNA|HLA-DPB1_uc011dqo.1_RNA|HLA-DPB1_uc011dqp.1_Silent_p.Y44Y|HLA-DPB1_uc011dqq.1_Translation_Start_Site	NM_002121	NP_002112	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP	45	Extracellular (Potential).|Beta-1.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex				ovary(1)	1																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33139591	33139591	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33139591G>T	uc003ocx.1	-	42	3277	c.3049C>A	c.(3049-3051)CCT>ACT	p.P1017T	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.P931T|COL11A2_uc003ocz.1_Missense_Mutation_p.P910T	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1017	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
FKBP5	2289	broad.mit.edu	37	6	35547992	35547992	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35547992T>C	uc011dte.1	-	9	1050	c.847A>G	c.(847-849)AAA>GAA	p.K283E	FKBP5_uc003okx.2_Missense_Mutation_p.K283E|FKBP5_uc011dtf.1_Missense_Mutation_p.K104E|FKBP5_uc003oky.2_Missense_Mutation_p.K283E	NM_001145776	NP_001139248	Q13451	FKBP5_HUMAN	FK506 binding protein 5 isoform 1	283	TPR 1.				protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
LHFPL5	222662	broad.mit.edu	37	6	35773711	35773711	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35773711C>A	uc003olg.1	+	1	641	c.264C>A	c.(262-264)TCC>TCA	p.S88S		NM_182548	NP_872354	Q8TAF8	TMHS_HUMAN	lipoma HMGIC fusion partner-like 5	88						integral to membrane				skin(1)	1																		---	---	---	---
SLC26A8	116369	broad.mit.edu	37	6	35960350	35960350	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35960350G>A	uc003olm.2	-	6	840	c.729C>T	c.(727-729)TCC>TCT	p.S243S	SLC26A8_uc003oln.2_Silent_p.S243S|SLC26A8_uc003oll.2_Intron	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	243	Helical; (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36168494	36168494	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36168494C>T	uc003olv.3	+	2	619	c.395C>T	c.(394-396)CCG>CTG	p.P132L	BRPF3_uc010jwb.2_Missense_Mutation_p.P132L|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.P132L	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	132					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38781845	38781845	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38781845G>A	uc003ooe.1	+	23	3222	c.2622G>A	c.(2620-2622)AAG>AAA	p.K874K		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																		---	---	---	---
TREML4	285852	broad.mit.edu	37	6	41196492	41196492	+	Missense_Mutation	SNP	C	T	T	rs141778511	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41196492C>T	uc003oqc.2	+	2	208	c.104C>T	c.(103-105)ACC>ATC	p.T35I	TREML4_uc003oqd.2_RNA	NM_198153	NP_937796	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid	35	Ig-like V-type.					extracellular region				breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)																	---	---	---	---
CRIP3	401262	broad.mit.edu	37	6	43275646	43275646	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43275646C>A	uc010jyn.1	-						CRIP3_uc003ouu.1_Intron	NM_206922	NP_996805			cysteine-rich protein 3							cytoplasm	zinc ion binding			skin(1)	1			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)															---	---	---	---
TCTE1	202500	broad.mit.edu	37	6	44250020	44250020	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44250020C>T	uc003oxi.2	-	4	1279	c.1123G>A	c.(1123-1125)GAG>AAG	p.E375K	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_182539	NP_872345	Q5JU00	TCTE1_HUMAN	t-complex-associated testis expressed 1	375	LRR 3.									ovary(2)|skin(2)	4	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
RUNX2	860	broad.mit.edu	37	6	45405710	45405710	+	Missense_Mutation	SNP	G	A	A	rs147009083		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45405710G>A	uc011dvx.1	+	5	817	c.607G>A	c.(607-609)GTC>ATC	p.V203I	RUNX2_uc011dvy.1_Missense_Mutation_p.V203I|RUNX2_uc003oxt.2_Missense_Mutation_p.V189I	NM_001024630	NP_001019801	Q13950	RUNX2_HUMAN	runt-related transcription factor 2 isoform a	203	Runt.				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3																		---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55142277	55142277	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55142277G>A	uc003pcl.2	+	5	1177	c.862G>A	c.(862-864)GCT>ACT	p.A288T	HCRTR2_uc010jzv.2_RNA	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	288	Cytoplasmic (Potential).				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)															---	---	---	---
DST	667	broad.mit.edu	37	6	56496731	56496731	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56496731G>T	uc003pdf.2	-	28	3842	c.3814C>A	c.(3814-3816)CTG>ATG	p.L1272M	DST_uc003pcz.3_Missense_Mutation_p.L1094M|DST_uc011dxj.1_Missense_Mutation_p.L1123M|DST_uc011dxk.1_Missense_Mutation_p.L1134M|DST_uc003pcy.3_Missense_Mutation_p.L768M|DST_uc003pdb.2_Missense_Mutation_p.L768M|DST_uc003pdc.3_Missense_Mutation_p.L768M|DST_uc003pdd.3_Missense_Mutation_p.L768M	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	1094					cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
COL9A1	1297	broad.mit.edu	37	6	70990716	70990716	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70990716C>T	uc003pfg.3	-	9	1062	c.903G>A	c.(901-903)CCG>CCA	p.P301P	COL9A1_uc003pfe.3_5'Flank|COL9A1_uc003pff.3_Silent_p.P58P	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	301	Triple-helical region (COL3).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75861629	75861629	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75861629T>C	uc003phs.2	-	20	4120	c.3954A>G	c.(3952-3954)GCA>GCG	p.A1318A	COL12A1_uc003pht.2_Silent_p.A154A	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1318	VWFA 3.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75899338	75899338	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75899338C>T	uc003phs.2	-	6	754	c.588G>A	c.(586-588)CAG>CAA	p.Q196Q	COL12A1_uc003pht.2_Intron|COL12A1_uc003phu.1_5'Flank	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	196	VWFA 1.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COX7A2	1347	broad.mit.edu	37	6	75950914	75950914	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75950914G>T	uc003phv.1	-	2	161	c.86C>A	c.(85-87)CCG>CAG	p.P29Q		NM_001865	NP_001856	P14406	CX7A2_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 2	29						mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0																		---	---	---	---
TTK	7272	broad.mit.edu	37	6	80718203	80718203	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80718203T>A	uc003pjc.2	+	4	537	c.463T>A	c.(463-465)TCA>ACA	p.S155T	TTK_uc003pjb.3_Missense_Mutation_p.S155T	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	155					mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)														---	---	---	---
UBE2CBP	90025	broad.mit.edu	37	6	83667139	83667139	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83667139G>A	uc003pjp.2	-	9	1149	c.1041C>T	c.(1039-1041)AGC>AGT	p.S347S	UBE2CBP_uc011dyx.1_RNA	NM_198920	NP_944602	Q7Z6J8	UB2CB_HUMAN	ubiquitin-conjugating enzyme E2C binding	347						cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)														---	---	---	---
PGM3	5238	broad.mit.edu	37	6	83884176	83884176	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83884176T>C	uc003pjv.2	-	10	1199	c.1159A>G	c.(1159-1161)ATA>GTA	p.I387V	PGM3_uc003pjw.2_Missense_Mutation_p.I306V|PGM3_uc011dyz.1_Missense_Mutation_p.I415V	NM_015599	NP_056414	O95394	AGM1_HUMAN	phosphoglucomutase 3	387					dolichol-linked oligosaccharide biosynthetic process|embryo development ending in birth or egg hatching|glucose 1-phosphate metabolic process|hemopoiesis|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	magnesium ion binding|phosphoacetylglucosamine mutase activity|phosphoglucomutase activity				0		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)														---	---	---	---
RIPPLY2	134701	broad.mit.edu	37	6	84563889	84563889	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84563889C>T	uc003pke.2	+							NM_001009994	NP_001009994			ripply2 protein						somite rostral/caudal axis specification	nucleus					0																		---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85472307	85472307	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85472307C>T	uc003pkl.1	-	2	452	c.452G>A	c.(451-453)CGC>CAC	p.R151H	TBX18_uc010kbq.1_5'UTR	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	151	T-box.				multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	p.R151C(1)		ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87964590	87964590	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87964590C>G	uc003plm.3	+	8	1284	c.1243C>G	c.(1243-1245)CAG>GAG	p.Q415E		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	415					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	90024926	90024926	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90024926C>G	uc003pnb.2	-	1	42	c.34G>C	c.(34-36)GGC>CGC	p.G12R		NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	12					synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)														---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	90024927	90024927	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90024927T>G	uc003pnb.2	-	1	41	c.33A>C	c.(31-33)ACA>ACC	p.T11T		NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	11					synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90494779	90494779	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90494779A>T	uc003pnn.1	-	9	1517	c.1401T>A	c.(1399-1401)TAT>TAA	p.Y467*	MDN1_uc003pno.1_Translation_Start_Site|MDN1_uc003pnp.1_Nonsense_Mutation_p.Y467*	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	467					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)														---	---	---	---
USP45	85015	broad.mit.edu	37	6	99958034	99958034	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99958034A>G	uc003ppx.2	-	2	596	c.63T>C	c.(61-63)ACT>ACC	p.T21T	USP45_uc003ppw.2_5'Flank|USP45_uc003ppy.2_RNA|USP45_uc010kcq.1_Silent_p.T21T|USP45_uc003ppz.2_Silent_p.T21T|USP45_uc003pqa.2_Silent_p.T21T	NM_001080481	NP_001073950	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	21					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|breast(1)	2		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100838636	100838636	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100838636C>T	uc003pqj.3	-	11	2109	c.1902G>A	c.(1900-1902)CAG>CAA	p.Q634Q	SIM1_uc010kcu.2_Silent_p.Q634Q	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	634	Single-minded C-terminal.				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)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101075830	101075830	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101075830A>G	uc003pqk.2	-	28	4738	c.4409T>C	c.(4408-4410)GTA>GCA	p.V1470A		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1470	Helicase ATP-binding 2.				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)														---	---	---	---
SCML4	256380	broad.mit.edu	37	6	108066255	108066255	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108066255G>T	uc010kdf.2	-	5	831	c.580C>A	c.(580-582)CGA>AGA	p.R194R	SCML4_uc003prz.3_Silent_p.R136R|SCML4_uc011eam.1_Silent_p.R194R|SCML4_uc003psa.3_Silent_p.R165R	NM_198081	NP_932347	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4	194					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)														---	---	---	---
ARMC2	84071	broad.mit.edu	37	6	109233764	109233764	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109233764A>G	uc003pss.3	+						ARMC2_uc011eao.1_Intron	NM_032131	NP_115507			armadillo repeat containing 2								binding				0		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)														---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111643889	111643889	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111643889T>C	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					---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111710360	111710360	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111710360G>A	uc003puy.3	-	7	1134	c.811C>T	c.(811-813)CGG>TGG	p.R271W	REV3L_uc003pux.3_Missense_Mutation_p.R193W|REV3L_uc003puz.3_Missense_Mutation_p.R193W	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	271					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					---	---	---	---
DSE	29940	broad.mit.edu	37	6	116747852	116747852	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116747852C>A	uc003pws.2	+	3	726	c.532C>A	c.(532-534)CTT>ATT	p.L178I	DSE_uc011ebf.1_Missense_Mutation_p.L178I|DSE_uc011ebg.1_Missense_Mutation_p.L197I|DSE_uc003pwt.2_Missense_Mutation_p.L178I	NM_001080976	NP_001074445	Q9UL01	DSE_HUMAN	dermatan sulfate epimerase precursor	178					dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
NCOA7	135112	broad.mit.edu	37	6	126240504	126240504	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:126240504T>C	uc010kes.2	+						NCOA7_uc003qae.3_Intron|NCOA7_uc003qah.2_Intron|NCOA7_uc003qai.2_Intron|NCOA7_uc010ket.2_Intron|NCOA7_uc003qak.2_Missense_Mutation_p.M1T	NM_181782	NP_861447			nuclear receptor coactivator 7 isoform 1						cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131247750	131247750	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131247750G>A	uc003qch.2	-	4	987	c.805C>T	c.(805-807)CAG>TAG	p.Q269*	EPB41L2_uc003qcg.1_Nonsense_Mutation_p.Q269*|EPB41L2_uc011eby.1_Nonsense_Mutation_p.Q269*|EPB41L2_uc003qci.2_Nonsense_Mutation_p.Q269*|EPB41L2_uc010kfk.2_Nonsense_Mutation_p.Q269*|EPB41L2_uc010kfl.1_Nonsense_Mutation_p.Q269*	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	269	FERM.				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)														---	---	---	---
STX7	8417	broad.mit.edu	37	6	132781989	132781989	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132781989G>A	uc003qdg.2	-	10	944	c.694C>T	c.(694-696)CGC>TGC	p.R232C	STX7_uc011ecg.1_RNA|STX7_uc011ech.1_Missense_Mutation_p.R57C	NM_003569	NP_003560	O15400	STX7_HUMAN	syntaxin 7	232	Cytoplasmic (Potential).				intracellular protein transport|post-Golgi vesicle-mediated transport	early endosome membrane|integral to membrane	SNAP receptor activity				0	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)														---	---	---	---
TNFAIP3	7128	broad.mit.edu	37	6	138196150	138196150	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138196150C>T	uc003qhr.2	+	3	530	c.464C>T	c.(463-465)ACG>ATG	p.T155M	TNFAIP3_uc003qhs.2_Missense_Mutation_p.T155M	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	155	TRAF-binding.|OTU.				anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding	p.0?(22)|p.T155T(1)		haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)				D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								---	---	---	---
ADAT2	134637	broad.mit.edu	37	6	143771793	143771793	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143771793C>A	uc003qjj.2	-	1	49	c.3G>T	c.(1-3)ATG>ATT	p.M1I	PEX3_uc011edx.1_5'Flank|PEX3_uc003qjl.2_5'Flank	NM_182503	NP_872309	Q7Z6V5	ADAT2_HUMAN	deaminase domain containing 1	1					tRNA processing		hydrolase activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144872230	144872230	+	Intron	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144872230A>T	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)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146243472	146243472	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146243472A>G	uc003qlf.2	-	20	4131	c.3732T>C	c.(3730-3732)TGT>TGC	p.C1244C	SHPRH_uc003qld.2_Silent_p.C1248C|SHPRH_uc003qle.2_Silent_p.C1248C|SHPRH_uc003qlg.1_Silent_p.C800C|SHPRH_uc003qlh.2_Silent_p.C169C|SHPRH_uc003qli.1_Silent_p.C169C	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1244					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146678795	146678795	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146678795G>C	uc010khw.1	+	6	2037	c.1567G>C	c.(1567-1569)GTG>CTG	p.V523L	GRM1_uc010khv.1_Missense_Mutation_p.V523L|GRM1_uc003qll.2_Missense_Mutation_p.V523L|GRM1_uc011edz.1_Missense_Mutation_p.V523L|GRM1_uc011eea.1_Missense_Mutation_p.V523L	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	523	Extracellular (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
RAB32	10981	broad.mit.edu	37	6	146865142	146865142	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146865142C>T	uc003qln.1	+	1	315	c.135C>T	c.(133-135)TAC>TAT	p.Y45Y		NM_006834	NP_006825	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	45					protein transport|small GTPase mediated signal transduction	mitochondrion	GTP binding				0		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)														---	---	---	---
ZC3H12D	340152	broad.mit.edu	37	6	149777945	149777945	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149777945G>A	uc003qmn.1	-	3	607	c.537C>T	c.(535-537)GAC>GAT	p.D179D	PPIL4_uc010kic.2_Intron|ZC3H12D_uc003qmm.2_Silent_p.D179D|ZC3H12D_uc010kid.2_Silent_p.D179D	NM_207360	NP_997243	A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	179						cytoplasm|nucleus	endonuclease activity|nucleic acid binding|zinc ion binding				0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152718029	152718029	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152718029T>G	uc010kiw.2	-	50	8039	c.7437A>C	c.(7435-7437)AAA>AAC	p.K2479N	SYNE1_uc003qot.3_Missense_Mutation_p.K2486N|SYNE1_uc003qou.3_Missense_Mutation_p.K2479N|SYNE1_uc010kjb.1_Missense_Mutation_p.K2462N	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2479	Spectrin 4.|Cytoplasmic (Potential).				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)			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155578187	155578187	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155578187G>A	uc003qqb.2	+	29	6311	c.5038G>A	c.(5038-5040)GTC>ATC	p.V1680I	TIAM2_uc003qqe.2_Missense_Mutation_p.V1680I|TIAM2_uc010kjj.2_Missense_Mutation_p.V1242I|TIAM2_uc003qqf.2_Missense_Mutation_p.V1056I|TIAM2_uc011efl.1_Missense_Mutation_p.V1024I|TIAM2_uc003qqg.2_Missense_Mutation_p.V992I|TIAM2_uc003qqh.2_Missense_Mutation_p.V605I|uc003qqi.1_5'Flank	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1680					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)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157405929	157405929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157405929C>T	uc003qqn.2	+	5	2110	c.1958C>T	c.(1957-1959)GCG>GTG	p.A653V	ARID1B_uc003qqo.2_Missense_Mutation_p.A666V|ARID1B_uc003qqp.2_Missense_Mutation_p.A653V|ARID1B_uc003qqq.1_Missense_Mutation_p.A95V	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	711	Ser-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158923930	158923930	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158923930G>A	uc003qrf.2	+	13	4592	c.3235G>A	c.(3235-3237)GAC>AAC	p.D1079N	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1079					intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160638452	160638452	+	3'UTR	SNP	C	T	T	rs150706757	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160638452C>T	uc003qtf.2	-	11					SLC22A2_uc003qte.1_Intron	NM_003058	NP_003049			solute carrier family 22 member 2						body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)														---	---	---	---
MAP3K4	4216	broad.mit.edu	37	6	161513073	161513073	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161513073G>T	uc003qtn.2	+	13	3309	c.3167G>T	c.(3166-3168)GGG>GTG	p.G1056V	MAP3K4_uc010kkc.1_Missense_Mutation_p.G1056V|MAP3K4_uc003qto.2_Missense_Mutation_p.G1056V|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_Missense_Mutation_p.G509V|MAP3K4_uc003qtp.2_Missense_Mutation_p.G46V	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1056					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161990440	161990440	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161990440G>A	uc003qtx.3	-	8	1014	c.880C>T	c.(880-882)CCC>TCC	p.P294S	PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Missense_Mutation_p.P103S|PARK2_uc003qtw.3_Missense_Mutation_p.P103S|PARK2_uc003qty.3_Missense_Mutation_p.P266S|PARK2_uc003qtz.3_Missense_Mutation_p.P145S|PARK2_uc010kke.1_Missense_Mutation_p.P313S|PARK2_uc011egf.1_5'UTR	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	294					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)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166864694	166864694	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166864694T>C	uc003qvb.1	-	13	1322	c.1103A>G	c.(1102-1104)AAC>AGC	p.N368S	RPS6KA2_uc011ego.1_Missense_Mutation_p.N279S|RPS6KA2_uc010kkl.1_Missense_Mutation_p.N279S|RPS6KA2_uc003qvc.1_Missense_Mutation_p.N376S|RPS6KA2_uc003qvd.1_Missense_Mutation_p.N393S	NM_021135	NP_066958	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	368	AGC-kinase C-terminal.				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)														---	---	---	---
KIF25	3834	broad.mit.edu	37	6	168430309	168430309	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168430309G>T	uc003qwk.1	+	2	306	c.44G>T	c.(43-45)AGG>ATG	p.R15M	KIF25_uc010kkt.1_RNA|KIF25_uc003qwl.1_Missense_Mutation_p.R15M	NM_030615	NP_085118	Q9UIL4	KIF25_HUMAN	kinesin family member 25 isoform 1	15	Kinesin-motor.				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(1)|pancreas(1)	2		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1527082	1527082	+	Silent	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1527082C>G	uc003skn.2	-	20	2621	c.2520G>C	c.(2518-2520)GGG>GGC	p.G840G	INTS1_uc003skp.1_Silent_p.G187G	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	840					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2418770	2418770	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2418770A>G	uc003slx.2	+	17	2317	c.2234A>G	c.(2233-2235)GAA>GGA	p.E745G	EIF3B_uc003sly.2_Missense_Mutation_p.E745G|EIF3B_uc003sma.2_Missense_Mutation_p.E473G|EIF3B_uc003smb.2_RNA	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	745					regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4218194	4218194	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4218194G>A	uc003smx.2	+	35	5213	c.5074G>A	c.(5074-5076)GTG>ATG	p.V1692M	SDK1_uc010kso.2_Missense_Mutation_p.V948M|SDK1_uc003smy.2_Missense_Mutation_p.V179M	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1692	Fibronectin type-III 10.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8062115	8062115	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8062115A>G	uc003srk.2	+	3	1171	c.612A>G	c.(610-612)ACA>ACG	p.T204T		NM_138426	NP_612435	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	204											0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8198199	8198199	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8198199C>T	uc003srm.2	-	7	730	c.663G>A	c.(661-663)GCG>GCA	p.A221A	ICA1_uc010ktr.2_Silent_p.A221A|ICA1_uc003srl.2_Silent_p.A209A|ICA1_uc003srn.3_Silent_p.A147A|ICA1_uc003srp.3_Silent_p.A220A|ICA1_uc010kts.2_RNA|ICA1_uc003srq.2_Silent_p.A221A|ICA1_uc003srr.2_Silent_p.A220A|ICA1_uc003sro.3_Silent_p.A221A|ICA1_uc011jxg.1_Silent_p.A221A|ICA1_uc003srs.1_Silent_p.A221A	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1	221	AH.				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)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11080314	11080314	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11080314G>A	uc003sry.1	+	12	2527	c.2092G>A	c.(2092-2094)GCA>ACA	p.A698T	PHF14_uc011jxi.1_Missense_Mutation_p.A413T|PHF14_uc003srz.2_Missense_Mutation_p.A698T|PHF14_uc011jxj.1_Missense_Mutation_p.A413T	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	698							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12668796	12668796	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12668796A>G	uc003ssn.3	+	9	1478	c.1268A>G	c.(1267-1269)GAC>GGC	p.D423G	SCIN_uc010ktt.2_RNA|SCIN_uc003sso.3_Missense_Mutation_p.D176G	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1	423	Ca(2+)-dependent actin binding.|Gelsolin-like 4.				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)														---	---	---	---
ABCB5	340273	broad.mit.edu	37	7	20793131	20793131	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20793131T>C	uc003suw.3	+	18	2787	c.2241_splice	c.e18+2	p.K747_splice	ABCB5_uc010kuh.2_Splice_Site_p.K1192_splice	NM_178559	NP_848654			ATP-binding cassette, sub-family B, member 5						regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21742378	21742378	+	Silent	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21742378T>A	uc003svc.2	+	38	6283	c.6252T>A	c.(6250-6252)GCT>GCA	p.A2084A		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2084					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DFNA5	1687	broad.mit.edu	37	7	24756983	24756983	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24756983G>A	uc010kus.1	-	5	675	c.587C>T	c.(586-588)ACG>ATG	p.T196M	DFNA5_uc003swz.2_Missense_Mutation_p.T32M|DFNA5_uc003sxa.1_Missense_Mutation_p.T196M|DFNA5_uc010kut.1_Missense_Mutation_p.T32M|DFNA5_uc003sxb.2_Missense_Mutation_p.T196M	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	196					sensory perception of sound					ovary(1)	1																		---	---	---	---
NFE2L3	9603	broad.mit.edu	37	7	26225407	26225407	+	3'UTR	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26225407G>A	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																		---	---	---	---
HOXA3	3200	broad.mit.edu	37	7	27148111	27148111	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27148111C>T	uc011jzl.1	-	3	955	c.755G>A	c.(754-756)GGC>GAC	p.G252D	HOXA3_uc011jzk.1_Missense_Mutation_p.G94D|HOXA3_uc003syk.2_Missense_Mutation_p.G252D	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	252					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2																		---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27855995	27855995	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27855995G>A	uc003szl.2	+	14	1950	c.1792G>A	c.(1792-1794)GCA>ACA	p.A598T	TAX1BP1_uc011jzo.1_Missense_Mutation_p.A598T|TAX1BP1_uc003szk.2_Missense_Mutation_p.A598T|TAX1BP1_uc011jzp.1_Missense_Mutation_p.A441T	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)	598	Potential.				anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)															---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	31862835	31862835	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31862835G>A	uc003tcm.1	-	14	1903	c.1434C>T	c.(1432-1434)GCC>GCT	p.A478A	PDE1C_uc003tcn.1_Silent_p.A478A|PDE1C_uc003tco.1_Silent_p.A538A|PDE1C_uc003tcr.2_Silent_p.A478A|PDE1C_uc003tcs.2_Silent_p.A478A	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	478	Catalytic (By similarity).				activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
SEPT7	989	broad.mit.edu	37	7	35872451	35872451	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35872451C>A	uc010kxc.2	+	2	303	c.110C>A	c.(109-111)CCA>CAA	p.P37Q	SEPT7_uc011kat.1_Missense_Mutation_p.P36Q|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_5'UTR	NM_001788	NP_001779	Q16181	SEPT7_HUMAN	cell division cycle 10 isoform 1	37					cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37251045	37251045	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37251045G>A	uc003tfk.1	-	13	1339	c.1032C>T	c.(1030-1032)AGC>AGT	p.S344S	ELMO1_uc011kbc.1_Silent_p.S248S|ELMO1_uc010kxg.1_Silent_p.S344S	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	344	ELMO.				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																		---	---	---	---
GPR141	353345	broad.mit.edu	37	7	37780456	37780456	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37780456G>T	uc003tfm.1	+	1	461	c.461G>T	c.(460-462)CGG>CTG	p.R154L	uc003tfl.2_Intron	NM_181791	NP_861456	Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	154	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40132819	40132819	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40132819C>A	uc003thh.3	+	13	3953	c.3671C>A	c.(3670-3672)CCT>CAT	p.P1224H	CDK13_uc003thi.3_Missense_Mutation_p.P1164H|CDK13_uc003thj.2_Missense_Mutation_p.P275H|CDK13_uc003thk.2_Missense_Mutation_p.P157H	NM_003718	NP_003709	Q14004	CDK13_HUMAN	cell division cycle 2-like 5 isoform 1	1224					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																		---	---	---	---
AEBP1	165	broad.mit.edu	37	7	44153301	44153301	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44153301T>C	uc003tkb.2	+	21	3223	c.2918T>C	c.(2917-2919)ATC>ACC	p.I973T	AEBP1_uc003tkc.3_Missense_Mutation_p.I548T|AEBP1_uc003tkd.2_Missense_Mutation_p.I223T	NM_001129	NP_001120	Q8IUX7	AEBP1_HUMAN	adipocyte enhancer binding protein 1 precursor	973	Interaction with PTEN (By similarity).|Required for transcriptional repression (By similarity).				cell adhesion|muscle organ development|proteolysis|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GCK	2645	broad.mit.edu	37	7	44187337	44187337	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44187337C>T	uc003tkl.2	-	7	1245	c.775G>A	c.(775-777)GCC>ACC	p.A259T	GCK_uc003tkh.1_5'Flank|GCK_uc003tki.1_5'Flank|GCK_uc003tkj.1_Missense_Mutation_p.A258T|GCK_uc003tkk.1_Missense_Mutation_p.A260T	NM_000162	NP_000153	P35557	HXK4_HUMAN	glucokinase isoform 1	259			A -> T (in MODY2).		cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4																		---	---	---	---
COBL	23242	broad.mit.edu	37	7	51098597	51098597	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51098597T>C	uc003tpr.3	-	9	1601	c.1416A>G	c.(1414-1416)AAA>AAG	p.K472K	COBL_uc003tps.2_Silent_p.K529K|COBL_uc011kcl.1_Silent_p.K472K|COBL_uc003tpp.3_Silent_p.K258K|COBL_uc003tpq.3_Silent_p.K413K|COBL_uc003tpo.3_Silent_p.K14K	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	472										skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
SEC61G	23480	broad.mit.edu	37	7	54823470	54823470	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54823470A>G	uc003tqf.2	-	3	288	c.197_splice	c.e3+1	p.V66_splice	SEC61G_uc003tqg.2_Splice_Site_p.V66_splice	NM_001012456	NP_001012474			Sec61 gamma subunit						protein targeting to ER	endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			lung(1)	1	Esophageal squamous(2;7.55e-08)|Breast(14;0.0654)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)															---	---	---	---
ZNF117	51351	broad.mit.edu	37	7	64452191	64452191	+	5'Flank	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64452191A>C	uc003ttr.2	-						ZNF117_uc011kdr.1_Missense_Mutation_p.L402R	NM_015852	NP_056936			zinc finger protein 117							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
ZNF92	168374	broad.mit.edu	37	7	64863705	64863705	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64863705A>G	uc003ttz.2	+	4	821	c.678A>G	c.(676-678)GAA>GAG	p.E226E	ZNF92_uc003tua.2_Silent_p.E157E|ZNF92_uc010kzu.2_Silent_p.E194E|ZNF92_uc003tub.2_Silent_p.E150E	NM_152626	NP_689839	Q03936	ZNF92_HUMAN	zinc finger protein 92 isoform 2	226						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(55;0.159)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66479405	66479405	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66479405C>A	uc003tvn.2	+	5	576	c.427C>A	c.(427-429)CTA>ATA	p.L143I	TYW1_uc010lai.2_RNA	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	143	Flavodoxin-like.				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)																---	---	---	---
POM121	9883	broad.mit.edu	37	7	72416158	72416158	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72416158C>A	uc010lam.1	+	15	3809	c.2768C>A	c.(2767-2769)CCT>CAT	p.P923H	POM121_uc003twj.2_Missense_Mutation_p.P923H	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	1188	Pore side (Potential).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)																---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72863875	72863875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72863875C>T	uc003tyc.2	-	15	4070	c.3725G>A	c.(3724-3726)GGC>GAC	p.G1242D		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1242					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)																---	---	---	---
SPDYE5	442590	broad.mit.edu	37	7	75131017	75131017	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75131017C>T	uc011kfy.1	+	6	1028	c.892C>T	c.(892-894)CGG>TGG	p.R298W		NM_001099435	NP_001092905	A6NIY4	SPDE5_HUMAN	speedy homolog E5	298	Arg-rich.										0																		---	---	---	---
TMEM120A	83862	broad.mit.edu	37	7	75617570	75617570	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75617570C>A	uc003ued.2	-	7	667	c.563G>T	c.(562-564)CGG>CTG	p.R188L	TMEM120A_uc003uee.2_Missense_Mutation_p.R92L|TMEM120A_uc003ueb.1_5'Flank|TMEM120A_uc003uec.2_Missense_Mutation_p.R92L	NM_031925	NP_114131	Q9BXJ8	T120A_HUMAN	transmembrane protein 120A	188	Extracellular (Potential).					integral to membrane					0																		---	---	---	---
FGL2	10875	broad.mit.edu	37	7	76825822	76825822	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76825822C>T	uc003ugb.2	-	2	1134	c.1094G>A	c.(1093-1095)CGA>CAA	p.R365Q	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	365	Fibrinogen C-terminal.				signal transduction	fibrinogen complex	receptor binding			skin(2)	2																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82580130	82580130	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82580130C>T	uc003uhx.2	-	6	10063	c.9774G>A	c.(9772-9774)GAG>GAA	p.E3258E	PCLO_uc003uhv.2_Silent_p.E3258E|PCLO_uc010lec.2_Silent_p.E223E	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3189	Gln-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82584742	82584742	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82584742G>A	uc003uhx.2	-	5	5816	c.5527C>T	c.(5527-5529)CGT>TGT	p.R1843C	PCLO_uc003uhv.2_Missense_Mutation_p.R1843C	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1774					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
STEAP4	79689	broad.mit.edu	37	7	87913386	87913386	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87913386A>G	uc003ujs.2	-	2	304	c.199T>C	c.(199-201)TAT>CAT	p.Y67H	STEAP4_uc010lek.2_Missense_Mutation_p.Y67H|STEAP4_uc003ujt.2_Missense_Mutation_p.Y67H	NM_024636	NP_078912	Q687X5	STEA4_HUMAN	tumor necrosis factor, alpha-induced protein 9	67					fat cell differentiation|ion transport|iron ion homeostasis	Golgi membrane|integral to membrane|plasma membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	Esophageal squamous(14;0.00802)																	---	---	---	---
PEX1	5189	broad.mit.edu	37	7	92141029	92141029	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92141029A>G	uc003uly.2	-						PEX1_uc011khr.1_Intron|PEX1_uc010ley.2_Intron|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_Intron	NM_000466	NP_000457			peroxin1						microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)															---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92926504	92926504	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92926504T>C	uc003umo.2	+	16	1438	c.1310T>C	c.(1309-1311)TTA>TCA	p.L437S	CCDC132_uc003umq.2_RNA|CCDC132_uc003ump.2_Missense_Mutation_p.L407S|CCDC132_uc003umr.2_RNA|CCDC132_uc011khz.1_Missense_Mutation_p.L157S	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	437											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
OCM2	4951	broad.mit.edu	37	7	97617763	97617763	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97617763G>A	uc003upc.2	-	2	159	c.159C>T	c.(157-159)AAC>AAT	p.N53N		NM_006188	NP_006179	P0CE71	OCM2_HUMAN	oncomodulin-like	53	EF-hand 1.|1 (Potential).						calcium ion binding				0																		---	---	---	---
CYP3A5	1577	broad.mit.edu	37	7	99262895	99262895	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99262895T>C	uc003urq.2	-	7	651	c.564A>G	c.(562-564)TCA>TCG	p.S188S	ZNF498_uc003urn.2_Intron|CYP3A5_uc003urp.2_Silent_p.S8S|CYP3A5_uc003urr.2_Silent_p.S75S|CYP3A5_uc011kiy.1_Silent_p.S178S|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron	NM_000777	NP_000768	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A,	188					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)													---	---	---	---
OR2AE1	81392	broad.mit.edu	37	7	99474306	99474306	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99474306G>A	uc003usc.1	-	1	351	c.351C>T	c.(349-351)GTC>GTT	p.V117V		NM_001005276	NP_001005276	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE,	117	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)																	---	---	---	---
ZNF3	7551	broad.mit.edu	37	7	99669329	99669329	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99669329C>T	uc003usq.2	-	6	1085	c.778G>A	c.(778-780)GAT>AAT	p.D260N	ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Missense_Mutation_p.D260N|ZNF3_uc010lgj.2_Missense_Mutation_p.D224N|ZNF3_uc003uss.2_Missense_Mutation_p.D267N|ZNF3_uc003ust.3_Missense_Mutation_p.D260N	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2	260	C2H2-type 3.				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)															---	---	---	---
MCM7	4176	broad.mit.edu	37	7	99695276	99695276	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99695276C>A	uc003usw.1	-	9	1588	c.1078G>T	c.(1078-1080)GGG>TGG	p.G360W	MCM7_uc003usv.1_Missense_Mutation_p.G184W|MCM7_uc003usx.1_Missense_Mutation_p.G184W	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	360	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)													---	---	---	---
GATS	352954	broad.mit.edu	37	7	99821527	99821527	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99821527G>A	uc003uua.3	-	3	638	c.389C>T	c.(388-390)ACG>ATG	p.T130M	GATS_uc003uty.3_RNA|GATS_uc003utz.3_RNA|GATS_uc010lgt.2_RNA|GATS_uc011kjl.1_5'Flank|GATS_uc010lgu.2_RNA	NM_178831	NP_849153	Q8NAP1	GATS_HUMAN	GATS, stromal antigen 3 opposite strand	130											0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
C7orf51	222950	broad.mit.edu	37	7	100086071	100086071	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100086071G>A	uc003uvd.1	+	4	886	c.727G>A	c.(727-729)GGC>AGC	p.G243S	C7orf51_uc003uve.1_Missense_Mutation_p.G25S	NM_173564	NP_775835	Q6ZVC0	CG051_HUMAN	hypothetical protein FLJ37538	243	Poly-Gly.									skin(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
EPHB4	2050	broad.mit.edu	37	7	100420130	100420130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100420130G>A	uc003uwn.1	-	4	1062	c.571C>T	c.(571-573)CAC>TAC	p.H191Y	EPHB4_uc003uwm.1_Missense_Mutation_p.H98Y|EPHB4_uc010lhj.1_Missense_Mutation_p.H191Y|EPHB4_uc011kkf.1_Missense_Mutation_p.H191Y|EPHB4_uc011kkg.1_Missense_Mutation_p.H191Y|EPHB4_uc011kkh.1_Missense_Mutation_p.H191Y	NM_004444	NP_004435	P54760	EPHB4_HUMAN	EPH receptor B4 precursor	191	Extracellular (Potential).|Cys-rich.				cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
SLC12A9	56996	broad.mit.edu	37	7	100453458	100453458	+	Silent	SNP	C	T	T	rs140479354	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100453458C>T	uc003uwp.2	+	4	589	c.447C>T	c.(445-447)GCC>GCT	p.A149A	SLC12A9_uc003uwo.1_Intron|SLC12A9_uc003uwq.2_Intron|SLC12A9_uc011kki.1_Intron|SLC12A9_uc003uwr.2_5'UTR|SLC12A9_uc003uws.2_5'UTR|SLC12A9_uc003uwt.2_5'Flank|SLC12A9_uc003uwv.2_5'Flank	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	149	Extracellular (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
SRRT	51593	broad.mit.edu	37	7	100478930	100478930	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100478930C>T	uc003uwy.2	+	4	415	c.147C>T	c.(145-147)CGC>CGT	p.R49R	SRRT_uc010lhl.1_Silent_p.R49R|SRRT_uc003uxa.2_Silent_p.R49R|SRRT_uc003uwz.2_Silent_p.R49R	NM_015908	NP_056992	Q9BXP5	SRRT_HUMAN	arsenate resistance protein 2 isoform a	49	Arg-rich.				cell proliferation|primary miRNA processing|response to arsenic-containing substance	cytoplasm|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	100606770	100606770	+	RNA	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100606770C>T	uc003uxk.1	+	3		c.2244C>T			uc003uxl.1_Silent_p.F520F|uc010lhn.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100678426	100678426	+	Silent	SNP	C	A	A	rs4729650	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100678426C>A	uc003uxp.1	+	3	3782	c.3729C>A	c.(3727-3729)CCC>CCA	p.P1243P	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1243	Extracellular (Potential).|Ser-rich.|18.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100679839	100679839	+	Silent	SNP	C	A	A	rs71557227	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100679839C>A	uc003uxp.1	+	3	5195	c.5142C>A	c.(5140-5142)CCC>CCA	p.P1714P	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1714	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|26.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100682851	100682851	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100682851C>T	uc003uxp.1	+	3	8207	c.8154C>T	c.(8152-8154)GAC>GAT	p.D2718D	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2718	Extracellular (Potential).|43.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
ORAI2	80228	broad.mit.edu	37	7	102087353	102087353	+	Missense_Mutation	SNP	G	A	A	rs149386719		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102087353G>A	uc010lhz.1	+	4	854	c.619G>A	c.(619-621)GTG>ATG	p.V207M	ORAI2_uc003uzj.2_Missense_Mutation_p.V207M|ORAI2_uc003uzk.2_Missense_Mutation_p.V207M|ORAI2_uc011kks.1_Missense_Mutation_p.V130M	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	207	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|kidney(1)	2																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103155701	103155701	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103155701G>A	uc003vca.2	-	50	8210	c.8050C>T	c.(8050-8052)CGC>TGC	p.R2684C	RELN_uc010liz.2_Missense_Mutation_p.R2684C	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2684					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104753431	104753431	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104753431C>A	uc003vcm.2	+	27	5762	c.5228C>A	c.(5227-5229)CCT>CAT	p.P1743H	MLL5_uc010ljc.2_Missense_Mutation_p.P1743H|MLL5_uc010ljf.1_Intron|MLL5_uc010ljg.2_Missense_Mutation_p.P477H	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1743	Pro-rich.				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																		---	---	---	---
CDHR3	222256	broad.mit.edu	37	7	105653434	105653434	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105653434G>A	uc003vdl.3	+	9	1289	c.1181G>A	c.(1180-1182)GGC>GAC	p.G394D	CDHR3_uc003vdk.2_Missense_Mutation_p.G42D|CDHR3_uc011kls.1_RNA|CDHR3_uc003vdm.3_Missense_Mutation_p.G381D|CDHR3_uc011klt.1_Missense_Mutation_p.G306D|CDHR3_uc003vdn.2_Missense_Mutation_p.G111D	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN	hypothetical protein LOC222256 precursor	394	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107580698	107580698	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107580698G>A	uc003vew.2	-	25	3832	c.3497C>T	c.(3496-3498)ACG>ATG	p.T1166M	LAMB1_uc003vev.2_Missense_Mutation_p.T1190M	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1166	Laminin EGF-like 13.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107807442	107807442	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107807442T>C	uc003vfb.2	-	30	3861	c.3390A>G	c.(3388-3390)ACA>ACG	p.T1130T	NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron|NRCAM_uc011kmj.1_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A	1130	Fibronectin type-III 5.|Extracellular (Potential).				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																		---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110762847	110762847	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110762847C>A	uc003vft.3	+	4	1065	c.19C>A	c.(19-21)CGA>AGA	p.R7R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Silent_p.R7R|LRRN3_uc003vfs.3_Silent_p.R7R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	7						integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110764283	110764283	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764283C>T	uc003vft.3	+	4	2501	c.1455C>T	c.(1453-1455)GGC>GGT	p.G485G	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Silent_p.G485G|LRRN3_uc003vfs.3_Silent_p.G485G	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	485	Extracellular (Potential).|Ig-like C2-type.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117417627	117417627	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117417627T>C	uc003vjf.2	-	8	2808	c.2716A>G	c.(2716-2718)ATT>GTT	p.I906V		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	906										ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
CPA5	93979	broad.mit.edu	37	7	130008355	130008355	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130008355G>A	uc010lmd.1	+	14	1848	c.1228G>A	c.(1228-1230)GCC>ACC	p.A410T	CPA5_uc003vps.2_Missense_Mutation_p.A410T|CPA5_uc003vpt.2_Silent_p.R381R|CPA5_uc010lme.1_Missense_Mutation_p.A410T|CPA5_uc003vpu.1_Missense_Mutation_p.A410T|uc003vpv.1_RNA	NM_001127441	NP_001120913	Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5 isoform 1	410					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)																	---	---	---	---
CPA1	1357	broad.mit.edu	37	7	130021944	130021944	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130021944C>A	uc003vpx.2	+						CPA1_uc011kpf.1_Intron|CPA1_uc003vpw.2_Intron	NM_001868	NP_001859			carboxypeptidase A1 precursor						proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)															OREG0018314	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131859587	131859587	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131859587G>A	uc003vra.3	-	21	4196	c.3967C>T	c.(3967-3969)CGG>TGG	p.R1323W		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1323	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135047678	135047678	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135047678G>T	uc011kpy.1	-	11	2193	c.2101C>A	c.(2101-2103)CCC>ACC	p.P701T	CNOT4_uc003vss.2_Missense_Mutation_p.P627T|CNOT4_uc011kpz.1_Missense_Mutation_p.P698T|CNOT4_uc003vst.2_Missense_Mutation_p.P630T	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	370					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135301989	135301989	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135301989T>C	uc003vsw.2	+	26	3715	c.3684T>C	c.(3682-3684)AAT>AAC	p.N1228N	NUP205_uc003vsx.2_5'Flank	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1228					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138603265	138603265	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138603265C>T	uc011kql.1	-	2	1156	c.1107G>A	c.(1105-1107)GCG>GCA	p.A369A	KIAA1549_uc003vuk.3_Silent_p.A319A|KIAA1549_uc011kqj.1_Silent_p.A369A	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	369						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139416405	139416405	+	Silent	SNP	G	A	A	rs113824554		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139416405G>A	uc003vvf.3	-	2	603	c.429C>T	c.(427-429)AGC>AGT	p.S143S	HIPK2_uc003vvd.3_Silent_p.S143S	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	143	Transcriptional corepression (By similarity).				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)																	---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140390620	140390620	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140390620G>A	uc003vvy.1	+						ADCK2_uc003vvz.2_Intron	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
TRPV6	55503	broad.mit.edu	37	7	142574257	142574257	+	Silent	SNP	G	A	A	rs138217574		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142574257G>A	uc003wbx.1	-	6	882	c.666C>T	c.(664-666)TAC>TAT	p.Y222Y	TRPV6_uc003wbw.1_Silent_p.Y8Y|TRPV6_uc010lou.1_Silent_p.Y93Y	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	222	Cytoplasmic (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(2)	2	Melanoma(164;0.059)																	---	---	---	---
EPHA1	2041	broad.mit.edu	37	7	143096842	143096842	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143096842C>T	uc003wcz.2	-	4	824	c.737G>A	c.(736-738)CGC>CAC	p.R246H		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	246	Extracellular (Potential).|Cys-rich.					integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)																---	---	---	---
OR2F2	135948	broad.mit.edu	37	7	143632553	143632553	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143632553C>T	uc011ktv.1	+	1	228	c.228C>T	c.(226-228)AGC>AGT	p.S76S		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	76	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	Melanoma(164;0.0903)																	---	---	---	---
OR2F2	135948	broad.mit.edu	37	7	143632955	143632955	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143632955T>C	uc011ktv.1	+	1	630	c.630T>C	c.(628-630)CCT>CCC	p.P210P		NM_001004685	NP_001004685	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	Melanoma(164;0.0903)																	---	---	---	---
OR2F1	26211	broad.mit.edu	37	7	143657708	143657708	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143657708T>G	uc003wds.1	+	1	689	c.645T>G	c.(643-645)CTT>CTG	p.L215L		NM_012369	NP_036501	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F,	215	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	Melanoma(164;0.0903)																	---	---	---	---
OR2A2	442361	broad.mit.edu	37	7	143806951	143806951	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143806951C>A	uc011ktz.1	+	1	276	c.276C>A	c.(274-276)TCC>TCA	p.S92S		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	92	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)																	---	---	---	---
ARHGEF5	7984	broad.mit.edu	37	7	144070331	144070331	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144070331C>T	uc003wel.2	+	10	4212	c.4094C>T	c.(4093-4095)ACA>ATA	p.T1365I	ARHGEF5_uc003wek.2_Missense_Mutation_p.T1365I|ARHGEF5_uc003wem.2_Missense_Mutation_p.T220I	NM_005435	NP_005426	Q12774	ARHG5_HUMAN	rho guanine nucleotide exchange factor 5	1365					intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity			skin(2)	2	Melanoma(164;0.14)																	---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148507436	148507436	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148507436T>C	uc003wfd.1	-	17	2169	c.2003A>G	c.(2002-2004)AAC>AGC	p.N668S	EZH2_uc011kug.1_Missense_Mutation_p.N617S|EZH2_uc003wfb.1_Missense_Mutation_p.N673S|EZH2_uc003wfc.1_Missense_Mutation_p.N629S|EZH2_uc011kuh.1_Missense_Mutation_p.N659S	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	668	SET.				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								---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148851131	148851131	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148851131C>T	uc003wfl.2	+	2	394	c.119C>T	c.(118-120)GCT>GTT	p.A40V	ZNF398_uc011kul.1_5'UTR|ZNF398_uc011kum.1_Missense_Mutation_p.A45V	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	40					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	148978653	148978653	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148978653G>A	uc003wfr.3	+						uc011kuo.1_5'Flank					Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																														---	---	---	---
ABP1	26	broad.mit.edu	37	7	150554063	150554063	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150554063A>G	uc003why.1	+	3	4723	c.505A>G	c.(505-507)ACC>GCC	p.T169A	ABP1_uc003whz.1_Missense_Mutation_p.T169A|ABP1_uc003wia.1_Missense_Mutation_p.T169A	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	169					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
ABP1	26	broad.mit.edu	37	7	150554734	150554734	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150554734G>A	uc003why.1	+	3	5394	c.1176G>A	c.(1174-1176)CCG>CCA	p.P392P	ABP1_uc003whz.1_Silent_p.P392P|ABP1_uc003wia.1_Silent_p.P392P	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	392					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
ASB10	136371	broad.mit.edu	37	7	150883498	150883498	+	Missense_Mutation	SNP	G	A	A	rs104886473	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150883498G>A	uc003wjm.1	-	2	826	c.700C>T	c.(700-702)CGG>TGG	p.R234W	ASB10_uc003wjl.1_Missense_Mutation_p.R234W|ASB10_uc003wjn.1_Missense_Mutation_p.R174W	NM_001142459	NP_001135931	Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box-containing 10	189	ANK 3.				intracellular signal transduction						0			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151860524	151860524	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151860524G>A	uc003wla.2	-	43	10357	c.10138C>T	c.(10138-10140)CCA>TCA	p.P3380S	MLL3_uc003wkz.2_Missense_Mutation_p.P2441S|MLL3_uc003wky.2_Missense_Mutation_p.P889S	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3380	Gln-rich.|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								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151962206	151962206	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151962206A>G	uc003wla.2	-	8	1320	c.1101T>C	c.(1099-1101)CAT>CAC	p.H367H		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	367	PHD-type 1.|RING-type.				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								---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2820754	2820754	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2820754G>A	uc011kwk.1	-	60	9837	c.9447C>T	c.(9445-9447)CCC>CCT	p.P3149P	CSMD1_uc011kwj.1_Silent_p.P2478P|CSMD1_uc010lrg.2_Silent_p.P1040P	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	3149	Sushi 25.|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)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2830689	2830689	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2830689C>T	uc011kwk.1	-	57	9266	c.8876G>A	c.(8875-8877)CGC>CAC	p.R2959H	CSMD1_uc011kwj.1_Missense_Mutation_p.R2288H|CSMD1_uc010lrg.2_Missense_Mutation_p.R969H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2959	Extracellular (Potential).|Sushi 22.					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)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6338243	6338243	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6338243A>G	uc003wqi.2	+	11	2050	c.1982A>G	c.(1981-1983)AAT>AGT	p.N661S		NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	661	BRCT 2.					microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6566240	6566240	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6566240C>A	uc003wqo.2	+	1	363	c.51C>A	c.(49-51)CCC>CCA	p.P17P	AGPAT5_uc011kwm.1_Silent_p.P17P	NM_018361	NP_060831	Q9NUQ2	PLCE_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 5	17	Helical; (Potential).				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)														---	---	---	---
PRSS55	203074	broad.mit.edu	37	8	10389000	10389000	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10389000C>A	uc003wta.2	+	3	558	c.543C>A	c.(541-543)CCC>CCA	p.P181P	uc010lru.2_Intron|PRSS55_uc003wtb.2_RNA	NM_198464	NP_940866	Q6UWB4	PRS55_HUMAN	hypothetical protein LOC203074 precursor	181	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10464615	10464615	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10464615C>A	uc003wtc.2	-	4	7222	c.6993G>T	c.(6991-6993)ACG>ACT	p.T2331T		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2331					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10755778	10755778	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10755778C>T	uc003wtk.1	-	3	1637	c.1610G>A	c.(1609-1611)CGG>CAG	p.R537Q		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	537						integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11614510	11614510	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11614510C>G	uc003wuc.2	+	6	1618	c.1064C>G	c.(1063-1065)ACC>AGC	p.T355S	GATA4_uc003wub.1_Missense_Mutation_p.T149S|GATA4_uc011kxc.1_Missense_Mutation_p.T356S	NM_002052	NP_002043	P43694	GATA4_HUMAN	GATA binding protein 4	355					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)														---	---	---	---
NEIL2	252969	broad.mit.edu	37	8	11637250	11637250	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11637250G>A	uc003wug.2	+	3	957	c.282G>A	c.(280-282)GGG>GGA	p.G94G	NEIL2_uc003wue.2_Silent_p.G94G|NEIL2_uc003wuf.2_Silent_p.G33G|NEIL2_uc011kxd.1_Intron	NM_145043	NP_659480	Q969S2	NEIL2_HUMAN	nei like 2 isoform a	94					base-excision repair|nucleotide-excision repair	nucleus	damaged DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|hydrolase activity, hydrolyzing N-glycosyl compounds|zinc ion binding				0	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)									BER_DNA_glycosylases					---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12878931	12878931	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12878931G>A	uc010lsq.2	+	5	1235	c.743G>A	c.(742-744)CGT>CAT	p.R248H	C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_Missense_Mutation_p.R161H|C8orf79_uc010lsr.2_Missense_Mutation_p.R122H	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1	248							methyltransferase activity				0																		---	---	---	---
STC1	6781	broad.mit.edu	37	8	23709885	23709885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23709885C>T	uc003xdw.1	-	2	415	c.131G>A	c.(130-132)CGT>CAT	p.R44H		NM_003155	NP_003146	P52823	STC1_HUMAN	stanniocalcin 1 precursor	44					cell surface receptor linked signaling pathway|cell-cell signaling|cellular calcium ion homeostasis		hormone activity	p.R44C(1)		skin(3)|upper_aerodigestive_tract(1)	4		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27279847	27279847	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27279847C>T	uc003xfn.1	+	10	1306	c.498C>T	c.(496-498)TAC>TAT	p.Y166Y	PTK2B_uc003xfo.1_Silent_p.Y166Y|PTK2B_uc003xfp.1_Silent_p.Y166Y|PTK2B_uc003xfq.1_Silent_p.Y166Y	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	166	FERM.				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)														---	---	---	---
FZD3	7976	broad.mit.edu	37	8	28413394	28413394	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28413394C>T	uc003xgx.2	+	7	2171	c.1693C>T	c.(1693-1695)CTG>TTG	p.L565L	FZD3_uc010lvb.2_Silent_p.L565L	NM_017412	NP_059108	Q9NPG1	FZD3_HUMAN	frizzled 3 precursor	565	Cytoplasmic (Potential).				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)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33367337	33367337	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33367337A>G	uc003xjl.3	-	2	1286	c.761T>C	c.(760-762)GTC>GCC	p.V254A	C8orf41_uc003xjk.3_Missense_Mutation_p.V254A|C8orf41_uc010lvv.2_Missense_Mutation_p.V254A|C8orf41_uc003xjm.3_Missense_Mutation_p.V254A|C8orf41_uc003xjn.1_Missense_Mutation_p.V254A	NM_025115	NP_079391	Q6NXR4	CH041_HUMAN	hypothetical protein LOC80185	254							binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38139077	38139077	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38139077C>T	uc003xli.2	-	20	4044	c.3526G>A	c.(3526-3528)GGT>AGT	p.G1176S	WHSC1L1_uc011lbm.1_Missense_Mutation_p.G1176S|WHSC1L1_uc010lwe.2_Missense_Mutation_p.G1127S|WHSC1L1_uc003xlh.2_5'Flank	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	1176	SET.				cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
ANK1	286	broad.mit.edu	37	8	41525866	41525866	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41525866G>T	uc003xok.2	-	39	5397	c.5313C>A	c.(5311-5313)TCC>TCA	p.S1771S	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.S925S|ANK1_uc003xoi.2_Silent_p.S1771S|ANK1_uc003xoj.2_Silent_p.S1771S|ANK1_uc003xol.2_Silent_p.S1609S|ANK1_uc003xom.2_Silent_p.S1812S	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1771	55 kDa regulatory domain.				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)															---	---	---	---
SGK196	84197	broad.mit.edu	37	8	42958705	42958705	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42958705C>T	uc003xpw.2	+	4	273	c.14C>T	c.(13-15)CCC>CTC	p.P5L		NM_032237	NP_115613	Q9H5K3	SG196_HUMAN	protein kinase-like protein SgK196	5						integral to membrane	ATP binding|protein kinase activity				0																		---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48706944	48706944	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48706944G>A	uc003xqi.2	-	75	10634	c.10577C>T	c.(10576-10578)CCG>CTG	p.P3526L	PRKDC_uc003xqj.2_Missense_Mutation_p.P3526L|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	3526	FAT.				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					---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54730032	54730032	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54730032G>A	uc003xrl.2	-	5	517	c.365C>T	c.(364-366)GCG>GTG	p.A122V	ATP6V1H_uc003xrk.2_Missense_Mutation_p.A82V|ATP6V1H_uc003xrm.2_Missense_Mutation_p.A122V|ATP6V1H_uc003xrn.2_Missense_Mutation_p.A122V|ATP6V1H_uc011ldv.1_Missense_Mutation_p.A42V|ATP6V1H_uc010lyd.2_Missense_Mutation_p.A58V	NM_213620	NP_998785	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1	122					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)															---	---	---	---
SOX17	64321	broad.mit.edu	37	8	55372486	55372486	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55372486C>T	uc003xsb.3	+	2	1380	c.1176C>T	c.(1174-1176)CAC>CAT	p.H392H		NM_022454	NP_071899	Q9H6I2	SOX17_HUMAN	SRY-box 17	392	Sox C-terminal.				angiogenesis|cardiac cell fate determination|endocardial cell differentiation|endocardium formation|endoderm formation|heart formation|heart looping|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell growth|outflow tract morphogenesis|positive regulation of transcription, DNA-dependent|protein destabilization|protein stabilization|regulation of embryonic development|renal system development|vasculogenesis|Wnt receptor signaling pathway	transcription factor complex	beta-catenin binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			lung(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)															---	---	---	---
RP1	6101	broad.mit.edu	37	8	55540063	55540063	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55540063T>C	uc003xsd.1	+	4	3769	c.3621T>C	c.(3619-3621)GAT>GAC	p.D1207D	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1207					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56015096	56015096	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56015096C>T	uc003xsf.2	+	1	80	c.48C>T	c.(46-48)GAC>GAT	p.D16D		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	16						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
CYP7A1	1581	broad.mit.edu	37	8	59404099	59404099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59404099C>T	uc003xtm.3	-	6	1513	c.1450G>A	c.(1450-1452)GCA>ACA	p.A484T		NM_000780	NP_000771	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A,	484					bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)												Neonatal_Giant_Cell_Hepatitis				---	---	---	---
CYP7A1	1581	broad.mit.edu	37	8	59410782	59410782	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59410782G>A	uc003xtm.3	-							NM_000780	NP_000771			cytochrome P450, family 7, subfamily A,						bile acid biosynthetic process|cellular lipid metabolic process|cellular response to cholesterol|cellular response to glucose stimulus|cholesterol catabolic process|cholesterol homeostasis|regulation of bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	cholesterol 7-alpha-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)												Neonatal_Giant_Cell_Hepatitis				---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61743037	61743037	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61743037A>G	uc003xue.2	+	15	4156	c.3679A>G	c.(3679-3681)ACA>GCA	p.T1227A		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1227					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
ASPH	444	broad.mit.edu	37	8	62588788	62588788	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62588788C>T	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_Missense_Mutation_p.G153D|ASPH_uc003xus.2_3'UTR	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)													---	---	---	---
ARMC1	55156	broad.mit.edu	37	8	66517566	66517566	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66517566C>T	uc003xvl.2	-	6	824	c.589G>A	c.(589-591)GCA>ACA	p.A197T	ARMC1_uc011leo.1_Missense_Mutation_p.A95T	NM_018120	NP_060590	Q9NVT9	ARMC1_HUMAN	armadillo repeat-containing protein	197					metal ion transport		metal ion binding			skin(1)	1			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)															---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67357660	67357660	+	Intron	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67357660T>A	uc003xwb.3	+						ADHFE1_uc003xwd.3_Intron|ADHFE1_uc003xwc.3_Intron|ADHFE1_uc003xwe.3_Intron|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Intron|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251			alcohol dehydrogenase, iron containing, 1						2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67364208	67364208	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67364208C>A	uc003xwb.3	+	9	789	c.755C>A	c.(754-756)ACC>AAC	p.T252N	ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Missense_Mutation_p.T204N|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_RNA|ADHFE1_uc011les.1_Missense_Mutation_p.T182N|ADHFE1_uc011leq.1_RNA|ADHFE1_uc011ler.1_RNA	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	252					2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69104648	69104648	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69104648T>C	uc003xxv.1	+	37	4519	c.4492T>C	c.(4492-4494)TGT>CGT	p.C1498R		NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	1498					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																		---	---	---	---
TRAM1	23471	broad.mit.edu	37	8	71495964	71495964	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71495964T>A	uc003xyo.1	-	9	981	c.811A>T	c.(811-813)ACT>TCT	p.T271S	TRAM1_uc011lfc.1_Missense_Mutation_p.T240S	NM_014294	NP_055109	Q15629	TRAM1_HUMAN	translocation associated membrane protein 1	271	Helical; (Potential).|TLC.				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)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73849496	73849496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73849496G>A	uc003xzb.2	+	3	2494	c.1906G>A	c.(1906-1908)GAC>AAC	p.D636N		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	636	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77767139	77767139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77767139G>A	uc003yav.2	+	10	8234	c.7847G>A	c.(7846-7848)AGG>AAG	p.R2616K	ZFHX4_uc003yau.1_Missense_Mutation_p.R2661K|ZFHX4_uc003yaw.1_Missense_Mutation_p.R2616K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2616	Homeobox 3.					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)			---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	87951921	87951921	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87951921T>G	uc003ydy.2	+	4	418	c.370T>G	c.(370-372)TTA>GTA	p.L124V		NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	124										ovary(3)	3																		---	---	---	---
NBN	4683	broad.mit.edu	37	8	90955598	90955598	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90955598T>C	uc003yej.1	-						NBN_uc003yei.1_Intron|NBN_uc011lgb.1_Intron	NM_002485	NP_002476			nibrin						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)										Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				---	---	---	---
NBN	4683	broad.mit.edu	37	8	90990491	90990491	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90990491G>T	uc003yej.1	-	5	651	c.541C>A	c.(541-543)CTG>ATG	p.L181M	NBN_uc003yei.1_Missense_Mutation_p.L99M|NBN_uc011lgb.1_Missense_Mutation_p.L181M	NM_002485	NP_002476	O60934	NBN_HUMAN	nibrin	181	BRCT.				cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)										Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	92998448	92998448	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92998448G>A	uc003yfd.2	-	8	1267	c.1183C>T	c.(1183-1185)CGG>TGG	p.R395W	RUNX1T1_uc003yfc.1_Missense_Mutation_p.R368W|RUNX1T1_uc003yfe.1_Missense_Mutation_p.R358W|RUNX1T1_uc010mao.2_Missense_Mutation_p.R368W|RUNX1T1_uc011lgi.1_Missense_Mutation_p.R406W|RUNX1T1_uc010man.1_5'UTR|RUNX1T1_uc003yfb.1_Missense_Mutation_p.R358W	NM_175634	NP_783552	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	395			R -> W (in a colorectal cancer sample; somatic mutation).		generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.R358W(1)		lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
TSPYL5	85453	broad.mit.edu	37	8	98289167	98289167	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98289167C>T	uc003yhy.2	-	1	1010	c.906G>A	c.(904-906)CCG>CCA	p.P302P		NM_033512	NP_277047	Q86VY4	TSYL5_HUMAN	TSPY-like 5	302					cellular response to gamma radiation|nucleosome assembly|positive regulation of cell proliferation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|regulation of growth	nucleus	protein binding			large_intestine(1)|ovary(1)	2	Breast(36;2.56e-06)																	---	---	---	---
KCNS2	3788	broad.mit.edu	37	8	99441361	99441361	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99441361C>T	uc003yin.2	+	2	1504	c.1154C>T	c.(1153-1155)ACG>ATG	p.T385M		NM_020697	NP_065748	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel,	385	Extracellular (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100147902	100147902	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100147902C>T	uc003yiv.2	+	11	1615	c.1504C>T	c.(1504-1506)CGA>TGA	p.R502*	VPS13B_uc003yiw.2_Nonsense_Mutation_p.R502*|VPS13B_uc003yit.2_Nonsense_Mutation_p.R502*|VPS13B_uc003yiu.1_Nonsense_Mutation_p.R502*|VPS13B_uc003yix.1_5'Flank	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	502					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	101065081	101065081	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101065081G>T	uc003yjb.1	-	10	1833	c.1638C>A	c.(1636-1638)ACC>ACA	p.T546T	RGS22_uc003yja.1_Silent_p.T365T|RGS22_uc003yjc.1_Silent_p.T534T|RGS22_uc011lgz.1_RNA|RGS22_uc010mbo.1_RNA	NM_015668	NP_056483	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	546					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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103293613	103293613	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103293613A>G	uc003ykr.1	-	41	5864	c.5831T>C	c.(5830-5832)TTG>TCG	p.L1944S	UBR5_uc003yks.1_Missense_Mutation_p.L1944S	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1944					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)															---	---	---	---
ODF1	4956	broad.mit.edu	37	8	103572812	103572812	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103572812G>A	uc003ykt.2	+	2	561	c.453G>A	c.(451-453)TCG>TCA	p.S151S		NM_024410	NP_077721	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	151					cell differentiation|multicellular organismal development|spermatogenesis	outer dense fiber	structural molecule activity			ovary(2)	2	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)															---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105456668	105456668	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105456668A>G	uc003yly.3	-							NM_001385	NP_001376			dihydropyrimidinase						protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106813750	106813750	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106813750C>A	uc003ymd.2	+	8	1463	c.1440C>A	c.(1438-1440)GCC>GCA	p.A480A	ZFPM2_uc011lhs.1_Silent_p.A211A	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	480					blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109215314	109215314	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109215314T>C	uc003ymu.2	-	12	1225	c.1197A>G	c.(1195-1197)TCA>TCG	p.S399S	EIF3E_uc003ymt.2_Silent_p.S350S|EIF3E_uc003ymv.2_Silent_p.S306S	NM_001568	NP_001559	P60228	EIF3E_HUMAN	eukaryotic translation initiation factor 3,	399	Sufficient for interaction with MCM7.				negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)															---	---	---	---
TRHR	7201	broad.mit.edu	37	8	110100047	110100047	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110100047T>G	uc003ymz.3	+	1	322	c.306T>G	c.(304-306)ACT>ACG	p.T102T		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	102	Helical; Name=3; (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110476610	110476610	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110476610A>G	uc003yne.2	+	49	7653	c.7549A>G	c.(7549-7551)ATT>GTT	p.I2517V		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2517	PbH1 1.|Extracellular (Potential).				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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113267597	113267597	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113267597T>C	uc003ynu.2	-	62	10081	c.9922A>G	c.(9922-9924)ATA>GTA	p.I3308V	CSMD3_uc003yns.2_Missense_Mutation_p.I2510V|CSMD3_uc003ynt.2_Missense_Mutation_p.I3268V|CSMD3_uc011lhx.1_Missense_Mutation_p.I3139V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3308	Extracellular (Potential).|Sushi 26.					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	118819472	118819472	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118819472C>T	uc003yok.1	-	9	2640	c.1867G>A	c.(1867-1869)GCT>ACT	p.A623T		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	623	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				---	---	---	---
NOV	4856	broad.mit.edu	37	8	120435303	120435303	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120435303C>T	uc003yoq.2	+	5	1226	c.1005C>T	c.(1003-1005)ACC>ACT	p.T335T		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	335	CTCK.				regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
ZHX1	11244	broad.mit.edu	37	8	124267603	124267603	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124267603C>T	uc003yqe.2	-	3	1014	c.584G>A	c.(583-585)CGG>CAG	p.R195Q	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Missense_Mutation_p.R195Q|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Missense_Mutation_p.R195Q	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	195					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)															---	---	---	---
TRIB1	10221	broad.mit.edu	37	8	126448362	126448362	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126448362C>A	uc003yrx.2	+	3	1350	c.768C>A	c.(766-768)ACC>ACA	p.T256T	TRIB1_uc011lis.1_Silent_p.T90T|TRIB1_uc010mdn.2_Silent_p.T25T	NM_025195	NP_079471	Q96RU8	TRIB1_HUMAN	G-protein-coupled receptor induced protein	256	Protein kinase.				JNK cascade|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell proliferation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|regulation of MAP kinase activity|response to lipopolysaccharide	cytoplasm|nucleus	ATP binding|mitogen-activated protein kinase kinase binding|protein kinase activity|protein kinase inhibitor activity|transcription factor binding|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			lung(1)	1	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133146585	133146585	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133146585T>G	uc003ytj.2	-	13	1976	c.1751A>C	c.(1750-1752)AAG>ACG	p.K584T	KCNQ3_uc010mdt.2_Missense_Mutation_p.K584T	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	584					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	134024285	134024285	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134024285G>T	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)														---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139153505	139153505	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139153505C>T	uc003yuy.2	-	17	3897	c.3726G>A	c.(3724-3726)ACG>ACA	p.T1242T	FAM135B_uc003yux.2_Silent_p.T1143T|FAM135B_uc003yuz.2_RNA	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1242										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139791754	139791754	+	Missense_Mutation	SNP	G	A	A	rs139654575	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139791754G>A	uc003yvd.2	-	14	2149	c.1702C>T	c.(1702-1704)CGG>TGG	p.R568W		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	568	Pro-rich.|Gly-rich.|Collagen-like 3.				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)			---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141803473	141803473	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141803473C>A	uc003yvu.2	-	13	1334	c.1104G>T	c.(1102-1104)CGG>CGT	p.R368R	PTK2_uc011ljq.1_Silent_p.R29R|PTK2_uc003yvp.2_Silent_p.R29R|PTK2_uc003yvq.2_5'UTR|PTK2_uc003yvr.2_Silent_p.R267R|PTK2_uc003yvs.2_Silent_p.R368R|PTK2_uc003yvt.2_Silent_p.R390R|PTK2_uc003yvv.2_Silent_p.R255R|PTK2_uc011ljr.1_Silent_p.R368R	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a	368					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)															---	---	---	---
ZFP41	286128	broad.mit.edu	37	8	144332457	144332457	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144332457C>T	uc003yxw.2	+	2	802	c.444C>T	c.(442-444)TGC>TGT	p.C148C	ZFP41_uc003yxv.2_RNA	NM_173832	NP_776193	Q8N8Y5	ZFP41_HUMAN	zinc finger protein 41 homolog	148	C2H2-type 3.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)															---	---	---	---
GRINA	2907	broad.mit.edu	37	8	145066937	145066937	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145066937G>A	uc003zan.1	+	7	1210	c.1044G>A	c.(1042-1044)GCG>GCA	p.A348A	GRINA_uc003zao.1_Silent_p.A348A|GRINA_uc003zap.1_Silent_p.A348A	NM_001009184	NP_001009184	Q7Z429	GRINA_HUMAN	glutamate receptor, ionotropic, N-methyl	348	Helical; (Potential).					integral to membrane				central_nervous_system(1)	1	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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145095846	145095846	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145095846C>T	uc011lkw.1	+	3	1246	c.1144C>T	c.(1144-1146)CCT>TCT	p.P382S	SPATC1_uc011lkx.1_Missense_Mutation_p.P382S	NM_198572	NP_940974	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	382										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)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145623823	145623823	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145623823G>A	uc003zcj.2	-	19	1838	c.1763C>T	c.(1762-1764)ACG>ATG	p.T588M		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	588					mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)															---	---	---	---
FOXD4	2298	broad.mit.edu	37	9	117535	117535	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117535C>T	uc003zfz.2	-	1	883	c.585G>A	c.(583-585)CGG>CGA	p.R195R		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	195	Fork-head.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system 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	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6604759	6604759	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6604759A>C	uc003zkc.2	-	7	1080	c.887T>G	c.(886-888)CTT>CGT	p.L296R		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	296					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)													---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8319960	8319960	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8319960G>A	uc003zkk.2	-	44	6252	c.5541C>T	c.(5539-5541)GGC>GGT	p.G1847G	PTPRD_uc003zkp.2_Silent_p.G1441G|PTPRD_uc003zkq.2_Silent_p.G1440G|PTPRD_uc003zkr.2_Silent_p.G1431G|PTPRD_uc003zks.2_Silent_p.G1440G|PTPRD_uc003zkl.2_Silent_p.G1838G|PTPRD_uc003zkm.2_Silent_p.G1834G|PTPRD_uc003zkn.2_Silent_p.G1436G|PTPRD_uc003zko.2_Silent_p.G1437G	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1847	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
TYRP1	7306	broad.mit.edu	37	9	12695847	12695847	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12695847A>G	uc003zkv.3	+							NM_000550	NP_000541			tyrosinase-related protein 1 precursor						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				---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20988425	20988425	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20988425C>T	uc003zog.1	+	43	5364	c.5001C>T	c.(4999-5001)GAC>GAT	p.D1667D	KIAA1797_uc003zoh.1_Silent_p.D1103D	NM_017794	NP_060264	Q5VW36	K1797_HUMAN	hypothetical protein LOC54914	1667						integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35706102	35706102	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35706102C>T	uc003zxt.2	-	41	5722	c.5368G>A	c.(5368-5370)GCT>ACT	p.A1790T		NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	1790	Interaction with SYNM.				axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
GNE	10020	broad.mit.edu	37	9	36227249	36227249	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36227249A>G	uc010mlh.2	-	7	1492	c.1277T>C	c.(1276-1278)ATG>ACG	p.M426T	CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_Missense_Mutation_p.M426T|GNE_uc011lpl.1_Missense_Mutation_p.M316T|GNE_uc010mli.2_Missense_Mutation_p.M457T|GNE_uc010mlj.2_Missense_Mutation_p.M421T	NM_005476	NP_005467	Q9Y223	GLCNE_HUMAN	UDP-N-acetylglucosamine-2-epimerase/N-	426	UDP-N-acetylglucosamine 2-epimerase.|N-acetylmannosamine kinase.				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)															---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993105	70993105	+	Intron	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993105G>C	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72833435	72833435	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72833435T>G	uc004ahm.2	+	12	2451	c.1834T>G	c.(1834-1836)TTA>GTA	p.L612V	MAMDC2_uc004ahn.2_RNA|uc004ahq.1_Intron	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor	612	MAM 4.					endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
ALDH1A1	216	broad.mit.edu	37	9	75545795	75545795	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75545795C>A	uc004ajd.2	-	3	365	c.312G>T	c.(310-312)GCG>GCT	p.A104A	ALDH1A1_uc011lsh.1_Silent_p.A25A	NM_000689	NP_000680	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1A1	104					cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79323912	79323912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79323912C>T	uc010mpk.2	-	8	3402	c.3278G>A	c.(3277-3279)CGA>CAA	p.R1093Q		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1093					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79841516	79841516	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79841516T>C	uc004akr.2	+	15	1617	c.1357_splice	c.e15+2	p.T453_splice	VPS13A_uc004akp.3_Splice_Site_p.T453_splice|VPS13A_uc004akq.3_Splice_Site_p.T453_splice|VPS13A_uc004aks.2_Splice_Site_p.T453_splice	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79910453	79910453	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79910453T>C	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron|VPS13A_uc010mpo.1_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84607460	84607460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84607460G>A	uc004amn.2	+	4	2122	c.2075G>A	c.(2074-2076)CGA>CAA	p.R692Q		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	692						integral to membrane					0																		---	---	---	---
RASEF	158158	broad.mit.edu	37	9	85607893	85607893	+	Silent	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85607893A>T	uc004amo.1	-	15	2229	c.1968T>A	c.(1966-1968)GCT>GCA	p.A656A		NM_152573	NP_689786	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	656	GTP (By similarity).				protein transport|small GTPase mediated signal transduction	perinuclear region of cytoplasm	calcium ion binding|GTP binding			upper_aerodigestive_tract(1)|lung(1)|breast(1)	3																		---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85863132	85863132	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85863132C>A	uc004ams.1	-	14	1697	c.1495G>T	c.(1495-1497)GAG>TAG	p.E499*	FRMD3_uc004amr.1_Nonsense_Mutation_p.E485*|FRMD3_uc004amq.1_Nonsense_Mutation_p.E156*	NM_174938	NP_777598	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	499						cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RMI1	80010	broad.mit.edu	37	9	86616999	86616999	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86616999C>G	uc004anq.3	+	3	1506	c.1098C>G	c.(1096-1098)TGC>TGG	p.C366W	RMI1_uc004anr.3_Missense_Mutation_p.C366W|RMI1_uc004anp.3_Missense_Mutation_p.C366W|RMI1_uc004ans.3_Missense_Mutation_p.C366W	NM_024945	NP_079221	Q9H9A7	RMI1_HUMAN	RMI1, RecQ mediated genome instability 1,	366					DNA replication	nucleus					0																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92020286	92020286	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92020286C>T	uc004aqo.1	-	5	658	c.86G>A	c.(85-87)CGG>CAG	p.R29Q	SEMA4D_uc011ltm.1_Missense_Mutation_p.R29Q|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Missense_Mutation_p.R27Q	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	29	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
FBP2	8789	broad.mit.edu	37	9	97321299	97321299	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97321299C>T	uc004auv.2	-	7	1008	c.941G>A	c.(940-942)CGA>CAA	p.R314Q	uc004aus.1_RNA|uc004aut.1_RNA|uc004auu.2_RNA	NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	314					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
FBP2	8789	broad.mit.edu	37	9	97355861	97355861	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97355861G>A	uc004auv.2	-	1	215	c.148C>T	c.(148-150)CGC>TGC	p.R50C		NM_003837	NP_003828	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	50					fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
ZNF510	22869	broad.mit.edu	37	9	99521052	99521052	+	3'UTR	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99521052T>G	uc004awn.1	-	6					ZNF510_uc004awo.1_3'UTR	NM_014930	NP_055745			zinc finger protein 510						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
CTSL2	1515	broad.mit.edu	37	9	99800233	99800233	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99800233C>T	uc004awt.2	-	2	290	c.93G>A	c.(91-93)CAG>CAA	p.Q31Q	CTSL2_uc010msi.2_Silent_p.Q31Q|CTSL2_uc004awu.2_Translation_Start_Site|CTSL2_uc010msj.1_Translation_Start_Site|CTSL2_uc010msk.2_Translation_Start_Site	NM_001333	NP_001324	O60911	CATL2_HUMAN	cathepsin L2 preproprotein	31						lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
NCBP1	4686	broad.mit.edu	37	9	100407390	100407390	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100407390C>T	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)																---	---	---	---
ALDOB	229	broad.mit.edu	37	9	104187169	104187169	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104187169C>T	uc004bbk.2	-	8	1037	c.955G>A	c.(955-957)GCA>ACA	p.A319T		NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	319					fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112017804	112017804	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112017804G>A	uc004bdz.1	-	11	1451	c.1156C>T	c.(1156-1158)CGC>TGC	p.R386C	EPB41L4B_uc004bea.2_Missense_Mutation_p.R386C	NM_019114	NP_061987	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	386						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112144688	112144688	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112144688C>T	uc004bed.2	-	24	2534	c.2422G>A	c.(2422-2424)GCA>ACA	p.A808T	PTPN3_uc004beb.2_Missense_Mutation_p.A677T|PTPN3_uc004bec.2_Missense_Mutation_p.A632T|PTPN3_uc010mtu.2_RNA|PTPN3_uc011lwg.1_Missense_Mutation_p.A763T|PTPN3_uc011lwh.1_Missense_Mutation_p.A654T|PTPN3_uc011lwd.1_Missense_Mutation_p.A276T|PTPN3_uc011lwe.1_Missense_Mutation_p.A521T|PTPN3_uc011lwf.1_Missense_Mutation_p.A476T	NM_002829	NP_002820	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type	808	Tyrosine-protein phosphatase.				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																		---	---	---	---
DNAJC25	548645	broad.mit.edu	37	9	114415422	114415422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114415422G>A	uc004bfl.2	+	4	1059	c.1003G>A	c.(1003-1005)GCA>ACA	p.A335T	DNAJC25-GNG10_uc004bfn.2_Intron|DNAJC25_uc004bfm.2_Missense_Mutation_p.A213T	NM_001015882	NP_001015882	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	335					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115166406	115166406	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115166406T>G	uc004bga.1	+	2	242	c.149T>G	c.(148-150)CTT>CGT	p.L50R	HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_5'UTR|HSDL2_uc004bgc.1_Missense_Mutation_p.L50R|HSDL2_uc011lww.1_5'UTR	NM_032303	NP_115679	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	50						peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116346004	116346004	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116346004C>A	uc004bhq.2	+	21	2521	c.2312C>A	c.(2311-2313)CCT>CAT	p.P771H	RGS3_uc004bhs.2_Missense_Mutation_p.P661H|RGS3_uc004bht.2_Missense_Mutation_p.P490H|RGS3_uc010muy.2_Intron|RGS3_uc004bhv.2_Missense_Mutation_p.P92H|RGS3_uc010muz.1_Missense_Mutation_p.P110H|RGS3_uc004bhw.2_Intron|RGS3_uc011lxh.1_Missense_Mutation_p.P81H|RGS3_uc004bhx.2_Missense_Mutation_p.P92H|RGS3_uc004bhy.1_Missense_Mutation_p.P81H|RGS3_uc004bhz.2_Missense_Mutation_p.P113H	NM_144488	NP_652759	P49796	RGS3_HUMAN	regulator of G-protein signalling 3 isoform 6	771	Pro-rich.				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																		---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123334315	123334315	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123334315G>T	uc004bkf.2	-	2	245	c.64C>A	c.(64-66)CTT>ATT	p.L22I	CDK5RAP2_uc004bkg.2_Missense_Mutation_p.L22I|CDK5RAP2_uc011lxw.1_5'UTR|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_5'UTR|CDK5RAP2_uc011lya.1_5'UTR|CDK5RAP2_uc004bkh.1_Missense_Mutation_p.L22I	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	22					brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
OR1Q1	158131	broad.mit.edu	37	9	125377600	125377600	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125377600A>G	uc011lyy.1	+	1	584	c.584A>G	c.(583-585)AAC>AGC	p.N195S		NM_012364	NP_036496	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q,	195	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR1K1	392392	broad.mit.edu	37	9	125563309	125563309	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125563309G>A	uc011lze.1	+	1	908	c.908G>A	c.(907-909)CGA>CAA	p.R303Q		NM_080859	NP_543135	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K,	303	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
CRB2	286204	broad.mit.edu	37	9	126132851	126132851	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126132851C>A	uc004bnx.1	+	7	1611	c.1519C>A	c.(1519-1521)CTG>ATG	p.L507M	CRB2_uc004bnw.1_Missense_Mutation_p.L507M	NM_173689	NP_775960	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 precursor	507	Extracellular (Potential).|Laminin G-like 1.					extracellular region|integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
NEK6	10783	broad.mit.edu	37	9	127089654	127089654	+	Silent	SNP	C	T	T	rs147517890		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127089654C>T	uc004bog.2	+	7	701	c.552C>T	c.(550-552)GGC>GGT	p.G184G	NEK6_uc004bof.2_Silent_p.G202G|NEK6_uc004boh.2_Silent_p.G218G|NEK6_uc010mwj.2_Silent_p.G137G|NEK6_uc010mwk.2_Silent_p.G184G|NEK6_uc004boi.2_Silent_p.G184G	NM_014397	NP_055212	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6 isoform 2	184	Protein kinase.				apoptosis|cell division|chromosome segregation|mitosis|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of mitotic metaphase/anaphase transition	cytoplasm|nucleus	ATP binding|kinesin binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|kidney(1)	3																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127650643	127650643	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127650643G>A	uc004bpc.2	-	19	2136	c.1794C>T	c.(1792-1794)TTC>TTT	p.F598F	GOLGA1_uc010mws.2_RNA	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	598	Potential.					Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129595614	129595614	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129595614G>A	uc004bql.2	+	3	1099	c.826G>A	c.(826-828)GTG>ATG	p.V276M	ZBTB43_uc010mxf.2_Missense_Mutation_p.V276M	NM_014007	NP_054726	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	276					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CIZ1	25792	broad.mit.edu	37	9	130941663	130941663	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130941663C>A	uc004btt.2	-	8	986	c.823G>T	c.(823-825)GGG>TGG	p.G275W	CIZ1_uc004btr.2_Missense_Mutation_p.G275W|CIZ1_uc004bts.2_Missense_Mutation_p.G246W|CIZ1_uc011maq.1_Missense_Mutation_p.G270W|CIZ1_uc004btu.2_Missense_Mutation_p.G251W|CIZ1_uc011mar.1_Missense_Mutation_p.G174W|CIZ1_uc011mas.1_Missense_Mutation_p.G305W|CIZ1_uc004btw.2_Missense_Mutation_p.G275W|CIZ1_uc004btv.2_Missense_Mutation_p.G275W|CIZ1_uc004btx.2_Missense_Mutation_p.G251W	NM_001131016	NP_001124488	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1 isoform	275						nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131395517	131395517	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131395517C>T	uc004bvl.3	+	56	7436	c.7323C>T	c.(7321-7323)TGC>TGT	p.C2441C	SPTAN1_uc004bvm.3_Silent_p.C2446C|SPTAN1_uc004bvn.3_Silent_p.C2421C|SPTAN1_uc004bvo.3_Silent_p.C208C|SPTAN1_uc004bvp.3_Silent_p.C184C	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	2441					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																		---	---	---	---
LRRC8A	56262	broad.mit.edu	37	9	131670897	131670897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131670897C>T	uc004bwl.3	+	3	1708	c.1454C>T	c.(1453-1455)GCG>GTG	p.A485V	LRRC8A_uc010myp.2_Missense_Mutation_p.A485V|LRRC8A_uc010myq.2_Missense_Mutation_p.A485V	NM_019594	NP_062540	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member	485	LRR 5.				pre-B cell differentiation	integral to membrane					0																		---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134340174	134340174	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134340174C>T	uc004can.3	+	11	1484	c.1429C>T	c.(1429-1431)CGG>TGG	p.R477W	BAT2L1_uc010mzj.1_Missense_Mutation_p.R60W	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	477							protein binding				0																		---	---	---	---
SETX	23064	broad.mit.edu	37	9	135139706	135139706	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135139706G>T	uc004cbk.2	-	26	8137	c.7954C>A	c.(7954-7956)CAC>AAC	p.H2652N	SETX_uc004cbj.2_Missense_Mutation_p.H2300N|SETX_uc010mzt.2_Missense_Mutation_p.H2238N	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	2652					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
GTF3C4	9329	broad.mit.edu	37	9	135555180	135555180	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135555180G>T	uc010mzv.2	+	2	2432	c.2174G>T	c.(2173-2175)AGA>ATA	p.R725I	GTF3C4_uc010mzw.2_RNA	NM_012204	NP_036336	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC 4	725					transcription initiation from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|enzyme activator activity|histone acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)														---	---	---	---
TSC1	7248	broad.mit.edu	37	9	135785954	135785954	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135785954G>A	uc004cca.2	-						TSC1_uc004ccb.3_Intron|TSC1_uc011mcq.1_Intron|TSC1_uc011mcr.1_Intron|TSC1_uc011mcs.1_Intron|TSC1_uc004ccc.1_Nonsense_Mutation_p.R423*	NM_000368	NP_000359			tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding	p.?(1)		lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)				D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				---	---	---	---
RPL7A	6130	broad.mit.edu	37	9	136218200	136218200	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136218200A>G	uc004cde.1	+	8	810	c.780A>G	c.(778-780)GAA>GAG	p.E260E	RPL7A_uc004cdf.1_Silent_p.E84E	NM_000972	NP_000963	P62424	RL7A_HUMAN	ribosomal protein L7a	260					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|membrane fraction|polysomal ribosome	RNA binding|structural constituent of ribosome				0				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)														---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138714112	138714112	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138714112C>T	uc004cgr.3	-	11	2395	c.2395G>A	c.(2395-2397)GCC>ACC	p.A799T	CAMSAP1_uc004cgq.3_Missense_Mutation_p.A689T|CAMSAP1_uc010nbg.2_Missense_Mutation_p.A521T	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	799						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
EDF1	8721	broad.mit.edu	37	9	139757844	139757844	+	Missense_Mutation	SNP	G	A	A	rs139723037		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139757844G>A	uc004cjt.1	-	3	215	c.187C>T	c.(187-189)CGG>TGG	p.R63W	EDF1_uc004cju.1_Missense_Mutation_p.R63W	NM_003792	NP_003783	O60869	EDF1_HUMAN	endothelial differentiation-related factor 1	63	Interaction with NR5A2, PPARG and NR1H3.				endothelial cell differentiation|multicellular organismal development|positive regulation of DNA binding|positive regulation of transcription, DNA-dependent|regulation of lipid metabolic process|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleus	calmodulin binding|protein binding|protein binding|sequence-specific DNA binding|transcription coactivator activity				0	all_cancers(76;0.0841)|all_epithelial(76;0.217)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140637990	140637990	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140637990G>A	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|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)														---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12006024	12006024	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12006024C>T	uc001ila.2	-	10	2642	c.2168G>A	c.(2167-2169)AGG>AAG	p.R723K	UPF2_uc001ilb.2_Missense_Mutation_p.R723K|UPF2_uc001ilc.2_Missense_Mutation_p.R723K|UPF2_uc009xiz.1_Missense_Mutation_p.R723K	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	723	MIF4G 2.|Sufficient for interaction with UPF3A and UPF3B.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
UPF2	26019	broad.mit.edu	37	10	12071324	12071324	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12071324A>C	uc001ila.2	-	2	1039	c.565T>G	c.(565-567)TTG>GTG	p.L189V	UPF2_uc001ilb.2_Missense_Mutation_p.L189V|UPF2_uc001ilc.2_Missense_Mutation_p.L189V|UPF2_uc009xiz.1_Missense_Mutation_p.L189V	NM_080599	NP_542166	Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog	189	MIF4G 1.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	exon-exon junction complex|perinuclear region of cytoplasm	identical protein binding|RNA binding			central_nervous_system(2)|ovary(1)	3		Renal(717;0.228)																---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16942758	16942758	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16942758A>G	uc001ioo.2	-	53	8328	c.8276T>C	c.(8275-8277)ATC>ACC	p.I2759T	CUBN_uc009xjq.1_RNA|CUBN_uc009xjr.1_Missense_Mutation_p.I115T	NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	2759	CUB 20.				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)													---	---	---	---
SLC39A12	221074	broad.mit.edu	37	10	18276457	18276457	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18276457G>A	uc001ipo.2	+	7	1419	c.1146G>A	c.(1144-1146)ATG>ATA	p.M382I	SLC39A12_uc001ipn.2_Missense_Mutation_p.M382I|SLC39A12_uc001ipp.2_Missense_Mutation_p.M382I|SLC39A12_uc010qck.1_Missense_Mutation_p.M248I	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	382	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2																		---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24874635	24874635	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24874635G>T	uc001isb.2	-	26	5070	c.4583C>A	c.(4582-4584)CCC>CAC	p.P1528H	ARHGAP21_uc010qdb.1_RNA	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1527					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27403477	27403477	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27403477G>A	uc001iti.2	-	19	2333	c.2151C>T	c.(2149-2151)ATC>ATT	p.I717I	YME1L1_uc001itj.2_Silent_p.I660I|YME1L1_uc010qdl.1_Silent_p.I627I|YME1L1_uc009xkv.2_RNA	NM_139312	NP_647473	Q96TA2	YMEL1_HUMAN	YME1-like 1 isoform 1	717					protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28420597	28420597	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28420597A>G	uc001iua.1	-	8	743	c.339T>C	c.(337-339)ACT>ACC	p.T113T	MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Silent_p.T113T|MPP7_uc009xla.2_Silent_p.T113T|MPP7_uc010qdv.1_RNA	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	113	L27 2.				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																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30317027	30317027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30317027G>A	uc001iux.2	-	2	2109	c.2050C>T	c.(2050-2052)CAC>TAC	p.H684Y	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.H546Y|KIAA1462_uc009xle.1_Missense_Mutation_p.H684Y	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	684										ovary(4)	4																		---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31791321	31791321	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31791321A>G	uc001ivs.3	+	4	428	c.365A>G	c.(364-366)CAT>CGT	p.H122R	ZEB1_uc001ivr.3_5'UTR|ZEB1_uc010qee.1_5'UTR|ZEB1_uc010qef.1_5'UTR|ZEB1_uc009xlh.1_RNA|ZEB1_uc009xli.1_RNA|ZEB1_uc009xlj.1_Intron|ZEB1_uc010qeg.1_Intron|ZEB1_uc009xlk.1_5'UTR|ZEB1_uc001ivt.3_5'UTR|ZEB1_uc001ivu.3_Missense_Mutation_p.H123R|ZEB1_uc001ivv.3_Missense_Mutation_p.H102R|ZEB1_uc010qeh.1_Missense_Mutation_p.H55R|ZEB1_uc009xll.2_RNA|ZEB1_uc009xlm.1_RNA|ZEB1_uc009xln.1_RNA|ZEB1_uc009xlo.1_Missense_Mutation_p.H105R|ZEB1_uc009xlp.2_Missense_Mutation_p.H106R	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	122					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)																---	---	---	---
CCDC7	221016	broad.mit.edu	37	10	32740668	32740668	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32740668C>A	uc001iwj.2	+	2	668	c.98C>A	c.(97-99)CCT>CAT	p.P33H	CCDC7_uc009xlu.1_RNA|CCDC7_uc001iwk.2_Missense_Mutation_p.P33H|CCDC7_uc009xlv.2_RNA|CCDC7_uc009xlw.1_RNA|CCDC7_uc009xlx.1_Missense_Mutation_p.P33H|CCDC7_uc009xly.1_RNA	NM_145023	NP_659460	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	33											0		Breast(68;0.000207)|Prostate(175;0.0107)																---	---	---	---
ITGB1	3688	broad.mit.edu	37	10	33209310	33209310	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33209310G>T	uc001iws.3	-	10	1268	c.1132C>A	c.(1132-1134)CTT>ATT	p.L378I	ITGB1_uc001iwp.3_Missense_Mutation_p.L378I|ITGB1_uc001iwq.3_Missense_Mutation_p.L378I|ITGB1_uc001iwr.3_Missense_Mutation_p.L378I|ITGB1_uc001iwt.3_Missense_Mutation_p.L378I|ITGB1_uc001iwu.1_Missense_Mutation_p.L378I	NM_133376	NP_596867	P05556	ITB1_HUMAN	integrin beta 1 isoform 1A precursor	378	Extracellular (Potential).|VWFA.				axon guidance|blood coagulation|cell-cell adhesion mediated by integrin|cell-matrix adhesion|cellular defense response|homophilic cell adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|leukocyte migration|positive regulation of apoptosis|regulation of immune response	cell surface|cleavage furrow|focal adhesion|melanosome|neuromuscular junction|ruffle|sarcolemma	identical protein binding|protein heterodimerization activity|receptor activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(717;1.34e-05)|Breast(68;0.0634)																---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33469287	33469287	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33469287G>A	uc001iwx.3	-	17	3012	c.2489C>T	c.(2488-2490)ACG>ATG	p.T830M	NRP1_uc001iwv.3_Missense_Mutation_p.T813M|NRP1_uc009xlz.2_Missense_Mutation_p.T824M|NRP1_uc001iww.3_Missense_Mutation_p.T642M|NRP1_uc001iwy.3_Missense_Mutation_p.T823M	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	830	Extracellular (Potential).				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43297650	43297650	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43297650G>T	uc001jaj.2	+	13	2671	c.2313G>T	c.(2311-2313)AAG>AAT	p.K771N		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	771					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
CSGALNACT2	55454	broad.mit.edu	37	10	43656003	43656003	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43656003G>T	uc001jan.2	+	4	1275	c.940G>T	c.(940-942)GGA>TGA	p.G314*	CSGALNACT2_uc001jam.1_Nonsense_Mutation_p.G314*	NM_018590	NP_061060	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate	314	Lumenal (Potential).				chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1																		---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45877991	45877991	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45877991G>A	uc001jce.2	+	2	310	c.211G>A	c.(211-213)GAG>AAG	p.E71K	ALOX5_uc009xmt.2_Missense_Mutation_p.E71K|ALOX5_uc010qfg.1_Missense_Mutation_p.E71K	NM_000698	NP_000689	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	71	PLAT.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)													---	---	---	---
RBP3	5949	broad.mit.edu	37	10	48390672	48390672	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48390672G>A	uc001jez.2	-	1	320	c.206C>T	c.(205-207)ACG>ATG	p.T69M		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	69	4 X approximate tandem repeats.|1.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)													---	---	---	---
FAM13C	220965	broad.mit.edu	37	10	61043190	61043190	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61043190C>T	uc001jkn.2	-	7	659	c.525G>A	c.(523-525)GTG>GTA	p.V175V	FAM13C_uc001jko.2_Silent_p.V175V|FAM13C_uc010qid.1_Silent_p.V92V|FAM13C_uc010qie.1_Silent_p.V92V|FAM13C_uc010qif.1_Silent_p.V197V|FAM13C_uc001jkp.2_Silent_p.V92V	NM_198215	NP_937858	Q8NE31	FA13C_HUMAN	hypothetical protein LOC220965 isoform 1	175										ovary(2)	2																		---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69647189	69647189	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69647189G>T	uc001jnd.2	+	2	498	c.445G>T	c.(445-447)GGT>TGT	p.G149C	SIRT1_uc010qis.1_5'UTR|SIRT1_uc009xpp.2_5'UTR	NM_012238	NP_036370	Q96EB6	SIRT1_HUMAN	sirtuin 1 isoform a	149	Interaction with HIST1H1E.				apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
HNRNPH3	3189	broad.mit.edu	37	10	70097668	70097668	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70097668A>C	uc001jnw.3	+	3	395	c.166A>C	c.(166-168)AGC>CGC	p.S56R	HNRNPH3_uc001jnx.3_Missense_Mutation_p.S56R|HNRNPH3_uc009xpu.2_5'UTR|HNRNPH3_uc010qiv.1_Intron|HNRNPH3_uc001jny.3_Missense_Mutation_p.S7R	NM_012207	NP_036339	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3	56	RRM 1.				nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2																		---	---	---	---
C10orf27	219793	broad.mit.edu	37	10	72539499	72539499	+	Splice_Site	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72539499C>T	uc001jrj.1	-	5	668	c.278_splice	c.e5-1	p.D93_splice	C10orf27_uc010qjm.1_Splice_Site_p.D93_splice|C10orf27_uc009xqh.1_Splice_Site|C10orf27_uc010qjn.1_Splice_Site_p.D93_splice|C10orf27_uc009xqi.1_Intron|C10orf27_uc010qjo.1_Splice_Site_p.D82_splice|C10orf27_uc009xqj.1_Silent_p.Q87Q|C10orf27_uc010qjp.1_Splice_Site_p.D82_splice	NM_152710	NP_689923			stromal protein associated with thymii and lymph						cell differentiation|multicellular organismal development|spermatogenesis	cytosol				skin(1)	1																		---	---	---	---
SLC29A3	55315	broad.mit.edu	37	10	73121832	73121832	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73121832C>T	uc001jrr.3	+	6	952	c.895C>T	c.(895-897)CGC>TGC	p.R299C	SLC29A3_uc001jrs.3_3'UTR|SLC29A3_uc010qjq.1_Missense_Mutation_p.R153C|SLC29A3_uc001jrt.3_Missense_Mutation_p.R93C|SLC29A3_uc001jru.3_Missense_Mutation_p.R111C	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside	299	Cytoplasmic (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0																		---	---	---	---
FUT11	170384	broad.mit.edu	37	10	75533570	75533570	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75533570A>G	uc001jva.2	+	2	1374	c.1331A>G	c.(1330-1332)GAC>GGC	p.D444G	FUT11_uc001juy.1_3'UTR|FUT11_uc001juz.1_Missense_Mutation_p.D444G	NM_173540	NP_775811	Q495W5	FUT11_HUMAN	fucosyltransferase 11 (alpha (1,3)	444	Lumenal (Potential).				protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	Prostate(51;0.0112)																	---	---	---	---
PPIF	10105	broad.mit.edu	37	10	81113488	81113488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81113488G>A	uc001kai.2	+	6	599	c.514G>A	c.(514-516)GGT>AGT	p.G172S	PPIF_uc001kaj.2_Silent_p.S146S	NM_005729	NP_005720	P30405	PPIF_HUMAN	peptidylprolyl isomerase F precursor	172	PPIase cyclophilin-type.				protein folding	membrane fraction|mitochondrial matrix	peptidyl-prolyl cis-trans isomerase activity			skin(1)	1	all_cancers(46;0.0893)|Breast(12;8.52e-05)|all_epithelial(25;0.00449)|Prostate(51;0.00985)		Epithelial(14;0.00242)|all cancers(16;0.0069)|Colorectal(32;0.229)		Dimethyl sulfoxide(DB01093)|L-Proline(DB00172)													---	---	---	---
PPIF	10105	broad.mit.edu	37	10	81113585	81113585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81113585G>A	uc001kai.2	+	6	696	c.611G>A	c.(610-612)GGC>GAC	p.G204D	PPIF_uc001kaj.2_3'UTR	NM_005729	NP_005720	P30405	PPIF_HUMAN	peptidylprolyl isomerase F precursor	204	PPIase cyclophilin-type.				protein folding	membrane fraction|mitochondrial matrix	peptidyl-prolyl cis-trans isomerase activity			skin(1)	1	all_cancers(46;0.0893)|Breast(12;8.52e-05)|all_epithelial(25;0.00449)|Prostate(51;0.00985)		Epithelial(14;0.00242)|all cancers(16;0.0069)|Colorectal(32;0.229)		Dimethyl sulfoxide(DB01093)|L-Proline(DB00172)													---	---	---	---
SFTPA2	729238	broad.mit.edu	37	10	81317088	81317088	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81317088G>A	uc001kal.3	-	6	721	c.624C>T	c.(622-624)TAC>TAT	p.Y208Y	SFTPA2_uc001kan.3_Silent_p.Y208Y	NM_006926	NP_008857	Q8IWL1	SFPA2_HUMAN	RecName: Full=Pulmonary surfactant-associated protein A2;          Short=SP-A2;          Short=SP-A;          Short=PSP-A;          Short=PSPA; AltName: Full=Alveolar proteinosis protein; AltName: Full=35 kDa pulmonary surfactant-associated protein; Flags: Precursor;	208	C-type lectin.				cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)											Pulmonary_Fibrosis_Idiopathic				---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483733	91483733	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91483733T>C	uc001kgs.1	+	14	1807	c.1735T>C	c.(1735-1737)TTA>CTA	p.L579L	KIF20B_uc001kgr.1_Silent_p.L579L|KIF20B_uc001kgt.1_5'UTR	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	579	Potential.				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94712135	94712135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94712135C>T	uc001kig.2	+	15	1588	c.1522C>T	c.(1522-1524)CGG>TGG	p.R508W	EXOC6_uc010qnr.1_Missense_Mutation_p.R524W|EXOC6_uc001kie.2_Missense_Mutation_p.R503W|EXOC6_uc009xub.2_Missense_Mutation_p.R507W|EXOC6_uc009xuc.2_Missense_Mutation_p.R405W|EXOC6_uc001kih.2_RNA|EXOC6_uc001kii.2_Missense_Mutation_p.R82W	NM_019053	NP_061926	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform a	508					protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95083098	95083098	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95083098C>A	uc001kin.2	-	47	5412	c.5289G>T	c.(5287-5289)TGG>TGT	p.W1763C	MYOF_uc001kio.2_Missense_Mutation_p.W1750C|MYOF_uc009xue.2_Intron	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1763	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																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95107511	95107511	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95107511G>T	uc001kin.2	-	37	4235	c.4112C>A	c.(4111-4113)CCC>CAC	p.P1371H	MYOF_uc001kio.2_Missense_Mutation_p.P1358H|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1371	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																		---	---	---	---
ENTPD1	953	broad.mit.edu	37	10	97624518	97624518	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97624518T>C	uc001klh.3	+	9	1550	c.1226T>C	c.(1225-1227)CTG>CCG	p.L409P	ENTPD1_uc001kli.3_Missense_Mutation_p.L416P|uc001klg.1_Intron|ENTPD1_uc010qoj.1_Missense_Mutation_p.L421P|ENTPD1_uc010qok.1_Missense_Mutation_p.L301P|ENTPD1_uc010qol.1_Missense_Mutation_p.L301P|ENTPD1_uc010qom.1_Missense_Mutation_p.L368P|ENTPD1_uc010qon.1_Missense_Mutation_p.L271P|ENTPD1_uc009xva.2_Missense_Mutation_p.L271P|ENTPD1_uc009xuz.2_RNA	NM_001776	NP_001767	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	409	Extracellular (Potential).				cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)														---	---	---	---
RRP12	23223	broad.mit.edu	37	10	99139083	99139083	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99139083A>C	uc001knf.2	-	15	1904	c.1765T>G	c.(1765-1767)TTC>GTC	p.F589V	RRP12_uc009xvm.2_Missense_Mutation_p.F307V|RRP12_uc010qou.1_Missense_Mutation_p.F528V|RRP12_uc009xvn.2_Missense_Mutation_p.F489V	NM_015179	NP_055994	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog isoform 1	589						integral to membrane|nuclear membrane|nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)														---	---	---	---
ANKRD2	26287	broad.mit.edu	37	10	99343491	99343491	+	3'UTR	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99343491C>T	uc001knw.2	+	9					DHDPSL_uc001knx.2_5'Flank|DHDPSL_uc001kny.2_5'Flank|DHDPSL_uc001knz.2_5'Flank|PI4K2A_uc010qoy.1_5'Flank|ANKRD2_uc009xvu.2_3'UTR	NM_020349	NP_065082			ankyrin repeat domain 2 isoform a						muscle contraction|muscle organ development		structural constituent of muscle				0		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)														---	---	---	---
AVPI1	60370	broad.mit.edu	37	10	99439420	99439420	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99439420C>T	uc001koh.1	-	2	354	c.243G>A	c.(241-243)AGG>AGA	p.R81R	AVPI1_uc001koi.2_Silent_p.R81R	NM_021732	NP_068378	Q5T686	AVPI1_HUMAN	vasopressin-induced protein, 32kDa	81				R -> K (in Ref. 3; BAD96819).	cell cycle					breast(1)	1		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)														---	---	---	---
LOXL4	84171	broad.mit.edu	37	10	100017916	100017916	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100017916C>T	uc001kpa.1	-	7	1078	c.927G>A	c.(925-927)CCG>CCA	p.P309P		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	309						extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)|skin(1)	5		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)														---	---	---	---
PYROXD2	84795	broad.mit.edu	37	10	100147059	100147059	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100147059C>T	uc001kpc.2	-	14	1539	c.1453G>A	c.(1453-1455)GAT>AAT	p.D485N	PYROXD2_uc001kpb.2_RNA|PYROXD2_uc001kpd.2_RNA	NM_032709	NP_116098	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase	485							oxidoreductase activity			central_nervous_system(1)	1																		---	---	---	---
CPN1	1369	broad.mit.edu	37	10	101823365	101823365	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101823365C>A	uc001kql.2	-							NM_001308	NP_001299			carboxypeptidase N, polypeptide 1 precursor						proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)														---	---	---	---
MIR608	693193	broad.mit.edu	37	10	102734779	102734779	+	RNA	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102734779C>T	hsa-mir-608|MI0003621	+			c.38C>T			SEMA4G_uc001krv.2_Intron|SEMA4G_uc010qpt.1_Intron|SEMA4G_uc001krw.1_Intron|SEMA4G_uc001krx.2_Intron																	0																		---	---	---	---
MGEA5	10724	broad.mit.edu	37	10	103558747	103558747	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103558747G>A	uc001ktv.2	-	9	2104	c.1661C>T	c.(1660-1662)ACC>ATC	p.T554I	MGEA5_uc001ktu.2_RNA|MGEA5_uc010qqe.1_Missense_Mutation_p.T501I|MGEA5_uc009xws.2_Missense_Mutation_p.T501I|MGEA5_uc001ktw.2_Missense_Mutation_p.T554I|MGEA5_uc009xwt.2_Missense_Mutation_p.T317I	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	554					glycoprotein catabolic process	cytoplasm|nucleus	histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)														---	---	---	---
NOLC1	9221	broad.mit.edu	37	10	103921390	103921390	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103921390A>G	uc001kuo.2	+	11	2054	c.1819A>G	c.(1819-1821)ACC>GCC	p.T607A	NOLC1_uc001kup.2_Missense_Mutation_p.T617A|NOLC1_uc001kuq.2_Missense_Mutation_p.T608A|NOLC1_uc009xxb.1_Missense_Mutation_p.T326A|NOLC1_uc001kur.2_Missense_Mutation_p.T326A	NM_004741	NP_004732	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	607	Nuclear localization signal (Potential).				mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104120057	104120057	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104120057C>T	uc001kux.1	+	12	1534	c.1294C>T	c.(1294-1296)CAT>TAT	p.H432Y	GBF1_uc001kuw.2_3'UTR|GBF1_uc001kuy.1_Missense_Mutation_p.H432Y|GBF1_uc001kuz.1_Missense_Mutation_p.H433Y	NM_004193	NP_004184	Q92538	GBF1_HUMAN	golgi-specific brefeldin A resistant guanine	432					COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
NFKB2	4791	broad.mit.edu	37	10	104156720	104156720	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104156720A>G	uc001kvb.2	+	6	568	c.303A>G	c.(301-303)CCA>CCG	p.P101P	NFKB2_uc001kva.2_Silent_p.P101P|NFKB2_uc010qqk.1_Silent_p.P101P|NFKB2_uc001kvd.2_Silent_p.P101P|NFKB2_uc009xxc.2_Silent_p.P101P	NM_001077494	NP_001070962	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene	101	RHD.				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	Bcl3/NF-kappaB2 complex|cytosol|nucleoplasm	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			lung(3)	3		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)				T	IGH@	B-NHL								---	---	---	---
PSD	5662	broad.mit.edu	37	10	104173950	104173950	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104173950C>A	uc001kvg.1	-	5	1656	c.1129G>T	c.(1129-1131)GGG>TGG	p.G377W	PSD_uc001kvh.1_Translation_Start_Site|PSD_uc009xxd.1_Missense_Mutation_p.G377W	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	377					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)														---	---	---	---
TMEM180	79847	broad.mit.edu	37	10	104230500	104230500	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104230500G>A	uc001kvt.2	+	5	549	c.330G>A	c.(328-330)GCG>GCA	p.A110A	TMEM180_uc001kvs.2_Intron|TMEM180_uc010qql.1_Intron|TMEM180_uc010qqm.1_Intron|TMEM180_uc001kvu.2_Silent_p.A110A	NM_024789	NP_079065	Q14CX5	TM180_HUMAN	transmembrane protein 180	110	Helical; (Potential).					integral to membrane				ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
OBFC1	79991	broad.mit.edu	37	10	105659861	105659861	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105659861C>T	uc001kxl.2	-	4	491	c.416G>A	c.(415-417)CGC>CAC	p.R139H	OBFC1_uc001kxm.2_Missense_Mutation_p.R139H|OBFC1_uc001kxn.2_RNA	NM_024928	NP_079204	Q9H668	STN1_HUMAN	oligonucleotide/oligosaccharide-binding fold	139	OB.				positive regulation of DNA replication|telomere maintenance via telomere lengthening		protein binding|single-stranded telomeric DNA binding			ovary(1)	1		Colorectal(252;0.178)		Epithelial(162;3.39e-10)|all cancers(201;1.32e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0151)														---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111630478	111630478	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111630478G>T	uc001kyp.1	-						XPNPEP1_uc009xxt.1_Intron|XPNPEP1_uc001kyq.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)														---	---	---	---
ZDHHC6	64429	broad.mit.edu	37	10	114194118	114194118	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114194118C>A	uc001kzv.2	-	7	1264	c.840G>T	c.(838-840)GGG>GGT	p.G280G	ZDHHC6_uc001kzw.2_Silent_p.G276G|ZDHHC6_uc009xya.1_Silent_p.G280G	NM_022494	NP_071939	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	280						integral to membrane	acyltransferase activity|zinc ion binding				0		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115338385	115338385	+	Splice_Site	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115338385G>T	uc001lai.3	+	7	672	c.569_splice	c.e7-1	p.G190_splice	HABP2_uc010qrz.1_Splice_Site|HABP2_uc010qry.1_Splice_Site	NM_004132	NP_004123			hyaluronan binding protein 2 preproprotein						cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115402723	115402723	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115402723G>A	uc001laj.2	-	12	1349	c.1185C>T	c.(1183-1185)AAC>AAT	p.N395N	NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Silent_p.N395N	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	395	Nebulin 9.			N -> D (in Ref. 3; CAD38623).		fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123276912	123276912	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123276912C>A	uc010qtk.1	-	8	1652	c.1005G>T	c.(1003-1005)GAG>GAT	p.E335D	FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Missense_Mutation_p.E220D|FGFR2_uc010qti.1_Missense_Mutation_p.E246D|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Missense_Mutation_p.E220D|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_RNA|FGFR2_uc010qtn.1_Missense_Mutation_p.E354D|FGFR2_uc010qto.1_Missense_Mutation_p.E239D|FGFR2_uc001lfo.1_3'UTR|FGFR2_uc001lfg.3_Translation_Start_Site	NM_000141	NP_000132	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2 isoform 1	335	Ig-like C2-type 3.|Extracellular (Potential).				angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124345846	124345846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124345846G>A	uc001lgk.1	+	16	1836	c.1730G>A	c.(1729-1731)GGC>GAC	p.G577D	DMBT1_uc001lgl.1_Missense_Mutation_p.G567D|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Missense_Mutation_p.G577D|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yaa.1_Intron	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	577	SRCR 4.				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)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124348500	124348500	+	Silent	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124348500T>A	uc001lgk.1	+	17	1930	c.1824T>A	c.(1822-1824)GGT>GGA	p.G608G	DMBT1_uc001lgl.1_Silent_p.G598G|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Silent_p.G608G|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yaa.1_Intron	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	608	SRCR 5.				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)																---	---	---	---
GPR26	2849	broad.mit.edu	37	10	125447476	125447476	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125447476G>A	uc001lhh.2	+	3	867	c.814G>A	c.(814-816)GGC>AGC	p.G272S		NM_153442	NP_703143	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	272	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)																---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128193584	128193584	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128193584T>G	uc001ljq.2	-	3	306	c.185A>C	c.(184-186)AAG>ACG	p.K62T	C10orf90_uc001ljp.2_Missense_Mutation_p.K15T|C10orf90_uc010qum.1_Missense_Mutation_p.K159T|C10orf90_uc009yao.2_Missense_Mutation_p.K159T|C10orf90_uc001ljs.1_Missense_Mutation_p.K15T	NM_001004298	NP_001004298	Q96M02	CJ090_HUMAN	hypothetical protein LOC118611	62										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)														---	---	---	---
DPYSL4	10570	broad.mit.edu	37	10	134006199	134006199	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134006199A>G	uc009ybb.2	+	3	320	c.166A>G	c.(166-168)AAG>GAG	p.K56E		NM_006426	NP_006417	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	56					axon guidance|pyrimidine base catabolic process	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			central_nervous_system(2)	2		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)														---	---	---	---
KNDC1	85442	broad.mit.edu	37	10	135013091	135013091	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135013091C>T	uc001llz.1	+	15	2889	c.2888C>T	c.(2887-2889)GCG>GTG	p.A963V	KNDC1_uc001lma.1_Missense_Mutation_p.A898V|KNDC1_uc001lmb.1_Missense_Mutation_p.A375V	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND)	963					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)														---	---	---	---
RIC8A	60626	broad.mit.edu	37	11	211289	211289	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:211289G>T	uc001log.2	+	5	1234	c.909G>T	c.(907-909)ATG>ATT	p.M303I	RIC8A_uc001lof.2_Missense_Mutation_p.M303I|RIC8A_uc001loh.2_Missense_Mutation_p.M296I	NM_021932	NP_068751	Q9NPQ8	RIC8A_HUMAN	resistance to inhibitors of cholinesterase 8	303						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	1264704	1264704	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1264704C>T	uc009ycr.1	+	48	8634	c.8508C>T	c.(8506-8508)CAC>CAT	p.H2836H	MUC5B_uc001ltb.2_Silent_p.H2201H	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	2198	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				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)														---	---	---	---
OR52A4	390053	broad.mit.edu	37	11	5142251	5142251	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5142251G>A	uc001lzz.1	-	1	558	c.558C>T	c.(556-558)CGC>CGT	p.R186R		NM_001005222	NP_001005222			olfactory receptor, family 52, subfamily A,											ovary(2)	2		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.7e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
OR51B5	282763	broad.mit.edu	37	11	5364322	5364322	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5364322C>A	uc001map.1	-	1	433	c.433G>T	c.(433-435)GGA>TGA	p.G145*	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Nonsense_Mutation_p.G145*	NM_001005567	NP_001005567	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B,	145	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM5	85363	broad.mit.edu	37	11	5701080	5701080	+	Missense_Mutation	SNP	C	T	T	rs146215995		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5701080C>T	uc001mbm.1	-	2	585	c.328G>A	c.(328-330)GGG>AGG	p.G110R	TRIM5_uc001mbq.1_Missense_Mutation_p.G110R|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Missense_Mutation_p.G110R|TRIM5_uc001mbo.2_Missense_Mutation_p.G110R|TRIM5_uc001mbp.2_Missense_Mutation_p.G110R	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	110	B box-type.		G -> E.		interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)														---	---	---	---
KCNJ11	3767	broad.mit.edu	37	11	17408965	17408965	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17408965C>T	uc001mna.2	-	1	1242	c.674G>A	c.(673-675)AGC>AAC	p.S225N	KCNJ11_uc001mnb.3_Missense_Mutation_p.S138N	NM_000525	NP_000516	B4DWI4	B4DWI4_HUMAN	potassium inwardly-rectifying channel J11	225						integral to membrane	ATP-activated inward rectifier potassium channel activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)												OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KCNA4	3739	broad.mit.edu	37	11	30033740	30033740	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30033740G>A	uc001msk.2	-	2	1638	c.486C>T	c.(484-486)GGC>GGT	p.G162G		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	162	Poly-Gly.					voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32624508	32624508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32624508G>A	uc001mtv.2	-	18	3133	c.3089C>T	c.(3088-3090)ACG>ATG	p.T1030M		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	1030										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
TCP11L1	55346	broad.mit.edu	37	11	33079684	33079684	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33079684A>G	uc001mud.2	+	5	1037	c.637A>G	c.(637-639)AGA>GGA	p.R213G	TCP11L1_uc009yju.2_Missense_Mutation_p.R28G|TCP11L1_uc010rei.1_Missense_Mutation_p.R213G|TCP11L1_uc001mue.2_Missense_Mutation_p.R213G|TCP11L1_uc001muf.1_5'Flank	NM_018393	NP_060863	Q9NUJ3	T11L1_HUMAN	t-complex 11 (mouse) like 1	213											0																		---	---	---	---
LMO2	4005	broad.mit.edu	37	11	33881074	33881074	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33881074C>T	uc001mve.2	-	3	744	c.305G>A	c.(304-306)CGT>CAT	p.R102H	LMO2_uc001mvc.2_Missense_Mutation_p.R95H|LMO2_uc001mvd.2_Missense_Mutation_p.R95H|LMO2_uc010rel.1_Missense_Mutation_p.R102H|LMO2_uc010rem.1_Missense_Mutation_p.R171H	NM_001142316	NP_001135788	P25791	RBTN2_HUMAN	LIM domain only 2 isoform 2	102	LIM zinc-binding 2.				multicellular organismal development	nucleus	protein binding|zinc ion binding			lung(1)	1								T	TRD@	T-ALL								---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36595310	36595310	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36595310G>A	uc001mwu.3	+	2	580	c.456G>A	c.(454-456)CCG>CCA	p.P152P	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	152	Interaction with importin alpha-1.				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				---	---	---	---
ALKBH3	221120	broad.mit.edu	37	11	43923097	43923097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43923097G>A	uc001mxs.2	+	8	934	c.491G>A	c.(490-492)CGC>CAC	p.R164H	ALKBH3_uc009ykp.2_RNA|ALKBH3_uc001mxt.2_RNA|ALKBH3_uc009ykq.2_Missense_Mutation_p.R17H	NM_139178	NP_631917	Q96Q83	ALKB3_HUMAN	AlkB homolog 3	164					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					---	---	---	---
ACCSL	390110	broad.mit.edu	37	11	44069844	44069844	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44069844C>T	uc001mxw.1	+	1	314	c.258C>T	c.(256-258)GCC>GCT	p.A86A	ACCSL_uc009ykr.2_5'UTR	NM_001031854	NP_001027025	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase	86							1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5																		---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47238526	47238526	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47238526G>A	uc001neb.2	+	3	577	c.382G>A	c.(382-384)GCT>ACT	p.A128T	DDB2_uc001nec.2_RNA|DDB2_uc009yli.1_Intron|DDB2_uc001ned.2_RNA|DDB2_uc001nee.2_Missense_Mutation_p.A128T|DDB2_uc001nef.2_Missense_Mutation_p.A114T|DDB2_uc001neg.2_5'UTR|DDB2_uc001neh.2_RNA	NM_000107	NP_000098	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2	128	WD 1.				nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV	nucleoplasm|protein complex	damaged DNA binding|protein binding			kidney(2)|ovary(1)	3								Mis|N			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
ACP2	53	broad.mit.edu	37	11	47269278	47269278	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47269278C>A	uc001nei.2	-	3	328	c.211G>T	c.(211-213)GAG>TAG	p.E71*	ACP2_uc010rhe.1_Nonsense_Mutation_p.E43*|ACP2_uc009ylj.2_5'UTR|ACP2_uc010rhf.1_Nonsense_Mutation_p.E39*|ACP2_uc010rhg.1_Nonsense_Mutation_p.E71*|ACP2_uc010rhh.1_5'UTR|ACP2_uc010rhi.1_5'UTR|ACP2_uc009ylk.2_Nonsense_Mutation_p.E71*|ACP2_uc010rhj.1_Nonsense_Mutation_p.E71*|NR1H3_uc009yll.1_5'Flank|NR1H3_uc010rhk.1_5'Flank|NR1H3_uc001nek.2_5'Flank|NR1H3_uc001nej.2_5'Flank|NR1H3_uc001nel.2_5'Flank	NM_001610	NP_001601	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal isoform 1	71	Lumenal (Potential).					integral to membrane|lysosomal lumen|lysosomal membrane	acid phosphatase activity			ovary(1)	1																		---	---	---	---
MYBPC3	4607	broad.mit.edu	37	11	47363661	47363661	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47363661G>A	uc001nfa.3	-	17	1726	c.1671C>T	c.(1669-1671)GGC>GGT	p.G557G	MYBPC3_uc010rhl.1_RNA	NM_000256	NP_000247	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	556	Ig-like C2-type 4.				cardiac muscle contraction|cell adhesion|muscle filament sliding|regulation of muscle filament sliding|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	C zone|cytosol|striated muscle myosin thick filament	actin binding|ATPase activator activity|metal ion binding|myosin heavy chain binding|structural constituent of muscle|titin binding			ovary(2)|central_nervous_system(1)	3				Lung(87;0.176)														---	---	---	---
SPI1	6688	broad.mit.edu	37	11	47377075	47377075	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47377075C>A	uc001nfc.1	-	5	739	c.516G>T	c.(514-516)CTG>CTT	p.L172L	MYBPC3_uc001nfa.3_5'Flank|SPI1_uc001nfb.1_Silent_p.L173L|SLC39A13_uc001nfd.2_Intron	NM_003120	NP_003111	P17947	SPI1_HUMAN	hematopoietic transcription factor PU.1 isoform	172	ETS.				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of erythrocyte differentiation	nucleus	protein binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)	2				Lung(87;0.0967)														---	---	---	---
PSMC3	5702	broad.mit.edu	37	11	47446697	47446697	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47446697G>A	uc001nfh.2	-	3	454	c.260C>T	c.(259-261)CCG>CTG	p.P87L	PSMC3_uc009ylr.1_Intron	NM_002804	NP_002795	P17980	PRS6A_HUMAN	proteasome 26S ATPase subunit 3	87					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 complex	ATP binding|nucleoside-triphosphatase activity|protein binding|transcription coactivator activity|transcription corepressor activity			ovary(4)	4				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
OR4S1	256148	broad.mit.edu	37	11	48328289	48328289	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48328289T>C	uc010rhu.1	+	1	515	c.515T>C	c.(514-516)ATA>ACA	p.I172T		NM_001004725	NP_001004725	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR4C12	283093	broad.mit.edu	37	11	50003875	50003875	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50003875A>G	uc010ria.1	-	1	163	c.163T>C	c.(163-165)TCC>CCC	p.S55P		NM_001005270	NP_001005270	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C,	55	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3																		---	---	---	---
OR4C46	119749	broad.mit.edu	37	11	51515486	51515486	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51515486G>T	uc010ric.1	+	1	205	c.205G>T	c.(205-207)GCC>TCC	p.A69S		NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C,	69	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR5D18	219438	broad.mit.edu	37	11	55587765	55587765	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55587765G>A	uc010rin.1	+	1	660	c.660G>A	c.(658-660)GCG>GCA	p.A220A		NM_001001952	NP_001001952	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D,	220	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3		all_epithelial(135;0.208)																---	---	---	---
OR9Q2	219957	broad.mit.edu	37	11	57958150	57958150	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57958150T>G	uc010rka.1	+	1	188	c.188T>G	c.(187-189)CTC>CGC	p.L63R		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	63	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)																---	---	---	---
OR10W1	81341	broad.mit.edu	37	11	58034831	58034831	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58034831T>C	uc001nmq.1	-	1	902	c.500A>G	c.(499-501)CAC>CGC	p.H167R		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)																---	---	---	---
GLYATL1	92292	broad.mit.edu	37	11	58722275	58722275	+	Silent	SNP	C	T	T	rs142174775		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58722275C>T	uc001nnf.2	+	6	595	c.219C>T	c.(217-219)AAC>AAT	p.N73N	uc001nng.1_Intron|GLYATL1_uc001nnh.1_Silent_p.N104N|GLYATL1_uc001nni.1_Silent_p.N73N|GLYATL1_uc001nnj.1_Silent_p.N73N			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	73						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
FAM111A	63901	broad.mit.edu	37	11	58920216	58920216	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58920216T>C	uc010rkp.1	+	5	1302	c.1075T>C	c.(1075-1077)TAC>CAC	p.Y359H	FAM111A_uc010rkq.1_Missense_Mutation_p.Y359H|FAM111A_uc010rkr.1_Missense_Mutation_p.Y359H|FAM111A_uc001nno.2_Missense_Mutation_p.Y359H|FAM111A_uc001nnp.2_Missense_Mutation_p.Y359H|FAM111A_uc001nnq.2_Missense_Mutation_p.Y359H	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	359					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)																---	---	---	---
OR4D9	390199	broad.mit.edu	37	11	59282557	59282557	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59282557C>T	uc010rkv.1	+	1	172	c.172C>T	c.(172-174)CCC>TCC	p.P58S		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	58	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
MS4A4A	51338	broad.mit.edu	37	11	60059718	60059718	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60059718C>T	uc001noz.2	+	2	72	c.62C>T	c.(61-63)ACA>ATA	p.T21I	MS4A4A_uc001npa.2_Missense_Mutation_p.T2I|MS4A4A_uc001npb.2_Missense_Mutation_p.T2I|MS4A4A_uc001npc.2_Missense_Mutation_p.T2I	NM_148975	NP_683876	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member	21	Cytoplasmic (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62297304	62297304	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62297304C>A	uc001ntl.2	-	5	4885	c.4585G>T	c.(4585-4587)GAG>TAG	p.E1529*	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1529					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
EEF1G	1937	broad.mit.edu	37	11	62338457	62338457	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62338457G>T	uc001ntm.1	-	5	648	c.502C>A	c.(502-504)CTG>ATG	p.L168M	EEF1G_uc010rlw.1_Missense_Mutation_p.L218M|EEF1G_uc001ntn.1_Missense_Mutation_p.L48M	NM_001404	NP_001395	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1	168	GST C-terminal.				response to virus	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0																		---	---	---	---
SLC22A6	9356	broad.mit.edu	37	11	62744336	62744336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62744336C>T	uc001nwk.2	-	10	1929	c.1622G>A	c.(1621-1623)CGA>CAA	p.R541Q	SLC22A6_uc001nwl.2_Missense_Mutation_p.R484Q|SLC22A6_uc001nwj.2_Missense_Mutation_p.R528Q|SLC22A6_uc001nwm.2_Missense_Mutation_p.R497Q	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	541	Cytoplasmic (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0																		---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63668038	63668038	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63668038G>T	uc001nxw.2	+	9	1355	c.776G>T	c.(775-777)CGG>CTG	p.R259L	MARK2_uc001nxx.2_Missense_Mutation_p.R259L|MARK2_uc001nxy.2_Missense_Mutation_p.R259L|MARK2_uc001nxv.3_Missense_Mutation_p.R259L|MARK2_uc001nxz.3_Missense_Mutation_p.R226L|MARK2_uc009yoy.2_Missense_Mutation_p.R226L	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	259	Protein kinase.				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																		---	---	---	---
CDC42BPG	55561	broad.mit.edu	37	11	64595231	64595231	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64595231A>G	uc001obs.3	-	31	3992	c.3992T>C	c.(3991-3993)GTG>GCG	p.V1331A		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	1331	CNH.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4																		---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64662442	64662442	+	3'UTR	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64662442G>T	uc001obx.2	-	41					uc009ypx.2_5'Flank|ATG2A_uc001obw.2_3'UTR	NM_015104	NP_055919			autophagy related 2A								protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
BATF2	116071	broad.mit.edu	37	11	64757176	64757176	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64757176A>G	uc001ocf.1	-	3	381	c.250T>C	c.(250-252)TGC>CGC	p.C84R	BATF2_uc001oce.1_5'UTR	NM_138456	NP_612465	Q8N1L9	BATF2_HUMAN	basic leucine zipper transcription factor,	84						nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
LTBP3	4054	broad.mit.edu	37	11	65319552	65319552	+	Silent	SNP	G	A	A	rs111330939		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65319552G>A	uc001oej.2	-	8	1691	c.1422C>T	c.(1420-1422)GGC>GGT	p.G474G	LTBP3_uc001oeh.2_5'Flank|LTBP3_uc010roi.1_Silent_p.G357G|LTBP3_uc001oei.2_Silent_p.G474G|LTBP3_uc010roj.1_Silent_p.G175G|LTBP3_uc010rok.1_Silent_p.G385G	NM_001130144	NP_001123616	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding	474						extracellular region	calcium ion binding|growth factor binding			central_nervous_system(2)|lung(1)	3																OREG0021081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EHBP1L1	254102	broad.mit.edu	37	11	65347891	65347891	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65347891A>G	uc001oeo.3	+	6	840	c.575A>G	c.(574-576)GAT>GGT	p.D192G	EHBP1L1_uc001oep.1_5'Flank	NM_001099409	NP_001092879	Q8N3D4	EH1L1_HUMAN	tangerin	192										central_nervous_system(1)	1																		---	---	---	---
EFEMP2	30008	broad.mit.edu	37	11	65634557	65634557	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65634557G>T	uc001ofy.3	-						EFEMP2_uc001ofz.2_Intron|EFEMP2_uc001oga.2_Intron	NM_016938	NP_058634			EGF-containing fibulin-like extracellular matrix						blood coagulation	basement membrane|membrane	calcium ion binding|extracellular matrix structural constituent|protein binding|transmembrane receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(159;0.169)														---	---	---	---
FIBP	9158	broad.mit.edu	37	11	65652091	65652091	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65652091G>A	uc001ogd.2	-	8	998	c.877C>T	c.(877-879)CTG>TTG	p.L293L	FIBP_uc009yqu.2_Silent_p.L283L|FIBP_uc001oge.2_Silent_p.L286L	NM_198897	NP_942600	O43427	FIBP_HUMAN	FGF intracellular binding protein isoform a	293					fibroblast growth factor receptor signaling pathway	endomembrane system|membrane|microsome|mitochondrion|nucleus	fibroblast growth factor binding			ovary(1)	1				READ - Rectum adenocarcinoma(159;0.166)												OREG0021089	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CATSPER1	117144	broad.mit.edu	37	11	65792929	65792929	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65792929C>T	uc001ogt.2	-	1	1060	c.922G>A	c.(922-924)GCG>ACG	p.A308T		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	308	His-rich.|Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2																		---	---	---	---
RAB1B	81876	broad.mit.edu	37	11	66039698	66039698	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66039698A>G	uc001ohf.2	+	3	253	c.158A>G	c.(157-159)GAT>GGT	p.D53G	uc001ohg.1_RNA	NM_030981	NP_112243	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	53					protein transport|small GTPase mediated signal transduction	Golgi apparatus|membrane	GTP binding|protein binding				0																		---	---	---	---
BRMS1	25855	broad.mit.edu	37	11	66109071	66109071	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66109071G>A	uc001ohp.1	-	3	310	c.163C>T	c.(163-165)CGA>TGA	p.R55*	BRMS1_uc001oho.1_Nonsense_Mutation_p.R55*|BRMS1_uc009yre.2_5'Flank	NM_015399	NP_056214	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1 isoform 1	55					apoptosis|negative regulation of anti-apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of anoikis|positive regulation of protein deacetylation|transcription, DNA-dependent	cytoplasm|nucleus	NF-kappaB binding				0																		---	---	---	---
RBM4B	83759	broad.mit.edu	37	11	66436136	66436136	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66436136G>A	uc001oja.2	-	2	1708	c.1039C>T	c.(1039-1041)CGG>TGG	p.R347W	RBM4B_uc001ojb.2_Missense_Mutation_p.R347W	NM_031492	NP_113680	Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	347	Interaction with TNPO3 (By similarity).				circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|RNA splicing	nucleolus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
CORO1B	57175	broad.mit.edu	37	11	67208646	67208646	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67208646T>C	uc001olj.1	-	5	742	c.706A>G	c.(706-708)ACC>GCC	p.T236A	CORO1B_uc009yrs.1_RNA|CORO1B_uc001olk.1_Missense_Mutation_p.T236A|CORO1B_uc009yrt.1_RNA|CORO1B_uc009yru.1_RNA|CORO1B_uc001oll.1_Missense_Mutation_p.T236A|CORO1B_uc010rps.1_Missense_Mutation_p.T236A	NM_020441	NP_065174	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	236	WD 4.				actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding			large_intestine(1)|ovary(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)															---	---	---	---
GPR152	390212	broad.mit.edu	37	11	67218801	67218801	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67218801C>T	uc001olm.2	-	1	1400	c.1395G>A	c.(1393-1395)CCG>CCA	p.P465P	uc009yrw.1_5'Flank|CABP4_uc001oln.2_5'Flank	NM_206997	NP_996880	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	465	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)															---	---	---	---
NUDT8	254552	broad.mit.edu	37	11	67395817	67395817	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67395817T>G	uc001omo.1	-	3	401	c.382A>C	c.(382-384)AGC>CGC	p.S128R	NUDT8_uc001omn.2_Missense_Mutation_p.S128R	NM_181843	NP_862826	Q8WV74	NUDT8_HUMAN	nudix-type motif 8	128	Nudix hydrolase.					mitochondrion	hydrolase activity|metal ion binding				0																		---	---	---	---
NDUFS8	4728	broad.mit.edu	37	11	67799650	67799650	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67799650G>T	uc001onc.2	+	2	139	c.32G>T	c.(31-33)CGG>CTG	p.R11L	NDUFS8_uc010rpz.1_Missense_Mutation_p.R11L|NDUFS8_uc009ysb.1_Intron|NDUFS8_uc009ysc.1_Missense_Mutation_p.R11L	NM_002496	NP_002487	O00217	NDUS8_HUMAN	NADH dehydrogenase ubiquinone Fe-S 8 precursor	11					mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|response to oxidative stress|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)													---	---	---	---
ANO1	55107	broad.mit.edu	37	11	70007826	70007826	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70007826T>C	uc001opj.2	+	18	2184	c.1879T>C	c.(1879-1881)TTC>CTC	p.F627L	ANO1_uc001opk.1_Missense_Mutation_p.F569L|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Missense_Mutation_p.F336L	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	627	Helical; (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
KRTAP5-9	3846	broad.mit.edu	37	11	71259987	71259987	+	Missense_Mutation	SNP	C	T	T	rs114705722	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71259987C>T	uc001oqs.1	+	1	522	c.284C>T	c.(283-285)TCC>TTC	p.S95F		NM_005553	NP_005544	P26371	KRA59_HUMAN	keratin associated protein 5-9	95	8 X 4 AA repeats of C-C-X-P.				epidermis development	keratin filament					0																		---	---	---	---
RNF121	55298	broad.mit.edu	37	11	71705854	71705854	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71705854A>C	uc001ora.2	+	7	1057	c.717A>C	c.(715-717)GAA>GAC	p.E239D	RNF121_uc001ord.2_Missense_Mutation_p.E158D|RNF121_uc001orb.2_Missense_Mutation_p.E207D|RNF121_uc009yst.2_Intron	NM_018320	NP_060790	Q9H920	RN121_HUMAN	ring finger protein 121	239	RING-type; atypical.					integral to membrane	zinc ion binding				0																		---	---	---	---
C11orf51	25906	broad.mit.edu	37	11	71822201	71822201	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71822201A>G	uc001orw.2	-	3	342	c.120_splice	c.e3+1	p.W40_splice	C11orf51_uc009ytc.1_Intron|C11orf51_uc001orv.2_Splice_Site_p.W40_splice	NM_014042	NP_054761			hypothetical protein LOC25906							intracellular					0																		---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72013356	72013356	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72013356G>A	uc001osj.2	-	11	1299	c.1249C>T	c.(1249-1251)CGA>TGA	p.R417*	CLPB_uc010rqx.1_Nonsense_Mutation_p.R372*|CLPB_uc010rqy.1_Nonsense_Mutation_p.R358*|CLPB_uc001osk.2_Nonsense_Mutation_p.R387*|CLPB_uc009ytg.2_RNA|CLPB_uc010rqz.1_Nonsense_Mutation_p.R216*|CLPB_uc001osi.2_Nonsense_Mutation_p.R25*	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	caseinolytic peptidase B	417					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1																		---	---	---	---
CTSC	1075	broad.mit.edu	37	11	88027550	88027550	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88027550C>T	uc001pck.3	-	7	1117	c.1016G>A	c.(1015-1017)CGT>CAT	p.R339H	CTSC_uc001pcl.3_Missense_Mutation_p.R191H	NM_001814	NP_001805	P53634	CATC_HUMAN	cathepsin C isoform a preproprotein	339			R -> C (in PLS).		immune response	lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92430571	92430571	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92430571G>T	uc001pdj.3	+	3	3646	c.3629G>T	c.(3628-3630)AGG>ATG	p.R1210M		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1210	Cadherin 11.|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)			---	---	---	---
FAM76B	143684	broad.mit.edu	37	11	95512300	95512300	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95512300C>A	uc001pfn.2	-						FAM76B_uc001pfm.2_Splice_Site	NM_144664	NP_653265			hypothetical protein LOC143684												0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95712275	95712275	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95712275C>A	uc001pfw.1	-	5	4593	c.3308G>T	c.(3307-3309)AGC>ATC	p.S1103I		NM_032427	NP_115803	Q8IZL2	MAML2_HUMAN	mastermind-like 2	1103					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								---	---	---	---
MMP1	4312	broad.mit.edu	37	11	102667472	102667472	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102667472T>C	uc001phi.2	-	4	691	c.548A>G	c.(547-549)CAT>CGT	p.H183R	uc001phh.1_Intron|MMP1_uc010ruv.1_Missense_Mutation_p.H117R	NM_002421	NP_002412	P03956	MMP1_HUMAN	matrix metalloproteinase 1 isoform 1	183	Metalloprotease.	Zinc 1.			blood coagulation|collagen catabolic process|interspecies interaction between organisms|leukocyte migration|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	all_epithelial(12;0.0127)	all_neural(303;0.000318)|all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.072)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.233)	OV - Ovarian serous cystadenocarcinoma(223;1.82e-07)|Epithelial(105;1.51e-06)|BRCA - Breast invasive adenocarcinoma(274;0.014)														---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106810870	106810870	+	Silent	SNP	A	G	G	rs61736490		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106810870A>G	uc001pjg.1	-	4	912	c.522T>C	c.(520-522)GGT>GGC	p.G174G	GUCY1A2_uc010rvo.1_Silent_p.G174G|GUCY1A2_uc009yxn.1_Silent_p.G174G	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	174					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)														---	---	---	---
ZC3H12C	85463	broad.mit.edu	37	11	110030105	110030105	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110030105G>A	uc009yxw.2	+	4	1089	c.1038G>A	c.(1036-1038)TCG>TCA	p.S346S	ZC3H12C_uc010rwc.1_Silent_p.S347S|ZC3H12C_uc010rwd.1_Silent_p.S347S|ZC3H12C_uc001pkr.3_Silent_p.S315S|ZC3H12C_uc001pkq.2_Silent_p.S315S	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	346							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	113934373	113934373	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113934373G>A	uc001pop.2	+	2	615	c.351G>A	c.(349-351)CAG>CAA	p.Q117Q	ZBTB16_uc001poo.1_Silent_p.Q117Q|ZBTB16_uc001poq.2_Silent_p.Q117Q	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	117					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)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114121133	114121133	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114121133C>T	uc001pop.2	+	7	2142	c.1878C>T	c.(1876-1878)GGC>GGT	p.G626G	ZBTB16_uc001poq.2_Silent_p.G626G	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	626					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)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115111047	115111047	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115111047A>G	uc001ppi.3	-	2	347	c.218T>C	c.(217-219)GTG>GCG	p.V73A	CADM1_uc001ppf.3_Missense_Mutation_p.V73A|CADM1_uc001ppk.3_Missense_Mutation_p.V73A|CADM1_uc001ppj.3_Missense_Mutation_p.V73A|CADM1_uc001ppl.2_Missense_Mutation_p.V73A	NM_014333	NP_055148	Q9BY67	CADM1_HUMAN	immunoglobulin superfamily, member 4D isoform 1	73	Ig-like V-type.|Extracellular (Potential).				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)														---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117222588	117222588	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117222588C>T	uc001prc.2	+	5	424	c.277C>T	c.(277-279)CGG>TGG	p.R93W	CEP164_uc001prb.2_Missense_Mutation_p.R93W|CEP164_uc001prd.2_Missense_Mutation_p.R93W|CEP164_uc010rxj.1_Missense_Mutation_p.R47W|CEP164_uc010rxk.1_Missense_Mutation_p.R93W	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	93	Interaction with ATRIP.				cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	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;4e-05)|Epithelial(105;0.0008)														---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117253641	117253641	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117253641G>A	uc001prc.2	+	14	1854	c.1707G>A	c.(1705-1707)CCG>CCA	p.P569P	CEP164_uc001prb.2_Silent_p.P572P|CEP164_uc010rxk.1_Silent_p.P543P|CEP164_uc001prf.2_RNA|CEP164_uc009yzp.1_RNA|CEP164_uc001prg.1_5'Flank	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	569	Glu-rich.				cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	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;4e-05)|Epithelial(105;0.0008)														---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119547871	119547871	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119547871G>A	uc001pwv.2	-	4	964	c.792C>T	c.(790-792)GAC>GAT	p.D264D	PVRL1_uc001pwu.1_Silent_p.D264D|PVRL1_uc001pww.2_Silent_p.D264D	NM_002855	NP_002846	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 1	264	Extracellular (Potential).|Ig-like C2-type 2.				adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)														---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123464792	123464792	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123464792G>A	uc001pyx.2	+	4	587	c.258G>A	c.(256-258)GTG>GTA	p.V86V	GRAMD1B_uc001pyw.2_Silent_p.V93V|GRAMD1B_uc010rzw.1_Silent_p.V46V|GRAMD1B_uc010rzx.1_Silent_p.V46V|GRAMD1B_uc009zbe.1_Silent_p.V82V	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	86						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
OR6M1	390261	broad.mit.edu	37	11	123676673	123676673	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123676673G>A	uc010rzz.1	-	1	385	c.385C>T	c.(385-387)CAC>TAC	p.H129Y		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	129	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)														---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126278260	126278260	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126278260C>T	uc001qds.2	+	8	715	c.496C>T	c.(496-498)CGT>TGT	p.R166C	ST3GAL4_uc001qdt.2_Missense_Mutation_p.R162C|ST3GAL4_uc009zcc.2_Missense_Mutation_p.R2C|ST3GAL4_uc009zcd.2_Missense_Mutation_p.R155C|ST3GAL4_uc001qdu.2_Missense_Mutation_p.R162C|ST3GAL4_uc001qdv.2_Missense_Mutation_p.R166C|ST3GAL4_uc009zce.2_Missense_Mutation_p.R162C|ST3GAL4_uc001qdw.2_Missense_Mutation_p.R155C|ST3GAL4_uc001qdx.1_Missense_Mutation_p.R123C|ST3GAL4_uc001qdy.2_Missense_Mutation_p.R2C|ST3GAL4_uc001qdz.2_Missense_Mutation_p.R2C	NM_006278	NP_006269	Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	166	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)														---	---	---	---
C11orf45	219833	broad.mit.edu	37	11	128774355	128774355	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128774355G>T	uc001qeu.2	-	2	301	c.107C>A	c.(106-108)CCC>CAC	p.P36H	KCNJ5_uc001qet.2_Intron|KCNJ5_uc009zck.2_Intron|C11orf45_uc009zcl.2_Missense_Mutation_p.P36H|C11orf45_uc001qev.2_Missense_Mutation_p.P36H	NM_145013	NP_659450	Q8TAV5	CK045_HUMAN	hypothetical protein LOC219833 precursor	36						extracellular region					0	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)														---	---	---	---
KCNJ5	3762	broad.mit.edu	37	11	128781942	128781942	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128781942C>T	uc001qet.2	+	2	1088	c.774C>T	c.(772-774)AAC>AAT	p.N258N	KCNJ5_uc009zck.2_Silent_p.N258N|KCNJ5_uc001qew.2_Silent_p.N258N	NM_000890	NP_000881	P48544	IRK5_HUMAN	potassium inwardly-rectifying channel J5	258	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glibenclamide(DB01016)													---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	660209	660209	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:660209G>A	uc001qii.1	+						B4GALNT3_uc001qij.1_Intron|B4GALNT3_uc001qik.1_5'Flank	NM_173593	NP_775864			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1213982	1213982	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1213982G>A	uc001qjb.2	+	4	1394	c.1153G>A	c.(1153-1155)GAG>AAG	p.E385K	ERC1_uc001qiz.2_RNA|ERC1_uc001qjc.2_Missense_Mutation_p.E385K|ERC1_uc001qja.2_RNA|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Missense_Mutation_p.E385K|ERC1_uc010sdv.1_Missense_Mutation_p.E161K|ERC1_uc009zdp.2_Missense_Mutation_p.E22K	NM_178040	NP_829884	Q8IUD2	RB6I2_HUMAN	RAB6-interacting protein 2 isoform epsilon	385	Potential.				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)															---	---	---	---
PARP11	57097	broad.mit.edu	37	12	3921464	3921464	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3921464C>A	uc001qmk.1	-	7	876	c.821G>T	c.(820-822)CGA>CTA	p.R274L	PARP11_uc001qml.2_Missense_Mutation_p.R281L|PARP11_uc009zef.2_RNA|PARP11_uc001qmm.2_Missense_Mutation_p.R200L|PARP11_uc001qmn.2_Missense_Mutation_p.R200L	NM_020367	NP_065100	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	274	PARP catalytic.						NAD+ ADP-ribosyltransferase activity			ovary(1)|central_nervous_system(1)	2			all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
VWF	7450	broad.mit.edu	37	12	6131131	6131131	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6131131G>A	uc001qnn.1	-	27	3859	c.3609C>T	c.(3607-3609)GGC>GGT	p.G1203G	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1203					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
VWF	7450	broad.mit.edu	37	12	6161758	6161758	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6161758C>T	uc001qnn.1	-	16	2387	c.2137G>A	c.(2137-2139)GGT>AGT	p.G713S	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	713					blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
NCAPD2	9918	broad.mit.edu	37	12	6627027	6627027	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6627027C>A	uc001qoo.2	+	13	1537	c.1491C>A	c.(1489-1491)CCC>CCA	p.P497P	NCAPD2_uc009zen.1_Silent_p.P369P|NCAPD2_uc010sfd.1_Silent_p.P452P	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	497	Interactions with SMC2 and SMC4.				cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5																		---	---	---	---
ACRBP	84519	broad.mit.edu	37	12	6749364	6749364	+	Silent	SNP	G	A	A	rs143853195		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6749364G>A	uc001qpu.1	-	8	1335	c.1287C>T	c.(1285-1287)TAC>TAT	p.Y429Y	LPAR5_uc010sff.1_5'Flank|ACRBP_uc001qpt.1_5'Flank|ACRBP_uc010sfg.1_Silent_p.Y396Y	NM_032489	NP_115878	Q8NEB7	ACRBP_HUMAN	proacrosin binding protein sp32 precursor	429						acrosomal vesicle|extracellular region				central_nervous_system(1)	1																		---	---	---	---
SPSB2	84727	broad.mit.edu	37	12	6981674	6981674	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6981674C>T	uc001qrl.2	-	2	548	c.392G>A	c.(391-393)TGG>TAG	p.W131*	SPSB2_uc001qrm.2_Nonsense_Mutation_p.W131*|SPSB2_uc010sfp.1_Nonsense_Mutation_p.W131*|LRRC23_uc001qrn.1_5'Flank	NM_001146316	NP_001139788	Q99619	SPSB2_HUMAN	splA/ryanodine receptor domain and SOCS box	131	B30.2/SPRY.				intracellular signal transduction	cytoplasm	protein binding			kidney(1)	1																OREG0021639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C1RL	51279	broad.mit.edu	37	12	7249058	7249058	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7249058C>A	uc001qsn.2	-	6	1410	c.1393G>T	c.(1393-1395)GGG>TGG	p.G465W	C1RL_uc009zft.2_3'UTR	NM_016546	NP_057630	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	465	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis		serine-type endopeptidase activity			pancreas(1)	1																		---	---	---	---
GPR19	2842	broad.mit.edu	37	12	12814577	12814577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12814577C>T	uc001rar.3	-	2	999	c.806G>A	c.(805-807)CGG>CAG	p.R269Q	GPR19_uc001raq.2_Missense_Mutation_p.R269Q	NM_006143	NP_006134	Q15760	GPR19_HUMAN	G protein-coupled receptor 19	269	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.048)														---	---	---	---
ATF7IP	55729	broad.mit.edu	37	12	14577496	14577496	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14577496C>A	uc001rbw.2	+	2	805	c.647C>A	c.(646-648)CCT>CAT	p.P216H	ATF7IP_uc010shs.1_Missense_Mutation_p.P216H|ATF7IP_uc001rbu.2_Missense_Mutation_p.P216H|ATF7IP_uc001rbv.1_Missense_Mutation_p.P216H|ATF7IP_uc001rbx.2_Missense_Mutation_p.P216H|ATF7IP_uc010sht.1_Missense_Mutation_p.P216H|ATF7IP_uc001rby.3_Missense_Mutation_p.P216H|ATF7IP_uc001rbz.1_Missense_Mutation_p.P216H|ATF7IP_uc001rca.2_Missense_Mutation_p.P216H|ATF7IP_uc001rcb.2_5'Flank	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	216					DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5																		---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15650227	15650227	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15650227C>T	uc001rcv.1	+	3	572	c.398C>T	c.(397-399)CCT>CTT	p.P133L	PTPRO_uc001rcw.1_Missense_Mutation_p.P133L|PTPRO_uc001rcu.1_Missense_Mutation_p.P133L	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	133	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)																---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18719882	18719882	+	Splice_Site	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18719882G>T	uc001rdt.2	+	28	3896	c.3780_splice	c.e28-1	p.E1260_splice	PIK3C2G_uc010sia.1_Splice_Site|PIK3C2G_uc010sib.1_Splice_Site_p.E1301_splice|PIK3C2G_uc010sic.1_Splice_Site_p.E1079_splice	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
SLCO1C1	53919	broad.mit.edu	37	12	20868189	20868189	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20868189G>A	uc001rej.3	+	7	1001	c.646G>A	c.(646-648)GCC>ACC	p.A216T	SLCO1C1_uc010sii.1_Missense_Mutation_p.A216T|SLCO1C1_uc010sij.1_Intron|SLCO1C1_uc009zip.2_Missense_Mutation_p.A50T|SLCO1C1_uc001rei.2_Missense_Mutation_p.A216T|SLCO1C1_uc010sik.1_Missense_Mutation_p.A98T	NM_017435	NP_059131	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family,	216	Cytoplasmic (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21242842	21242842	+	Silent	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242842A>T	uc010sil.1	+	16	2114	c.2049A>T	c.(2047-2049)GGA>GGT	p.G683G	LST-3TM12_uc010sim.1_Silent_p.G622G|LST-3TM12_uc010sin.1_Silent_p.G575G			Q9NPD5	SO1B3_HUMAN	SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
IAPP	3375	broad.mit.edu	37	12	21531349	21531349	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21531349T>A	uc001rev.2	+	3	411	c.259T>A	c.(259-261)TTG>ATG	p.L87M	SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron	NM_000415	NP_000406	P10997	IAPP_HUMAN	islet amyloid polypeptide precursor	87					apoptosis|cell-cell signaling|endocrine pancreas development|signal transduction	extracellular region|soluble fraction	hormone activity				0					Perindopril(DB00790)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	21971084	21971084	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21971084C>T	uc001rfi.1	-	30	3791	c.3771G>A	c.(3769-3771)ACG>ACA	p.T1257T	ABCC9_uc001rfh.2_Silent_p.T1257T|ABCC9_uc001rfj.1_Silent_p.T1221T	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1257	Helical; Name=15; (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
CASC1	55259	broad.mit.edu	37	12	25302613	25302613	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25302613C>T	uc001rgl.2	-	6	598	c.516G>A	c.(514-516)CTG>CTA	p.L172L	CASC1_uc001rgk.2_Silent_p.L178L|CASC1_uc001rgm.3_Silent_p.L236L|CASC1_uc001rgj.2_Silent_p.L132L|CASC1_uc010sje.1_Silent_p.L113L|CASC1_uc010sjf.1_Silent_p.L60L|CASC1_uc010sjg.1_Silent_p.L172L	NM_001082973	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1 isoform b	172										ovary(2)	2	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)															---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26636652	26636652	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26636652C>A	uc001rhg.2	-	42	6408	c.5991G>T	c.(5989-5991)CAG>CAT	p.Q1997H	ITPR2_uc009zjg.1_Missense_Mutation_p.Q148H	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	1997	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27842020	27842020	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27842020C>T	uc001ric.1	+	26	2964	c.2587C>T	c.(2587-2589)CGA>TGA	p.R863*	PPFIBP1_uc010sjr.1_Nonsense_Mutation_p.R694*|PPFIBP1_uc001rib.1_Nonsense_Mutation_p.R857*|PPFIBP1_uc001ria.2_Nonsense_Mutation_p.R832*|PPFIBP1_uc001rid.1_Nonsense_Mutation_p.R710*|PPFIBP1_uc001rif.1_Nonsense_Mutation_p.R370*	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	863	SAM 3.				cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)																	---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32861078	32861078	+	Intron	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32861078A>T	uc001rld.2	+						DNM1L_uc010skf.1_Intron|DNM1L_uc010skg.1_Intron|DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
KIF21A	55605	broad.mit.edu	37	12	39703384	39703384	+	Intron	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39703384T>G	uc001rly.2	-						KIF21A_uc001rlv.2_Intron|KIF21A_uc001rlw.2_Intron|KIF21A_uc001rlx.2_Intron|KIF21A_uc001rlz.2_Intron|KIF21A_uc010skl.1_Intron|KIF21A_uc001rlt.2_Intron|KIF21A_uc001rlu.2_Intron	NM_017641	NP_060111			kinesin family member 21A						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)																---	---	---	---
ADCY6	112	broad.mit.edu	37	12	49165630	49165630	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49165630A>G	uc001rsh.3	-	18	3574	c.2914T>C	c.(2914-2916)TAT>CAT	p.Y972H	ADCY6_uc001rsj.3_Missense_Mutation_p.Y972H|ADCY6_uc001rsi.3_Missense_Mutation_p.Y919H|ADCY6_uc010slw.1_Missense_Mutation_p.Y203H	NM_015270	NP_056085	O43306	ADCY6_HUMAN	adenylate cyclase 6 isoform a	972	Cytoplasmic (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 membrane	ATP binding|metal ion binding				0																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49415918	49415918	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49415918A>C	uc001rta.3	-	53	16429	c.16429T>G	c.(16429-16431)TGT>GGT	p.C5477G		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	5477	SET.	Zinc (By similarity).			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	49436377	49436377	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49436377G>T	uc001rta.3	-	27	5834	c.5834C>A	c.(5833-5835)CCA>CAA	p.P1945Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1945					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)			---	---	---	---
KCNH3	23416	broad.mit.edu	37	12	49948282	49948282	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49948282G>A	uc001ruh.1	+	11	2341	c.2081G>A	c.(2080-2082)CGT>CAT	p.R694H	KCNH3_uc010smj.1_Missense_Mutation_p.R634H	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	694	cNMP.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0																		---	---	---	---
PRPF40B	25766	broad.mit.edu	37	12	50025218	50025218	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50025218C>T	uc001rur.1	+	2	117	c.53C>T	c.(52-54)CCG>CTG	p.P18L	PRPF40B_uc001rup.1_Missense_Mutation_p.P40L|PRPF40B_uc001ruq.1_Missense_Mutation_p.P12L|PRPF40B_uc001rus.1_5'Flank	NM_001031698	NP_001026868	Q6NWY9	PR40B_HUMAN	Huntingtin interacting protein C isoform 1	18	Pro-rich.				mRNA processing|RNA splicing	nuclear speck				skin(2)|ovary(1)|pancreas(1)|kidney(1)	5																		---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50047585	50047585	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50047585C>A	uc001ruv.1	-	12	1378	c.1144G>T	c.(1144-1146)GGG>TGG	p.G382W	FMNL3_uc001ruw.1_Missense_Mutation_p.G331W|FMNL3_uc001rut.1_5'Flank|FMNL3_uc001ruu.1_Missense_Mutation_p.G232W	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1	382	GBD/FH3.				actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51882498	51882498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51882498C>T	uc001rys.1	+	18	2480	c.2302C>T	c.(2302-2304)CGC>TGC	p.R768C	SLC4A8_uc001rym.2_Missense_Mutation_p.R715C|SLC4A8_uc001ryn.2_Missense_Mutation_p.R715C|SLC4A8_uc001ryo.2_Missense_Mutation_p.R715C|SLC4A8_uc010snj.1_Missense_Mutation_p.R795C|SLC4A8_uc001ryr.2_Missense_Mutation_p.R768C	NM_001039960	NP_001035049	Q2Y0W8	S4A8_HUMAN	solute carrier family 4, sodium bicarbonate	768	Extracellular (Potential).				bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
KRT6B	3854	broad.mit.edu	37	12	52841554	52841554	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52841554T>C	uc001sak.2	-							NM_005555	NP_005546			keratin 6B						ectoderm development	keratin filament	structural constituent of cytoskeleton			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.083)														---	---	---	---
CSAD	51380	broad.mit.edu	37	12	53565756	53565756	+	Missense_Mutation	SNP	C	T	T	rs138203066	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53565756C>T	uc001sby.2	-	6	487	c.361G>A	c.(361-363)GCC>ACC	p.A121T	CSAD_uc001sbw.2_Intron|CSAD_uc009zmt.2_5'UTR|CSAD_uc010snx.1_Missense_Mutation_p.A148T|CSAD_uc001sbz.2_Missense_Mutation_p.A121T|CSAD_uc009zmu.2_Intron|CSAD_uc001sca.3_RNA|CSAD_uc010sny.1_Missense_Mutation_p.A121T	NM_015989	NP_057073	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	121					carboxylic acid metabolic process		pyridoxal phosphate binding|sulfinoalanine decarboxylase activity			ovary(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)									Hereditary_Prostate_Cancer				---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53686188	53686188	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53686188C>T	uc001sck.2	+						ESPL1_uc001scj.2_Intron	NM_012291	NP_036423			separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																		---	---	---	---
CALCOCO1	57658	broad.mit.edu	37	12	54115307	54115307	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54115307C>A	uc001sef.2	-	6	846	c.702G>T	c.(700-702)GAG>GAT	p.E234D	CALCOCO1_uc010som.1_Missense_Mutation_p.E201D|CALCOCO1_uc010son.1_Missense_Mutation_p.E111D|CALCOCO1_uc001seh.2_Missense_Mutation_p.E234D|CALCOCO1_uc009znd.2_Missense_Mutation_p.E234D|CALCOCO1_uc001seg.2_Missense_Mutation_p.E111D|CALCOCO1_uc010soo.1_Missense_Mutation_p.E227D	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	234	Potential.				steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
HOXC6	3223	broad.mit.edu	37	12	54422366	54422366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422366C>T	uc001sev.2	+	1	173	c.61C>T	c.(61-63)CTC>TTC	p.L21F	HOXC6_uc001ses.2_5'UTR|HOXC5_uc001set.2_Intron|HOXC4_uc001seu.2_Intron	NM_004503	NP_004494	P09630	HXC6_HUMAN	homeobox C6 isoform 1	21					regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
NCKAP1L	3071	broad.mit.edu	37	12	54913073	54913073	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54913073G>A	uc001sgc.3	+	16	1661	c.1582G>A	c.(1582-1584)GTA>ATA	p.V528I	NCKAP1L_uc010sox.1_Missense_Mutation_p.V70I|NCKAP1L_uc010soy.1_Missense_Mutation_p.V478I	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	528					actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
NCKAP1L	3071	broad.mit.edu	37	12	54920460	54920460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54920460G>A	uc001sgc.3	+	21	2384	c.2305G>A	c.(2305-2307)GCC>ACC	p.A769T	NCKAP1L_uc010sox.1_Missense_Mutation_p.A311T|NCKAP1L_uc010soy.1_Missense_Mutation_p.A719T	NM_005337	NP_005328	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	769				NA -> KP (in Ref. 1; AAA35964).	actin polymerization-dependent cell motility|B cell homeostasis|B cell receptor signaling pathway|cortical actin cytoskeleton organization|erythrocyte development|maintenance of cell polarity|myeloid cell homeostasis|negative regulation of apoptosis|negative regulation of interleukin-17 production|negative regulation of interleukin-6 production|negative regulation of myosin-light-chain-phosphatase activity|neutrophil chemotaxis|positive regulation of actin filament polymerization|positive regulation of B cell differentiation|positive regulation of B cell proliferation|positive regulation of CD4-positive, alpha-beta T cell differentiation|positive regulation of CD8-positive, alpha-beta T cell differentiation|positive regulation of cell adhesion mediated by integrin|positive regulation of erythrocyte differentiation|positive regulation of gamma-delta T cell differentiation|positive regulation of neutrophil chemotaxis|positive regulation of phagocytosis, engulfment|positive regulation of T cell proliferation|protein complex assembly|response to drug|T cell homeostasis	cytosol|integral to plasma membrane|membrane fraction|SCAR complex	protein complex binding|protein kinase activator activity|Rac GTPase activator activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
OR6C70	390327	broad.mit.edu	37	12	55863562	55863562	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55863562A>G	uc010spn.1	-	1	361	c.361T>C	c.(361-363)TAT>CAT	p.Y121H		NM_001005499	NP_001005499	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56487323	56487323	+	Missense_Mutation	SNP	G	A	A	rs149951770		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56487323G>A	uc001sjh.2	+	12	1662	c.1469G>A	c.(1468-1470)CGC>CAC	p.R490H	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.R431H|ERBB3_uc009zok.2_5'Flank|ERBB3_uc001sjk.2_5'Flank|ERBB3_uc001sjj.1_Missense_Mutation_p.R58H	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	490	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)															---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56495459	56495459	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56495459C>A	uc001sjh.2	+	28	3842	c.3649C>A	c.(3649-3651)CTT>ATT	p.L1217I	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Missense_Mutation_p.L574I|ERBB3_uc010sqc.1_Missense_Mutation_p.L1158I|ERBB3_uc009zok.2_Missense_Mutation_p.L482I|ERBB3_uc001sjk.2_Missense_Mutation_p.L458I|ERBB3_uc001sjl.2_Missense_Mutation_p.L337I|PA2G4_uc001sjm.2_5'Flank|PA2G4_uc009zol.2_5'Flank|PA2G4_uc009zom.2_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	1217	Cytoplasmic (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)															---	---	---	---
ESYT1	23344	broad.mit.edu	37	12	56532561	56532561	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56532561G>A	uc001sjq.2	+	23	2493	c.2443G>A	c.(2443-2445)GGC>AGC	p.G815S	ESYT1_uc001sjr.2_Missense_Mutation_p.G825S	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	815	C2 4.					integral to membrane				ovary(4)|skin(1)	5																		---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56811689	56811689	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56811689A>G	uc001slf.2	-	28	3724	c.3556_splice	c.e28+1	p.A1186_splice		NM_003920	NP_003911			timeless homolog						cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56817369	56817369	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56817369G>A	uc001slf.2	-	17	2257	c.2089C>T	c.(2089-2091)CGC>TGC	p.R697C		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	697					cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
PRIM1	5557	broad.mit.edu	37	12	57128007	57128007	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57128007T>C	uc001smd.2	-	12	1231	c.1167A>G	c.(1165-1167)GCA>GCG	p.A389A		NM_000946	NP_000937	P49642	PRI1_HUMAN	DNA primase polypeptide 1	389					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	DNA primase activity|metal ion binding				0																		---	---	---	---
MARS	4141	broad.mit.edu	37	12	57906639	57906639	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57906639A>G	uc001sog.2	+	15	1882	c.1859A>G	c.(1858-1860)TAT>TGT	p.Y620C	MARS_uc001sof.1_RNA|MARS_uc010srq.1_Missense_Mutation_p.Y386C|MARS_uc001soh.1_Missense_Mutation_p.Y15C	NM_004990	NP_004981	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	620					methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)													---	---	---	---
DYRK2	8445	broad.mit.edu	37	12	68051258	68051258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68051258C>T	uc001str.3	+	3	973	c.571C>T	c.(571-573)CGC>TGC	p.R191C	DYRK2_uc001sts.3_Missense_Mutation_p.R118C	NM_006482	NP_006473	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	191					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|smoothened signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)														---	---	---	---
DYRK2	8445	broad.mit.edu	37	12	68052038	68052038	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68052038C>T	uc001str.3	+	3	1753	c.1351C>T	c.(1351-1353)CGA>TGA	p.R451*	DYRK2_uc001sts.3_Nonsense_Mutation_p.R378*	NM_006482	NP_006473	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	451	Protein kinase.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|smoothened signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)														---	---	---	---
BBS10	79738	broad.mit.edu	37	12	76739774	76739774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76739774G>A	uc001syd.1	-	2	2075	c.1991C>T	c.(1990-1992)GCA>GTA	p.A664V		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	664					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2														Bardet-Biedl_syndrome				---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78400518	78400518	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78400518G>A	uc001syp.2	+	8	1373	c.1200G>A	c.(1198-1200)CCG>CCA	p.P400P	NAV3_uc001syo.2_Silent_p.P400P	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	400						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
ACSS3	79611	broad.mit.edu	37	12	81528592	81528592	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81528592T>C	uc001szl.1	+						ACSS3_uc001szm.1_Intron	NM_024560	NP_078836			acyl-CoA synthetase short-chain family member 3							mitochondrion	acetate-CoA ligase activity|ATP binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94631565	94631565	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94631565C>A	uc001tdc.2	+	10	2355	c.2106C>A	c.(2104-2106)ACC>ACA	p.T702T		NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	702	Extracellular (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
LTA4H	4048	broad.mit.edu	37	12	96412962	96412962	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96412962G>A	uc001ten.1	-	7	763	c.695C>T	c.(694-696)GCT>GTT	p.A232V	LTA4H_uc010suy.1_Missense_Mutation_p.A194V|LTA4H_uc010suz.1_Missense_Mutation_p.A194V|LTA4H_uc010sva.1_RNA	NM_000895	NP_000886	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	232					hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
LTA4H	4048	broad.mit.edu	37	12	96422827	96422827	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96422827T>C	uc001ten.1	-						LTA4H_uc010suy.1_Intron|LTA4H_uc010suz.1_Intron|LTA4H_uc010sva.1_Intron	NM_000895	NP_000886			leukotriene A4 hydrolase						hormone biosynthetic process|inflammatory response|leukotriene biosynthetic process|peptide catabolic process|prostanoid metabolic process|proteolysis	cytosol|nucleus	aminopeptidase activity|epoxide hydrolase activity|leukotriene-A4 hydrolase activity|metallopeptidase activity|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(1)	1																		---	---	---	---
DRAM1	55332	broad.mit.edu	37	12	102302036	102302036	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102302036C>A	uc001tix.2	+	4	878	c.415C>A	c.(415-417)CTA>ATA	p.L139I	DRAM1_uc010svv.1_Intron	NM_018370	NP_060840	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	139					apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104160109	104160109	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104160109C>G	uc001tjw.2	+	69	7837	c.7651C>G	c.(7651-7653)CTG>GTG	p.L2551V	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2551	Cytoplasmic (Potential).				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																		---	---	---	---
NUAK1	9891	broad.mit.edu	37	12	106464587	106464587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106464587C>T	uc001tlj.1	-	6	2177	c.797G>A	c.(796-798)AGC>AAC	p.S266N		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	266	Protein kinase.						ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NUAK1	9891	broad.mit.edu	37	12	106480539	106480539	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106480539G>A	uc001tlj.1	-	3	1866	c.486C>T	c.(484-486)ATC>ATT	p.I162I		NM_014840	NP_055655	O60285	NUAK1_HUMAN	AMPK-related protein kinase 5	162	Protein kinase.						ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109604665	109604665	+	Splice_Site	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109604665G>T	uc001tob.2	+	3	773	c.654_splice	c.e3-1	p.R218_splice	ACACB_uc001toc.2_Splice_Site_p.R218_splice	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ACACB	32	broad.mit.edu	37	12	109675059	109675059	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109675059C>T	uc001tob.2	+	34	4655	c.4536C>T	c.(4534-4536)GCC>GCT	p.A1512A	ACACB_uc001toc.2_Silent_p.A1512A|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Silent_p.A178A	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1512					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ACACB	32	broad.mit.edu	37	12	109680283	109680283	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109680283C>T	uc001tob.2	+	37	5183	c.5064C>T	c.(5062-5064)CAC>CAT	p.H1688H	ACACB_uc001toc.2_Silent_p.H1688H|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Silent_p.H354H	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1688					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110781180	110781180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110781180G>A	uc001tqk.3	+	16	3025	c.2462G>A	c.(2461-2463)CGG>CAG	p.R821Q	ATP2A2_uc001tql.3_Missense_Mutation_p.R821Q|ATP2A2_uc010sxy.1_Missense_Mutation_p.R794Q|ATP2A2_uc001tqn.3_5'Flank|ATP2A2_uc009zvn.2_5'Flank	NM_170665	NP_733765	P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, slow twitch 2 isoform	821	Cytoplasmic (By similarity).				ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111748279	111748279	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111748279C>A	uc001tsa.1	+	15	1846	c.1693C>A	c.(1693-1695)CAG>AAG	p.Q565K		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	565	CUT 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111893896	111893896	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111893896C>T	uc001tsj.2	-	23	3843	c.3681G>A	c.(3679-3681)ACG>ACA	p.T1227T	ATXN2_uc001tsh.2_Silent_p.T962T|ATXN2_uc001tsi.2_Silent_p.T920T|ATXN2_uc001tsk.2_RNA|ATXN2_uc001tsg.2_Silent_p.T415T|ATXN2_uc001tsl.1_Silent_p.T228T	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2	1227					cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112140085	112140085	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112140085C>T	uc001tsq.2	+	3	507	c.307C>T	c.(307-309)CGA>TGA	p.R103*	ACAD10_uc009zvw.2_Nonsense_Mutation_p.R103*|ACAD10_uc001tso.3_Nonsense_Mutation_p.R103*|ACAD10_uc001tsp.2_Nonsense_Mutation_p.R103*|ACAD10_uc009zvx.2_Nonsense_Mutation_p.R103*	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	103							acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112650367	112650367	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112650367T>C	uc009zwc.2	-	42	6305	c.6287A>G	c.(6286-6288)TAC>TGC	p.Y2096C	C12orf51_uc001ttr.1_Missense_Mutation_p.Y271C	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
DTX1	1840	broad.mit.edu	37	12	113532908	113532908	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113532908C>T	uc001tuk.1	+	7	1784	c.1448C>T	c.(1447-1449)CCG>CTG	p.P483L		NM_004416	NP_004407	Q86Y01	DTX1_HUMAN	deltex homolog 1	483					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																		---	---	---	---
DTX1	1840	broad.mit.edu	37	12	113533015	113533015	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113533015T>C	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																		---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115120662	115120662	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115120662T>C	uc001tvt.1	-	1	1308	c.344A>G	c.(343-345)CAG>CGG	p.Q115R	TBX3_uc001tvu.1_Missense_Mutation_p.Q115R|TBX3_uc010syw.1_Missense_Mutation_p.Q115R	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	115	T-box; first part.				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)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117685162	117685162	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117685162C>A	uc001twm.1	-	18	3500	c.2814G>T	c.(2812-2814)AAG>AAT	p.K938N		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	938	Flavodoxin-like.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
RSRC2	65117	broad.mit.edu	37	12	123001921	123001921	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123001921C>T	uc001ucr.2	-	5	601	c.455G>A	c.(454-456)CGG>CAG	p.R152Q	RSRC2_uc001uco.2_5'UTR|RSRC2_uc001ucp.2_Missense_Mutation_p.R93Q|RSRC2_uc001ucq.2_5'UTR|RSRC2_uc001ucs.2_5'UTR|RSRC2_uc001uct.2_Missense_Mutation_p.R104Q|RSRC2_uc001ucu.2_Missense_Mutation_p.R152Q	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a	152	Ser-rich.									ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)														---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123286325	123286325	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123286325G>T	uc001udc.2	+	9	1777	c.1632G>T	c.(1630-1632)CAG>CAT	p.Q544H	CCDC62_uc010tah.1_RNA|CCDC62_uc001udf.2_Missense_Mutation_p.Q544H|CCDC62_uc001ude.2_Missense_Mutation_p.Q305H	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	544						cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124258738	124258738	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124258738T>G	uc001uft.3	+	5	390	c.365T>G	c.(364-366)ATT>AGT	p.I122S		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	122	Stem (By similarity).				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)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124341746	124341746	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124341746G>A	uc001uft.3	+	36	6253	c.6228G>A	c.(6226-6228)GCG>GCA	p.A2076A		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2076	AAA 2 (By similarity).				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)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124857107	124857107	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124857107A>G	uc010tba.1	-	20	2385	c.2268T>C	c.(2266-2268)ACT>ACC	p.T756T	NCOR2_uc010tay.1_Silent_p.T756T|NCOR2_uc010taz.1_Silent_p.T739T|NCOR2_uc010tbb.1_Silent_p.T756T|NCOR2_uc010tbc.1_Silent_p.T738T|NCOR2_uc001ugj.1_Silent_p.T756T	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	756					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)														---	---	---	---
FZD10	11211	broad.mit.edu	37	12	130648883	130648883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130648883C>T	uc001uii.2	+	1	1852	c.1396C>T	c.(1396-1398)CGC>TGC	p.R466C	uc001uig.1_5'Flank|uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor	466	Extracellular (Potential).				brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)														---	---	---	---
PGAM5	192111	broad.mit.edu	37	12	133295367	133295367	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133295367G>A	uc009zyv.2	+						PGAM5_uc010tbr.1_Intron|PGAM5_uc001uku.2_Missense_Mutation_p.A247T	NM_138575	NP_612642			phosphoglycerate mutase family member 5							integral to membrane|mitochondrial outer membrane	phosphoprotein phosphatase activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20221160	20221160	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20221160G>A	uc001umh.2	+	3	956	c.947G>A	c.(946-948)AGT>AAT	p.S316N	MPHOSPH8_uc001umf.1_Missense_Mutation_p.S316N|MPHOSPH8_uc001umg.2_Missense_Mutation_p.S316N|MPHOSPH8_uc001umi.2_Missense_Mutation_p.S13N	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	316					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)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21396376	21396376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21396376C>T	uc001unq.3	-	8	929	c.893G>A	c.(892-894)TGC>TAC	p.C298Y		NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	298					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)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25077812	25077812	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25077812C>T	uc001upl.2	-	2	209	c.103G>A	c.(103-105)GGA>AGA	p.G35R	PARP4_uc010tdc.1_Missense_Mutation_p.G35R	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	35	BRCT.				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
FAM123A	219287	broad.mit.edu	37	13	25745590	25745590	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25745590G>A	uc001uqb.2	-	1	268	c.168C>T	c.(166-168)GCC>GCT	p.A56A	FAM123A_uc001uqa.2_Silent_p.A56A|FAM123A_uc001uqc.2_Silent_p.A56A	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	56	Gly-rich.									ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)														---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29598991	29598991	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29598991G>A	uc001usl.3	+	1	244	c.186G>A	c.(184-186)AAG>AAA	p.K62K		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	52						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31719831	31719831	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31719831T>C	uc001utj.2	-	11	1851	c.1453A>G	c.(1453-1455)AAC>GAC	p.N485D	HSPH1_uc001utk.2_Missense_Mutation_p.N485D|HSPH1_uc010aaw.2_Missense_Mutation_p.N444D|HSPH1_uc001utl.2_Missense_Mutation_p.N487D|HSPH1_uc010tds.1_Missense_Mutation_p.N409D	NM_006644	NP_006635	Q92598	HS105_HUMAN	heat shock 105kD	485					positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32761804	32761804	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32761804G>A	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	33258137	33258137	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33258137A>T	uc010abf.2	+	11	1338	c.1180A>T	c.(1180-1182)AGA>TGA	p.R394*	PDS5B_uc001uuo.2_Nonsense_Mutation_p.R394*|PDS5B_uc010abg.2_RNA|PDS5B_uc010teb.1_Nonsense_Mutation_p.R96*	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	394	HEAT.			R -> G (in Ref. 2; AAD22134).	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)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33344698	33344698	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33344698G>T	uc010abf.2	+	32	4222	c.4064G>T	c.(4063-4065)AGA>ATA	p.R1355I	PDS5B_uc010abg.2_RNA	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1355					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)														---	---	---	---
SPG20	23111	broad.mit.edu	37	13	36905589	36905589	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36905589C>A	uc001uvn.2	-	4	1225	c.955G>T	c.(955-957)GAT>TAT	p.D319Y	SPG20_uc010ten.1_Missense_Mutation_p.D319Y|SPG20_uc001uvm.2_Missense_Mutation_p.D319Y|SPG20_uc001uvo.2_Missense_Mutation_p.D319Y|SPG20_uc001uvq.2_Missense_Mutation_p.D319Y|SPG20_uc001uvp.2_Missense_Mutation_p.D319Y	NM_001142296	NP_001135768	Q8N0X7	SPG20_HUMAN	spartin	319					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)														---	---	---	---
CCNA1	8900	broad.mit.edu	37	13	37012843	37012843	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37012843C>T	uc001uvr.3	+	5	1082	c.732C>T	c.(730-732)CGC>CGT	p.R244R	CCNA1_uc010teo.1_Silent_p.R200R|CCNA1_uc010abq.2_Silent_p.R200R|CCNA1_uc010abp.2_Silent_p.R200R|CCNA1_uc001uvs.3_Silent_p.R243R|CCNA1_uc010abr.2_Intron	NM_003914	NP_003905	P78396	CCNA1_HUMAN	cyclin A1 isoform a	244					cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		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;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)														---	---	---	---
FAM48A	55578	broad.mit.edu	37	13	37618213	37618213	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37618213A>G	uc001uwg.2	-	7	644	c.396_splice	c.e7+1	p.Q132_splice	FAM48A_uc010abt.2_Splice_Site_p.Q133_splice|FAM48A_uc001uwh.2_Splice_Site_p.Q133_splice|FAM48A_uc001uwi.2_Splice_Site_p.Q132_splice|FAM48A_uc001uwj.2_Splice_Site_p.Q133_splice|FAM48A_uc001uwk.2_Splice_Site_p.Q132_splice|FAM48A_uc010tes.1_Splice_Site_p.Q120_splice|FAM48A_uc001uwl.1_Splice_Site_p.Q132_splice	NM_001014286	NP_001014308			family with sequence similarity 48, member A						autophagy|gastrulation	SAGA-type complex	protein binding				0		Lung NSC(96;2.09e-06)|Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.0959)		all cancers(112;6.06e-07)|Epithelial(112;1.87e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00794)|BRCA - Breast invasive adenocarcinoma(63;0.0128)|GBM - Glioblastoma multiforme(144;0.0477)														---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38158194	38158194	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38158194C>T	uc001uwo.3	-	9	1273	c.1155G>A	c.(1153-1155)ACG>ACA	p.T385T	POSTN_uc001uwp.3_Silent_p.T385T|POSTN_uc001uwr.2_Silent_p.T385T|POSTN_uc001uwq.2_Silent_p.T385T|POSTN_uc010teu.1_Silent_p.T385T|POSTN_uc010tev.1_Silent_p.T385T|POSTN_uc010tew.1_Silent_p.T385T|POSTN_uc010tex.1_Silent_p.T300T	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	385	FAS1 3.				cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39263555	39263555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39263555C>T	uc001uwv.2	+	1	2383	c.2074C>T	c.(2074-2076)CGT>TGT	p.R692C		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	692	CSPG 4.|Extracellular (Potential).				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
MRPS31	10240	broad.mit.edu	37	13	41303612	41303612	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41303612G>T	uc001uxm.3	-	7	1159	c.1084C>A	c.(1084-1086)CCA>ACA	p.P362T	MIR320D-1_hsa-mir-320d-1|MI0008190_5'Flank	NM_005830	NP_005821	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31 precursor	362						mitochondrion|ribosome	protein domain specific binding				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)														---	---	---	---
WBP4	11193	broad.mit.edu	37	13	41650292	41650292	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41650292G>A	uc001uxt.2	+	8	788	c.675G>A	c.(673-675)TCG>TCA	p.S225S	WBP4_uc010tfd.1_Silent_p.S204S	NM_007187	NP_009118	O75554	WBP4_HUMAN	WW domain-containing binding protein 4	225					nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)														---	---	---	---
KBTBD6	89890	broad.mit.edu	37	13	41705321	41705321	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41705321G>A	uc001uxu.1	-	1	1616	c.1327C>T	c.(1327-1329)CGA>TGA	p.R443*	KBTBD6_uc010ace.1_Intron|KBTBD6_uc010tfe.1_Nonsense_Mutation_p.R377*|uc001uxv.1_5'Flank	NM_152903	NP_690867	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain-containing 6	443	Kelch 2.						protein binding			ovary(1)|skin(1)	2		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42303703	42303703	+	Silent	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42303703T>A	uc001uyj.2	-	23	2683	c.2613A>T	c.(2611-2613)CTA>CTT	p.L871L	KIAA0564_uc001uyk.2_Silent_p.L871L	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	871						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	42407654	42407654	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42407654C>T	uc001uyj.2	-	13	1509	c.1439G>A	c.(1438-1440)CGT>CAT	p.R480H	KIAA0564_uc001uyk.2_Missense_Mutation_p.R480H	NM_015058	NP_055873	A3KMH1	K0564_HUMAN	hypothetical protein LOC23078 isoform a	480						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)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42793377	42793377	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42793377G>A	uc001uyl.1	+	27	3246	c.3225G>A	c.(3223-3225)TCG>TCA	p.S1075S	DGKH_uc010tfh.1_Silent_p.S1075S|DGKH_uc001uym.1_Silent_p.S1075S|DGKH_uc010tfi.1_Silent_p.S830S|DGKH_uc010tfj.1_Silent_p.S930S|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Silent_p.S930S|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	1075					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
EPSTI1	94240	broad.mit.edu	37	13	43500558	43500558	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43500558C>A	uc001uyw.1	-	7	647	c.571G>T	c.(571-573)GCT>TCT	p.A191S	EPSTI1_uc001uyx.1_Missense_Mutation_p.A191S	NM_001002264	NP_001002264	Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 isoform 1	191										ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47315858	47315858	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47315858G>T	uc001vbj.2	+	19	2298	c.2062G>T	c.(2062-2064)GGG>TGG	p.G688W	LRCH1_uc001vbk.2_Missense_Mutation_p.G723W|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH)	688	CH.									ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52509129	52509129	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52509129C>A	uc001vfw.2	-	21	4318	c.4161G>T	c.(4159-4161)CAG>CAT	p.Q1387H	ATP7B_uc010adv.2_Missense_Mutation_p.Q957H|ATP7B_uc001vfx.2_Missense_Mutation_p.Q1180H|ATP7B_uc001vfy.2_Missense_Mutation_p.Q1276H|ATP7B_uc010tgt.1_Missense_Mutation_p.Q1322H|ATP7B_uc010tgu.1_Missense_Mutation_p.Q1339H|ATP7B_uc010tgv.1_Missense_Mutation_p.Q1309H|ATP7B_uc001vfv.2_Missense_Mutation_p.Q659H|ATP7B_uc010tgs.1_Missense_Mutation_p.Q598H	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1387	Cytoplasmic (Potential).				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				---	---	---	---
PIBF1	10464	broad.mit.edu	37	13	73369613	73369613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73369613G>A	uc001vjc.2	+	4	775	c.470G>A	c.(469-471)CGT>CAT	p.R157H	PIBF1_uc001vja.1_Missense_Mutation_p.R157H|PIBF1_uc010aeo.1_RNA|PIBF1_uc001vjb.2_Missense_Mutation_p.R157H|PIBF1_uc010aep.2_Intron	NM_006346	NP_006337	Q8WXW3	PIBF1_HUMAN	progesterone-induced blocking factor 1	157						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)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77655968	77655968	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77655968T>C	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron|MYCBP2_uc001vke.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)														---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92345711	92345711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92345711G>A	uc010tif.1	+	3	962	c.596G>A	c.(595-597)CGG>CAG	p.R199Q		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	199						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)																---	---	---	---
IPO5	3843	broad.mit.edu	37	13	98642694	98642694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98642694C>T	uc001vnf.1	+	6	637	c.572C>T	c.(571-573)ACG>ATG	p.T191M	IPO5_uc001vne.2_Missense_Mutation_p.T209M|IPO5_uc010tik.1_Intron|IPO5_uc010til.1_Missense_Mutation_p.T131M	NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5	191					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																		---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103281921	103281921	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103281921C>T	uc001vpi.3	+	9	1209	c.1106C>T	c.(1105-1107)ACA>ATA	p.T369I		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	369					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)																	---	---	---	---
DAOA	267012	broad.mit.edu	37	13	106142341	106142341	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106142341C>T	uc001vqb.2	+	4	647	c.373C>T	c.(373-375)CCT>TCT	p.P125S	DAOA_uc010tjf.1_Missense_Mutation_p.P54S|DAOA_uc001vpz.2_RNA|DAOA_uc010agd.2_RNA|DAOA_uc010tjg.1_Missense_Mutation_p.P97S|DAOA_uc001vqc.2_RNA|DAOA_uc001vqe.2_RNA	NM_172370	NP_758958	P59103	DAOA_HUMAN	D-amino acid oxidase activator isoform 1	125						Golgi apparatus					0	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)																	---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111083146	111083146	+	Intron	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111083146G>T	uc001vqx.2	+							NM_001846	NP_001837			alpha 2 type IV collagen preproprotein						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)															---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113478731	113478731	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113478731C>T	uc001vsi.3	+	10	952	c.864C>T	c.(862-864)GCC>GCT	p.A288A	ATP11A_uc001vsj.3_Silent_p.A288A|ATP11A_uc001vsm.1_Silent_p.A164A	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	288	Cytoplasmic (Potential).				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)																---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113481177	113481177	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113481177C>T	uc001vsi.3	+	12	1281	c.1193C>T	c.(1192-1194)ACG>ATG	p.T398M	ATP11A_uc001vsj.3_Missense_Mutation_p.T398M|ATP11A_uc001vsm.1_Missense_Mutation_p.T274M	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	398	Cytoplasmic (Potential).				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)																---	---	---	---
GRTP1	79774	broad.mit.edu	37	13	114005269	114005269	+	Silent	SNP	G	T	T	rs113325393		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114005269G>T	uc001vtn.2	-	4	457	c.360C>A	c.(358-360)CCC>CCA	p.P120P	GRTP1_uc010tkb.1_Silent_p.P42P|GRTP1_uc010tkc.1_Silent_p.P120P|GRTP1_uc010agv.1_RNA	NM_024719	NP_078995	Q5TC63	GRTP1_HUMAN	growth hormone regulated TBC protein 1	120	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0314)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0978)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114265347	114265347	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114265347T>A	uc001vtw.2	+	3	261	c.49T>A	c.(49-51)TTC>ATC	p.F17I	TFDP1_uc010tkd.1_5'UTR|TFDP1_uc010tke.1_5'UTR|TFDP1_uc001vty.3_Missense_Mutation_p.F17I|TFDP1_uc010agx.2_Missense_Mutation_p.F17I	NM_007111	NP_009042	Q14186	TFDP1_HUMAN	transcription factor Dp-1	17					cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)												TSP Lung(29;0.18)			---	---	---	---
OR4Q3	441669	broad.mit.edu	37	14	20216515	20216515	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20216515C>G	uc010tkt.1	+	1	929	c.929C>G	c.(928-930)CCA>CGA	p.P310R		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	310	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20871938	20871938	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20871938A>G	uc001vxe.2	-	6	1178	c.1138T>C	c.(1138-1140)TAC>CAC	p.Y380H	TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Intron	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	380	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22476151	22476151	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22476151G>A	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wct.3_3'UTR|uc001wcu.3_Silent_p.A29A					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
AP1G2	8906	broad.mit.edu	37	14	24033782	24033782	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24033782C>T	uc001wkl.2	-	9	1247	c.910G>A	c.(910-912)GCT>ACT	p.A304T	AP1G2_uc001wkj.2_5'UTR|AP1G2_uc001wkk.3_Missense_Mutation_p.A232T|AP1G2_uc001wkn.2_5'UTR|uc001wko.1_Intron|AP1G2_uc001wkp.1_RNA|AP1G2_uc010tnp.1_Missense_Mutation_p.A304T	NM_003917	NP_003908	O75843	AP1G2_HUMAN	adaptor-related protein complex 1, gamma 2	304					interspecies interaction between organisms|intracellular protein transport|vesicle-mediated transport	AP-1 adaptor complex|endosome membrane	protein binding|protein transporter activity			ovary(1)	1	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00672)														---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24664214	24664214	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24664214T>C	uc001wnb.1	-	2	360	c.12A>G	c.(10-12)GTA>GTG	p.V4V	TM9SF1_uc010toa.1_Intron|TM9SF1_uc001wna.1_RNA|TM9SF1_uc010tob.1_Silent_p.V239V|TM9SF1_uc001wnc.2_Silent_p.V4V|TM9SF1_uc001wnd.2_5'Flank	NM_006405	NP_006396	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1 isoform a	4					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0183)														---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	27064621	27064621	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27064621T>C	uc001wpy.2	-	2	593	c.275A>G	c.(274-276)TAC>TGC	p.Y92C	NOVA1_uc001wpz.2_Missense_Mutation_p.Y92C|NOVA1_uc001wqa.2_5'UTR|NOVA1_uc001wqb.2_Missense_Mutation_p.Y92C	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1	95	KH 1.				locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
ARHGAP5	394	broad.mit.edu	37	14	32561215	32561215	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32561215G>A	uc001wrl.2	+	2	1579	c.1340G>A	c.(1339-1341)GGG>GAG	p.G447E	ARHGAP5_uc001wrm.2_Missense_Mutation_p.G447E|ARHGAP5_uc001wrn.2_Missense_Mutation_p.G447E|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	447	FF 3.				cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)														---	---	---	---
ARHGAP5	394	broad.mit.edu	37	14	32561281	32561281	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32561281C>T	uc001wrl.2	+	2	1645	c.1406C>T	c.(1405-1407)GCT>GTT	p.A469V	ARHGAP5_uc001wrm.2_Missense_Mutation_p.A469V|ARHGAP5_uc001wrn.2_Missense_Mutation_p.A469V|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	469	FF 3.				cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)														---	---	---	---
ARHGAP5	394	broad.mit.edu	37	14	32623920	32623920	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32623920A>G	uc001wrl.2	+	7	4514	c.4275A>G	c.(4273-4275)CGA>CGG	p.R1425R	ARHGAP5_uc001wrm.2_Silent_p.R1424R|ARHGAP5_uc001wrn.2_Silent_p.R1425R|ARHGAP5_uc001wro.2_Silent_p.R164R|ARHGAP5_uc001wrp.2_Silent_p.R160R	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	1425	Rho-GAP.				cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)														---	---	---	---
PAX9	5083	broad.mit.edu	37	14	37145642	37145642	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37145642G>A	uc001wty.3	+	5	1728	c.1011G>A	c.(1009-1011)ACG>ACA	p.T337T	PAX9_uc010amq.2_RNA	NM_006194	NP_006185	P55771	PAX9_HUMAN	paired box 9	337					multicellular organismal development|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)														---	---	---	---
PNN	5411	broad.mit.edu	37	14	39650999	39650999	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39650999C>T	uc001wuw.3	+	9	2183	c.2086C>T	c.(2086-2088)CGA>TGA	p.R696*		NM_002687	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	696	Ser-rich.|Arg-rich.|Necessary for interaction with PPIG.				cell adhesion|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|desmosome|intermediate filament|nuclear speck	DNA binding|protein binding|structural molecule activity			ovary(1)	1	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)														---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45432443	45432443	+	Silent	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45432443T>G	uc001wvv.2	+	1	1028	c.819T>G	c.(817-819)TCT>TCG	p.S273S	FAM179B_uc001wvw.2_Silent_p.S273S|FAM179B_uc010anc.2_RNA|KLHL28_uc001wvq.2_5'Flank|KLHL28_uc001wvr.2_5'Flank|FAM179B_uc010anb.1_Silent_p.S273S|FAM179B_uc001wvu.2_Silent_p.S273S	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	273							binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FKBP3	2287	broad.mit.edu	37	14	45599948	45599948	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45599948T>G	uc010tqf.1	-	2	237	c.164A>C	c.(163-165)AAC>ACC	p.N55T		NM_002013	NP_002004	Q00688	FKBP3_HUMAN	FK506 binding protein 3, 25kDa	55					protein folding	membrane|nucleus	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor activity				0																		---	---	---	---
NID2	22795	broad.mit.edu	37	14	52520915	52520915	+	Missense_Mutation	SNP	G	A	A	rs147980330		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52520915G>A	uc001wzo.2	-	4	1126	c.892C>T	c.(892-894)CGT>TGT	p.R298C	NID2_uc010tqs.1_Missense_Mutation_p.R298C|NID2_uc010tqt.1_Missense_Mutation_p.R298C|NID2_uc001wzp.2_Missense_Mutation_p.R298C	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	298						basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)																	---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56757145	56757145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56757145A>G	uc001xch.2	+	5	953	c.667A>G	c.(667-669)ACC>GCC	p.T223A		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	223					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																		---	---	---	---
GPR135	64582	broad.mit.edu	37	14	59930803	59930803	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59930803G>A	uc010apj.2	-	1	1257	c.1142C>T	c.(1141-1143)GCC>GTC	p.A381V	GPR135_uc001xed.2_RNA	NM_022571	NP_072093	Q8IZ08	GP135_HUMAN	G protein-coupled receptor 135	381	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.134)														---	---	---	---
RTN1	6252	broad.mit.edu	37	14	60074086	60074086	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60074086G>A	uc001xen.1	-	4	2099	c.1890C>T	c.(1888-1890)GCC>GCT	p.A630A	RTN1_uc001xem.1_Silent_p.A210A|RTN1_uc001xek.1_Silent_p.A62A|RTN1_uc001xel.1_RNA|RTN1_uc010apl.1_Silent_p.A47A	NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	630	Reticulon.				neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)														---	---	---	---
SIX6	4990	broad.mit.edu	37	14	60976498	60976498	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60976498G>A	uc001xfa.3	+	1	561	c.382G>A	c.(382-384)GGC>AGC	p.G128S		NM_007374	NP_031400	O95475	SIX6_HUMAN	SIX homeobox 6	128	Homeobox.				organ morphogenesis|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.088)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63417018	63417018	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63417018C>T	uc001xfx.2	-	7	1253	c.1202G>A	c.(1201-1203)CGC>CAC	p.R401H	KCNH5_uc001xfy.2_Missense_Mutation_p.R401H|KCNH5_uc001xfz.1_Missense_Mutation_p.R343H|KCNH5_uc001xga.2_Missense_Mutation_p.R343H	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	401	Extracellular (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64518919	64518919	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64518919C>T	uc001xgm.2	+	48	8518	c.8288C>T	c.(8287-8289)TCA>TTA	p.S2763L	SYNE2_uc001xgl.2_Missense_Mutation_p.S2763L	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2763	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
PLEKHG3	26030	broad.mit.edu	37	14	65208660	65208660	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65208660C>T	uc001xho.1	+	16	2694	c.2425C>T	c.(2425-2427)CGC>TGC	p.R809C	PLEKHG3_uc001xhn.1_Missense_Mutation_p.R753C|PLEKHG3_uc001xhp.2_Missense_Mutation_p.R930C|PLEKHG3_uc010aqh.1_Missense_Mutation_p.R351C|PLEKHG3_uc001xhq.1_Missense_Mutation_p.R314C	NM_015549	NP_056364	A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G,	809					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73538375	73538375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73538375G>A	uc001xno.2	+	2	234	c.26G>A	c.(25-27)CGC>CAC	p.R9H	RBM25_uc001xnn.3_Missense_Mutation_p.R9H|RBM25_uc010ttu.1_Missense_Mutation_p.R9H|RBM25_uc001xnp.2_5'UTR	NM_021239	NP_067062	P49756	RBM25_HUMAN	RNA binding motif protein 25	9					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)														---	---	---	---
FAM161B	145483	broad.mit.edu	37	14	74411468	74411468	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74411468C>A	uc001xpd.1	-	3	601	c.495G>T	c.(493-495)TGG>TGT	p.W165C		NM_152445	NP_689658			hypothetical protein LOC145483											ovary(1)	1																		---	---	---	---
TMEM90A	646658	broad.mit.edu	37	14	74874351	74874351	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74874351T>C	uc001xpx.2	-	4	852	c.604A>G	c.(604-606)ACC>GCC	p.T202A		NM_001105579	NP_001099049	A6NDD5	SYN1L_HUMAN	transmembrane protein 90A	202					response to biotic stimulus	Golgi apparatus|integral to membrane					0				BRCA - Breast invasive adenocarcinoma(234;0.00159)														---	---	---	---
ISM2	145501	broad.mit.edu	37	14	77941933	77941933	+	3'UTR	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77941933C>A	uc001xtz.2	-	7					ISM2_uc001xua.2_3'UTR|ISM2_uc001xty.2_3'UTR|ISM2_uc010tvl.1_3'UTR	NM_199296	NP_954993			isthmin 2 homolog isoform 1							extracellular region				skin(1)	1																		---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81251580	81251580	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81251580C>T	uc001xux.2	-	14	2041	c.1870G>A	c.(1870-1872)GCC>ACC	p.A624T	C14orf145_uc010asz.1_RNA	NM_152446	NP_689659	Q6ZU80	CE128_HUMAN	hypothetical protein LOC145508	624	Potential.					centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
ZC3H14	79882	broad.mit.edu	37	14	89073629	89073629	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89073629T>A	uc001xww.2	+	13	2015	c.1790T>A	c.(1789-1791)CTT>CAT	p.L597H	ZC3H14_uc010twd.1_Missense_Mutation_p.L597H|ZC3H14_uc010twe.1_Missense_Mutation_p.L592H|ZC3H14_uc001xwx.2_Missense_Mutation_p.L441H|ZC3H14_uc010twf.1_Missense_Mutation_p.L311H|ZC3H14_uc001xwy.2_Missense_Mutation_p.L432H|ZC3H14_uc010twg.1_Missense_Mutation_p.L286H|ZC3H14_uc001xxa.2_Missense_Mutation_p.L142H|ZC3H14_uc001xxc.2_Missense_Mutation_p.L141H|ZC3H14_uc001xxb.2_Missense_Mutation_p.L168H	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1	597	C3H1-type 1.					cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89878829	89878829	+	5'UTR	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89878829A>T	uc001xxo.3	-	2					FOXN3_uc001xxn.3_5'UTR|FOXN3_uc010atk.2_5'UTR|FOXN3_uc001xxp.2_5'UTR	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|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|protein C-terminus 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(2)|ovary(1)	3																		---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91773527	91773527	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91773527C>T	uc010aty.2	-	18	3149	c.3050G>A	c.(3049-3051)GGG>GAG	p.G1017E		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	1017	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)																---	---	---	---
SERPINA9	327657	broad.mit.edu	37	14	94936051	94936051	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94936051G>A	uc001ydf.2	-	2	342	c.181C>T	c.(181-183)CAG>TAG	p.Q61*	SERPINA9_uc001yde.2_Nonsense_Mutation_p.Q61*|SERPINA9_uc010avc.2_Intron|SERPINA9_uc001ydg.2_Intron|SERPINA9_uc001ydh.1_Nonsense_Mutation_p.Q61*|SERPINA9_uc001ydi.1_Intron	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN	serine (or cysteine) proteinase inhibitor, clade	43					regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity			lung(1)|central_nervous_system(1)	2		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)														---	---	---	---
SERPINA12	145264	broad.mit.edu	37	14	94964289	94964289	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94964289T>G	uc001ydj.2	-	3	1242	c.446A>C	c.(445-447)AAG>ACG	p.K149T		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	149					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)														---	---	---	---
SERPINA3	12	broad.mit.edu	37	14	95090098	95090098	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95090098G>A	uc001ydp.2	+	5	1298	c.1219G>A	c.(1219-1221)GAC>AAC	p.D407N	SERPINA3_uc001ydo.3_Missense_Mutation_p.D432N|SERPINA3_uc001ydr.2_RNA|SERPINA3_uc001ydq.2_Missense_Mutation_p.D407N|SERPINA3_uc001yds.2_Missense_Mutation_p.D407N|SERPINA3_uc010avg.2_Missense_Mutation_p.D407N	NM_001085	NP_001076	P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A, member 3	407					acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis	extracellular region|nucleus	DNA binding|protein binding|serine-type endopeptidase inhibitor activity	p.D407N(1)		ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1)	6		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)														---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95569719	95569719	+	Silent	SNP	C	T	T	rs143454689		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95569719C>T	uc001ydw.2	-	22	4196	c.4014G>A	c.(4012-4014)GCG>GCA	p.A1338A	DICER1_uc010avh.1_Silent_p.A236A|DICER1_uc001ydv.2_Silent_p.A1328A|DICER1_uc001ydx.2_Silent_p.A1338A|DICER1_uc001ydy.1_Silent_p.A190A	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1338	RNase III 1.				negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
WARS	7453	broad.mit.edu	37	14	100835438	100835438	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100835438C>T	uc001yhf.1	-	1	169	c.85G>A	c.(85-87)GGA>AGA	p.G29R	WARS_uc001yhg.1_Missense_Mutation_p.G29R|WARS_uc001yhh.1_Missense_Mutation_p.G29R|WARS_uc001yhi.1_Intron|WARS_uc001yhj.1_Intron|WARS_uc001yhk.1_Intron|WARS_uc001yhl.1_Missense_Mutation_p.G29R|WARS_uc010twz.1_Missense_Mutation_p.G29R	NM_173701	NP_776049	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase isoform a	29	WHEP-TRS.				angiogenesis|negative regulation of cell proliferation|regulation of angiogenesis|tryptophanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|protein binding|tryptophan-tRNA ligase activity			breast(1)	1		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)													---	---	---	---
WDR25	79446	broad.mit.edu	37	14	100847811	100847811	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100847811C>T	uc010avx.2	+	2	643	c.550C>T	c.(550-552)CGG>TGG	p.R184W	WDR25_uc001yhm.2_Missense_Mutation_p.R176W|WDR25_uc001yhn.2_Missense_Mutation_p.R184W|WDR25_uc010avy.2_RNA|WDR25_uc001yho.2_5'Flank	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25	184											0		Melanoma(154;0.212)																---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105412736	105412736	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105412736G>A	uc010axc.1	-	7	9172	c.9052C>T	c.(9052-9054)CAG>TAG	p.Q3018*	AHNAK2_uc001ypx.2_Nonsense_Mutation_p.Q2918*	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3018						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105677548	105677548	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105677548T>C	uc001yqp.2	-	17	2270	c.1907A>G	c.(1906-1908)TAC>TGC	p.Y636C	BRF1_uc010tyo.1_Missense_Mutation_p.Y521C|BRF1_uc010typ.1_Missense_Mutation_p.Y543C|BRF1_uc001yqk.2_Missense_Mutation_p.Y162C|BRF1_uc001yql.2_Missense_Mutation_p.Y432C|BRF1_uc001yqo.2_Missense_Mutation_p.Y398C|BRF1_uc010axg.1_Missense_Mutation_p.Y609C|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.1_3'UTR	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	636					positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27772702	27772702	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27772702C>T	uc001zbg.1	+	8	1155	c.989C>T	c.(988-990)GCG>GTG	p.A330V		NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	330	Helical; (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28422236	28422236	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28422236T>C	uc001zbj.2	-	61	9398	c.9292A>G	c.(9292-9294)ACC>GCC	p.T3098A		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3098	RCC1 8.				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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34130674	34130674	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34130674C>A	uc001zhi.2	+	89	12563	c.12493C>A	c.(12493-12495)CTC>ATC	p.L4165I	RYR3_uc010bar.2_Missense_Mutation_p.L4160I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	4165					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)														---	---	---	---
PGBD4	161779	broad.mit.edu	37	15	34396075	34396075	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34396075A>G	uc001zho.2	+	1	1802	c.1343A>G	c.(1342-1344)CAC>CGC	p.H448R	C15orf24_uc001zhm.2_5'Flank|C15orf24_uc001zhn.2_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	448											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)														---	---	---	---
C15orf55	256646	broad.mit.edu	37	15	34646818	34646818	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34646818C>T	uc001zif.2	+	5	1318	c.1163C>T	c.(1162-1164)TCA>TTA	p.S388L	C15orf55_uc010ucc.1_Missense_Mutation_p.S416L|C15orf55_uc010ucd.1_Missense_Mutation_p.S406L	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	388						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								---	---	---	---
LPCAT4	254531	broad.mit.edu	37	15	34654982	34654982	+	Splice_Site	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34654982C>T	uc001zig.2	-	8	895	c.801_splice	c.e8+1	p.E267_splice		NM_153613	NP_705841			lysophosphatidylcholine acyltransferase 4						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity|calcium ion binding				0																		---	---	---	---
GOLGA8A	23015	broad.mit.edu	37	15	34673666	34673666	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34673666G>A	uc001zii.2	-	16	1867	c.1758C>T	c.(1756-1758)AGC>AGT	p.S586S	GOLGA8A_uc001zih.2_Silent_p.S442S|uc001zil.2_5'Flank	NM_181077	NP_851422	A7E2F4	GOG8A_HUMAN	golgi autoantigen, golgin subfamily a, 8A	614	Golgi-targeting domain (By similarity).					Golgi cisterna membrane					0		all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)														---	---	---	---
AQR	9716	broad.mit.edu	37	15	35163101	35163101	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35163101A>G	uc001ziv.2	-	31	3801	c.3620T>C	c.(3619-3621)GTA>GCA	p.V1207A		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	1207						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)														---	---	---	---
AQR	9716	broad.mit.edu	37	15	35202476	35202476	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35202476G>A	uc001ziv.2	-	17	1704	c.1523C>T	c.(1522-1524)GCG>GTG	p.A508V		NM_014691	NP_055506	O60306	AQR_HUMAN	aquarius	508						catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)														---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40254062	40254062	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40254062G>T	uc001zkm.1	+	7	871	c.821G>T	c.(820-822)AGT>ATT	p.S274I	EIF2AK4_uc001zkl.2_Missense_Mutation_p.S274I|EIF2AK4_uc010bbj.1_Missense_Mutation_p.S3I	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	274					translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)														---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40942786	40942786	+	Intron	SNP	G	T	T	rs115900739	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40942786G>T	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)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41379814	41379814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41379814G>A	uc001zni.2	-	6	817	c.604C>T	c.(604-606)CGG>TGG	p.R202W	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	202	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.				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																		---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44175946	44175946	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44175946C>T	uc001ztl.2	-	13	1267	c.1090G>A	c.(1090-1092)GTC>ATC	p.V364I	FRMD5_uc001ztj.1_Missense_Mutation_p.V37I|FRMD5_uc001ztk.1_Missense_Mutation_p.V270I|FRMD5_uc010uef.1_Missense_Mutation_p.V37I|FRMD5_uc001ztm.2_Missense_Mutation_p.V37I|FRMD5_uc001ztn.2_Missense_Mutation_p.V130I	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2	364						cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
SQRDL	58472	broad.mit.edu	37	15	45968356	45968356	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45968356G>T	uc001zvt.2	+	7	901	c.712G>T	c.(712-714)GGG>TGG	p.G238W	SQRDL_uc001zvu.2_Missense_Mutation_p.G238W|SQRDL_uc001zvv.2_Missense_Mutation_p.G238W	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor	238							oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)														---	---	---	---
CYP19A1	1588	broad.mit.edu	37	15	51514600	51514600	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51514600G>A	uc001zyz.3	-	6	825	c.574C>T	c.(574-576)CGT>TGT	p.R192C	CYP19A1_uc001zza.3_Missense_Mutation_p.R192C|CYP19A1_uc001zzb.2_Missense_Mutation_p.R192C|CYP19A1_uc001zzd.2_Missense_Mutation_p.R192C|CYP19A1_uc010bey.1_Missense_Mutation_p.R192C	NM_031226	NP_112503	P11511	CP19A_HUMAN	cytochrome P450, family 19	192					estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)													---	---	---	---
KIAA1370	56204	broad.mit.edu	37	15	52877031	52877031	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52877031T>C	uc002acg.3	-	12	3141	c.2988A>G	c.(2986-2988)GTA>GTG	p.V996V	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Silent_p.V908V|KIAA1370_uc002acf.3_Silent_p.V26V|KIAA1370_uc010ugf.1_Silent_p.V1003V	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	996											0				all cancers(107;0.0803)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55652559	55652559	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55652559C>T	uc002acv.1	-	8	1577	c.1412G>A	c.(1411-1413)GGC>GAC	p.G471D	CCPG1_uc002acy.2_Missense_Mutation_p.G471D|CCPG1_uc002acu.1_Missense_Mutation_p.G327D|CCPG1_uc002acw.1_Missense_Mutation_p.G196D|CCPG1_uc002acx.2_Intron|CCPG1_uc010bfk.1_Missense_Mutation_p.G471D|CCPG1_uc002acz.1_Missense_Mutation_p.G471D	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	471	Lumenal (Potential).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
PRTG	283659	broad.mit.edu	37	15	55912260	55912260	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55912260C>T	uc002adg.2	-	20	3451	c.3403G>A	c.(3403-3405)GAT>AAT	p.D1135N		NM_173814	NP_776175	Q2VWP7	PRTG_HUMAN	protogenin precursor	1135					multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)														---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57731440	57731440	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57731440A>C	uc002aeg.2	+	2	1319	c.1243A>C	c.(1243-1245)AGC>CGC	p.S415R	CGNL1_uc010bfw.2_Missense_Mutation_p.S415R	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	415	Head.					myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62950012	62950012	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62950012G>A	uc002alb.3	+	6	703	c.703G>A	c.(703-705)GAG>AAG	p.E235K		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	235	FERM.				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																		---	---	---	---
MTFMT	123263	broad.mit.edu	37	15	65308768	65308768	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65308768A>G	uc002aof.3	-							NM_139242	NP_640335			mitochondrial methionyl-tRNA formyltransferase							mitochondrion	methionyl-tRNA formyltransferase activity|methyltransferase activity			ovary(2)	2					Tetrahydrofolic acid(DB00116)													---	---	---	---
FEM1B	10116	broad.mit.edu	37	15	68582325	68582325	+	Missense_Mutation	SNP	G	A	A	rs142755987	byFrequency;by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68582325G>A	uc002arg.2	+	2	1244	c.629G>A	c.(628-630)CGT>CAT	p.R210H	FEM1B_uc002arh.2_Missense_Mutation_p.R130H	NM_015322	NP_056137	Q9UK73	FEM1B_HUMAN	fem-1 homolog b	210	ANK 5.				apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity				0																		---	---	---	---
GRAMD2	196996	broad.mit.edu	37	15	72456008	72456008	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72456008A>G	uc002atq.2	-	9	715	c.691T>C	c.(691-693)TCA>CCA	p.S231P	GRAMD2_uc010bis.2_Missense_Mutation_p.S231P|GRAMD2_uc010ukh.1_Missense_Mutation_p.S25P	NM_001012642	NP_001012660	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	231						integral to membrane					0																		---	---	---	---
ISLR2	57611	broad.mit.edu	37	15	74425657	74425657	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74425657G>A	uc002axd.2	+	4	1331	c.562G>A	c.(562-564)GGC>AGC	p.G188S	ISLR2_uc002axe.2_Missense_Mutation_p.G188S|ISLR2_uc010bjg.2_Missense_Mutation_p.G188S|ISLR2_uc010bjf.2_Missense_Mutation_p.G188S	NM_001130136	NP_001123608	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing	188	Extracellular (Potential).|LRRCT.				positive regulation of axon extension	cell surface|integral to membrane|plasma membrane					0																		---	---	---	---
CYP1A1	1543	broad.mit.edu	37	15	75012940	75012940	+	Missense_Mutation	SNP	G	A	A	rs56240201	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75012940G>A	uc002ayp.3	-	7	1551	c.1429C>T	c.(1429-1431)CGG>TGG	p.R477W	CYP1A1_uc010bjv.2_RNA|CYP1A1_uc010bjw.2_RNA|CYP1A1_uc010bju.2_Missense_Mutation_p.R213W|CYP1A1_uc010bjx.2_Missense_Mutation_p.R213W|CYP1A1_uc002ayq.3_Missense_Mutation_p.R477W|CYP1A1_uc010bjy.2_Missense_Mutation_p.R448W	NM_000499	NP_000490	P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A,	477					cellular lipid metabolic process|drug metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|vitamin D 24-hydroxylase activity	p.R477W(1)		ovary(2)|breast(2)|pancreas(1)	5					Arsenic trioxide(DB01169)|Benzphetamine(DB00865)|Bleomycin(DB00290)|Chlorzoxazone(DB00356)|Dacarbazine(DB00851)|Dactinomycin(DB00970)|Esomeprazole(DB00736)|Estrone(DB00655)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Ginseng(DB01404)|Granisetron(DB00889)|Ketoconazole(DB01026)|Menadione(DB00170)|Picrotoxin(DB00466)|Primaquine(DB01087)|Quinidine(DB00908)|Quinine(DB00468)|Thiabendazole(DB00730)									Endometrial_Cancer_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia				---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75772249	75772249	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75772249A>G	uc002bal.2	-	9	1577	c.1069T>C	c.(1069-1071)TAC>CAC	p.Y357H		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	357	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
LINGO1	84894	broad.mit.edu	37	15	77906539	77906539	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77906539G>A	uc002bct.1	-	2	1762	c.1710C>T	c.(1708-1710)GGC>GGT	p.G570G	LINGO1_uc002bcu.1_Silent_p.G564G	NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A	570	Helical; (Potential).				negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2																		---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78921959	78921959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78921959G>A	uc002bed.1	-	5	800	c.688C>T	c.(688-690)CGC>TGC	p.R230C	CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Missense_Mutation_p.R48C	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4	230	Extracellular (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																		---	---	---	---
TMC3	342125	broad.mit.edu	37	15	81636296	81636296	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81636296A>G	uc002bgo.1	-	14	1609	c.1609T>C	c.(1609-1611)TTA>CTA	p.L537L	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Silent_p.L537L	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	537	Extracellular (Potential).					integral to membrane				ovary(1)|liver(1)	2																		---	---	---	---
EFTUD1	79631	broad.mit.edu	37	15	82444608	82444608	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82444608A>G	uc002bgt.1	-	18	2356	c.2187T>C	c.(2185-2187)CCT>CCC	p.P729P	EFTUD1_uc002bgs.1_Silent_p.P100P|EFTUD1_uc002bgu.1_Silent_p.P678P	NM_024580	NP_078856	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain	729					mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1																		---	---	---	---
SCARNA15	677778	broad.mit.edu	37	15	83424779	83424779	+	RNA	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83424779C>A	uc002bjc.2	+	1		c.83C>A				NR_003011				Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 898037.												0																		---	---	---	---
ZSCAN2	54993	broad.mit.edu	37	15	85163909	85163909	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85163909G>A	uc002bkr.2	+	3	709	c.483G>A	c.(481-483)TCG>TCA	p.S161S	ZSCAN2_uc010bmz.1_Silent_p.S159S|ZSCAN2_uc010bna.2_Silent_p.S11S|ZSCAN2_uc010uox.1_Silent_p.S160S|ZSCAN2_uc010uoy.1_Silent_p.S160S|ZSCAN2_uc010uoz.1_Silent_p.S160S	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1	161					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)														---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85487996	85487996	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85487996A>G	uc002blg.2	+	18	1974	c.1772A>G	c.(1771-1773)TAC>TGC	p.Y591C	SLC28A1_uc010bnb.2_Missense_Mutation_p.Y591C|SLC28A1_uc010upe.1_Missense_Mutation_p.Y425C|SLC28A1_uc010upf.1_Missense_Mutation_p.Y591C|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204	O00337	S28A1_HUMAN	solute carrier family 28, member 1 isoform 1	591	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88679207	88679207	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88679207T>C	uc002bme.1	-	8	992	c.830A>G	c.(829-831)GAC>GGC	p.D277G	NTRK3_uc002bmh.2_Missense_Mutation_p.D277G|NTRK3_uc002bmf.1_Missense_Mutation_p.D277G|NTRK3_uc010upl.1_Missense_Mutation_p.D179G|NTRK3_uc010bnh.1_Missense_Mutation_p.D277G|NTRK3_uc002bmg.2_Missense_Mutation_p.D277G	NM_001012338	NP_001012338	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	277	Ig-like C2-type 1.|Extracellular (Potential).				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)			---	---	---	---
WDR93	56964	broad.mit.edu	37	15	90286554	90286554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90286554G>A	uc002boj.2	+	17	2094	c.1993G>A	c.(1993-1995)GAG>AAG	p.E665K	WDR93_uc010bnr.2_Missense_Mutation_p.E637K|WDR93_uc010upz.1_Missense_Mutation_p.E382K	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	665					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
MAN2A2	4122	broad.mit.edu	37	15	91450533	91450533	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91450533C>A	uc010bnz.2	+						MAN2A2_uc010boa.2_Intron|MAN2A2_uc002bqc.2_Intron|MAN2A2_uc010uql.1_Intron|MAN2A2_uc010uqm.1_5'Flank	NM_006122	NP_006113			mannosidase, alpha, class 2A, member 2						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			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)															---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93524143	93524143	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93524143T>C	uc002bsp.2	+	23	3548	c.2973_splice	c.e23+2	p.Q991_splice	CHD2_uc002bso.1_Splice_Site_p.Q991_splice	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)															---	---	---	---
NR2F2	7026	broad.mit.edu	37	15	96877465	96877465	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96877465G>A	uc010uri.1	+	2	1827	c.603G>A	c.(601-603)ATG>ATA	p.M201I	NR2F2_uc002btp.2_Missense_Mutation_p.M68I|NR2F2_uc010urj.1_Missense_Mutation_p.M48I|NR2F2_uc010urk.1_Missense_Mutation_p.M48I	NM_021005	NP_066285	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	201	Interaction with ZFPM2 (By similarity).|Ligand-binding (By similarity).				lipid metabolic process|negative regulation of cyclin-dependent protein kinase activity|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment	nucleus	ligand-regulated transcription factor activity|protein homodimerization activity|retinoic acid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity|zinc ion binding			ovary(2)|breast(1)	3	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)															---	---	---	---
ASB7	140460	broad.mit.edu	37	15	101188577	101188577	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101188577T>C	uc002bwk.2	+	6	1636	c.867T>C	c.(865-867)TGT>TGC	p.C289C		NM_198243	NP_937886	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box-containing protein 7	289	SOCS box.				intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)															---	---	---	---
RHBDF1	64285	broad.mit.edu	37	16	108543	108543	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:108543G>T	uc002cfl.3	-	21	2512	c.2364C>A	c.(2362-2364)CCC>CCA	p.P788P		NM_022450	NP_071895	Q96CC6	RHDF1_HUMAN	rhomboid family 1	788	Helical; (Potential).				cell migration|cell proliferation|negative regulation of protein secretion|protein transport|proteolysis|regulation of epidermal growth factor receptor signaling pathway|regulation of proteasomal protein catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	growth factor binding|serine-type endopeptidase activity			ovary(1)|pancreas(1)	2		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)																---	---	---	---
NHLRC4	283948	broad.mit.edu	37	16	618400	618400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:618400G>A	uc002chl.2	+	2	949	c.353G>A	c.(352-354)GGC>GAC	p.G118D	PIGQ_uc010bqw.2_Intron|PIGQ_uc002chm.2_5'Flank|PIGQ_uc002chn.2_5'Flank|PIGQ_uc002cho.2_5'Flank	NM_176677	NP_788850	P0CG21	NHLC4_HUMAN	hypothetical protein LOC283948	118	NHL 2.										0																		---	---	---	---
WDR24	84219	broad.mit.edu	37	16	739536	739536	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:739536G>A	uc002ciz.1	-	1	865	c.105C>T	c.(103-105)TGC>TGT	p.C35C		NM_032259	NP_115635	Q96S15	WDR24_HUMAN	WD repeat domain 24	97										ovary(1)|central_nervous_system(1)	2		Hepatocellular(780;0.0218)																---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1817232	1817232	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1817232C>T	uc002cmk.2	+	26	3288	c.3168C>T	c.(3166-3168)TAC>TAT	p.Y1056Y	MAPK8IP3_uc002cml.2_Silent_p.Y1050Y|MAPK8IP3_uc010uvl.1_Silent_p.Y1057Y	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	1056					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
SPSB3	90864	broad.mit.edu	37	16	1827807	1827807	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1827807C>T	uc002cmr.2	-	5	695	c.662G>A	c.(661-663)GGC>GAC	p.G221D	SPSB3_uc002cms.2_Missense_Mutation_p.G93D|SPSB3_uc002cmt.2_Missense_Mutation_p.G93D|SPSB3_uc002cmu.2_Missense_Mutation_p.G221D|SPSB3_uc002cmv.2_Missense_Mutation_p.G93D	NM_080861	NP_543137	Q6PJ21	SPSB3_HUMAN	splA/ryanodine receptor domain and SOCS box	221	B30.2/SPRY.				intracellular signal transduction						0																		---	---	---	---
PAQR4	124222	broad.mit.edu	37	16	3021725	3021725	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3021725C>A	uc002csj.3	+	3	932	c.598C>A	c.(598-600)CCA>ACA	p.P200T	PAQR4_uc002csk.3_Missense_Mutation_p.P161T|PAQR4_uc002csl.3_Missense_Mutation_p.P126T|PAQR4_uc010uwm.1_Missense_Mutation_p.P131T	NM_152341	NP_689554	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	200	Helical; (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
NLRC3	197358	broad.mit.edu	37	16	3591887	3591887	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3591887C>T	uc010btn.2	-	21	3547	c.3136G>A	c.(3136-3138)GGG>AGG	p.G1046R		NM_178844	NP_849172	Q7RTR2	NLRC3_HUMAN	NOD3 protein	1046	LRR 16.				I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation	cytoplasm	ATP binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3656500	3656500	+	Silent	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3656500A>C	uc002cvp.2	-	3	1362	c.735T>G	c.(733-735)CCT>CCG	p.P245P	BTBD12_uc002cvq.1_Silent_p.P245P	NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	245	Interaction with C20orf94, ERCC4 and MSH2.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3790455	3790455	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3790455G>A	uc002cvv.2	-	24	4282	c.4078C>T	c.(4078-4080)CGA>TGA	p.R1360*	CREBBP_uc002cvw.2_Nonsense_Mutation_p.R1322*	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1360	Cys/His-rich.				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	p.R1360*(1)		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				---	---	---	---
ALG1	56052	broad.mit.edu	37	16	5132575	5132575	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5132575G>C	uc002cym.2	+	11	1129	c.1088G>C	c.(1087-1089)GGT>GCT	p.G363A	ALG1_uc002cyj.2_Missense_Mutation_p.G252A|ALG1_uc002cyn.2_Missense_Mutation_p.G364A|ALG1_uc010bue.2_Missense_Mutation_p.G252A|ALG1_uc010uxy.1_Missense_Mutation_p.G252A	NM_019109	NP_061982	Q9BT22	ALG1_HUMAN	beta-1,4-mannosyltransferase	363	Lumenal (Potential).				dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			upper_aerodigestive_tract(1)|ovary(1)	2		Ovarian(90;0.0164)																---	---	---	---
ABAT	18	broad.mit.edu	37	16	8866730	8866730	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8866730G>A	uc002czc.3	+	12	1076	c.910G>A	c.(910-912)GCA>ACA	p.A304T	ABAT_uc002czd.3_Missense_Mutation_p.A304T|ABAT_uc010buh.2_Missense_Mutation_p.A246T|ABAT_uc010bui.2_Missense_Mutation_p.A304T	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor	304					behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)													---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11785695	11785695	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11785695C>T	uc010buu.1	-	9	1494	c.1432G>A	c.(1432-1434)GGG>AGG	p.G478R	TXNDC11_uc002dbg.1_Missense_Mutation_p.G451R	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	478					cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14340951	14340951	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14340951C>T	uc010uza.1	+	12	1989	c.1834C>T	c.(1834-1836)CGG>TGG	p.R612W	MKL2_uc002dcg.2_Missense_Mutation_p.R612W|MKL2_uc002dcj.2_5'Flank	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	601	Potential.				cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
PLA2G10	8399	broad.mit.edu	37	16	14766560	14766560	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14766560C>A	uc002dcq.2	-	4	842	c.402G>T	c.(400-402)CAG>CAT	p.Q134H		NM_003561	NP_003552	O15496	PA2GX_HUMAN	phospholipase A2, group X precursor	134					arachidonic acid metabolic process|axon guidance|cholesterol homeostasis|lipid catabolic process|lysophospholipid transport|negative regulation of cholesterol efflux|negative regulation of sequence-specific DNA binding transcription factor activity|phospholipid metabolic process|positive regulation of arachidonic acid secretion|positive regulation of cellular protein metabolic process|positive regulation of lipid storage|positive regulation of prostaglandin secretion|regulation of macrophage activation	extracellular region	calcium ion binding|phospholipase A2 activity				0																		---	---	---	---
NOMO1	23420	broad.mit.edu	37	16	14958558	14958558	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14958558A>G	uc002dcv.2	+	13	1578	c.1512A>G	c.(1510-1512)TCA>TCG	p.S504S		NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor	504	Extracellular (Potential).					integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1																		---	---	---	---
KIAA0430	9665	broad.mit.edu	37	16	15704907	15704907	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15704907C>T	uc002ddr.2	-	19	3869	c.3676G>A	c.(3676-3678)GTA>ATA	p.V1226I	KIAA0430_uc002ddq.2_Missense_Mutation_p.V1060I|KIAA0430_uc010uzv.1_Missense_Mutation_p.V1222I|KIAA0430_uc010uzw.1_Missense_Mutation_p.V1225I	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	1225						peroxisome	nucleotide binding|RNA binding				0																		---	---	---	---
ACSM2B	348158	broad.mit.edu	37	16	20576071	20576071	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20576071G>T	uc002dhj.3	-	3	307	c.97C>A	c.(97-99)CTG>ATG	p.L33M	ACSM2B_uc002dhk.3_Missense_Mutation_p.L33M|ACSM2B_uc010bwf.1_Missense_Mutation_p.L33M	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	33					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5																		---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22271848	22271848	+	Silent	SNP	C	A	A	rs56137739		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22271848C>A	uc002dki.2	+	11	1782	c.1297C>A	c.(1297-1299)CGG>AGG	p.R433R	EEF2K_uc002dkh.2_RNA	NM_013302	NP_037434	O00418	EF2K_HUMAN	elongation factor-2 kinase	433					insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)														---	---	---	---
SCNN1G	6340	broad.mit.edu	37	16	23200704	23200704	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23200704T>C	uc002dlm.1	+	3	469	c.330T>C	c.(328-330)GTT>GTC	p.V110V		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	110	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
RBBP6	5930	broad.mit.edu	37	16	24580751	24580751	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24580751A>G	uc002dmh.2	+	17	3780	c.2740A>G	c.(2740-2742)ACA>GCA	p.T914A	RBBP6_uc010vcb.1_Missense_Mutation_p.T781A|RBBP6_uc002dmi.2_Missense_Mutation_p.T880A|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Missense_Mutation_p.T747A	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	914					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)														---	---	---	---
IL21R	50615	broad.mit.edu	37	16	27460161	27460161	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27460161T>G	uc002doq.1	+	9	1407	c.1174T>G	c.(1174-1176)TGC>GGC	p.C392G	IL21R_uc002dor.1_Missense_Mutation_p.C392G|IL21R_uc002dos.1_Missense_Mutation_p.C392G|uc002dot.2_RNA	NM_181078	NP_851564	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor precursor	392	Cytoplasmic (Potential).				natural killer cell activation	integral to membrane	interleukin-21 receptor activity			ovary(2)|lung(1)|breast(1)	4								T	BCL6	NHL								---	---	---	---
MVP	9961	broad.mit.edu	37	16	29842329	29842329	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29842329G>A	uc002dui.2	+	3	340	c.256G>A	c.(256-258)GCT>ACT	p.A86T	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc010bzh.1_RNA|MVP_uc010vdz.1_Intron|MVP_uc002duj.2_Missense_Mutation_p.A86T|MVP_uc010vea.1_5'UTR	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein	86	MVP 2.				mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
ZNF48	197407	broad.mit.edu	37	16	30409177	30409177	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30409177G>A	uc002dya.1	+	2	665	c.606G>A	c.(604-606)CGG>CGA	p.R202R	ZNF48_uc002dxz.1_Silent_p.R79R	NM_152652	NP_689865	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	202	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRR14	78994	broad.mit.edu	37	16	30665594	30665594	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30665594G>T	uc002dyy.2	+	7	850	c.592G>T	c.(592-594)GGG>TGG	p.G198W	PRR14_uc002dyz.2_Missense_Mutation_p.G43W|PRR14_uc002dza.2_Missense_Mutation_p.G198W|PRR14_uc002dzb.1_Missense_Mutation_p.G12W	NM_024031	NP_076936	Q9BWN1	PRR14_HUMAN	proline rich 14	198	Pro-rich.										0			Colorectal(24;0.103)															---	---	---	---
PRSS36	146547	broad.mit.edu	37	16	31161349	31161349	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31161349C>A	uc002ebd.2	-	1	67	c.8G>T	c.(7-9)CGG>CTG	p.R3L	PRSS36_uc010vff.1_5'Flank|PRSS36_uc010vfg.1_Missense_Mutation_p.R3L|PRSS36_uc010vfh.1_Missense_Mutation_p.R3L	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	3					proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48227793	48227793	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48227793C>T	uc002eff.1	-	18	2855	c.2505G>A	c.(2503-2505)TCG>TCA	p.S835S	ABCC11_uc002efg.1_Silent_p.S835S|ABCC11_uc002efh.1_Silent_p.S835S|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	835	ABC transmembrane type-1 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances	p.S835S(1)		ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52484318	52484318	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52484318G>A	uc002egw.2	-	4	720	c.549C>T	c.(547-549)AGC>AGT	p.S183S	TOX3_uc010vgt.1_Silent_p.S178S|TOX3_uc010vgu.1_Silent_p.S183S	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	183					apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
RPGRIP1L	23322	broad.mit.edu	37	16	53682876	53682876	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53682876C>T	uc002ehp.2	-	16	2368	c.2304G>A	c.(2302-2304)TCG>TCA	p.S768S	RPGRIP1L_uc002eho.3_Silent_p.S768S|RPGRIP1L_uc010vgy.1_Silent_p.S768S|RPGRIP1L_uc010cbx.2_Silent_p.S768S|RPGRIP1L_uc010vgz.1_Silent_p.S768S	NM_015272	NP_056087	Q68CZ1	FTM_HUMAN	RPGRIP1-like isoform a	768					negative regulation of G-protein coupled receptor protein signaling pathway	cell-cell junction|centrosome|cilium axoneme|microtubule basal body	thromboxane A2 receptor binding			ovary(1)	1		all_cancers(37;0.0973)																---	---	---	---
MMP2	4313	broad.mit.edu	37	16	55513508	55513508	+	Silent	SNP	C	T	T	rs139082366		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55513508C>T	uc002ehz.3	+	1	428	c.117C>T	c.(115-117)GGC>GGT	p.G39G	MMP2_uc010vhd.1_5'Flank|MMP2_uc010ccc.2_5'Flank	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	39					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)													---	---	---	---
CES7	221223	broad.mit.edu	37	16	55880490	55880490	+	Missense_Mutation	SNP	G	A	A	rs142487845	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55880490G>A	uc002eip.2	-	13	1750	c.1601C>T	c.(1600-1602)CCG>CTG	p.P534L	CES7_uc002eio.2_Missense_Mutation_p.P484L|CES7_uc002eiq.2_Missense_Mutation_p.P295L|CES7_uc002eir.2_Missense_Mutation_p.P428L	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	534						extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)														---	---	---	---
CES7	221223	broad.mit.edu	37	16	55893464	55893464	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55893464G>A	uc002eip.2	-	8	1200	c.1051C>T	c.(1051-1053)CCT>TCT	p.P351S	CES7_uc002eio.2_Missense_Mutation_p.P351S|CES7_uc002eiq.2_Missense_Mutation_p.P112S|CES7_uc002eir.2_Missense_Mutation_p.P245S	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	351						extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)														---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57054633	57054633	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57054633C>A	uc002ekk.1	+	3	234	c.9C>A	c.(7-9)CCC>CCA	p.P3P	NLRC5_uc010ccq.1_RNA	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	3					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)																---	---	---	---
DOK4	55715	broad.mit.edu	37	16	57507884	57507884	+	Missense_Mutation	SNP	C	T	T	rs146675149		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57507884C>T	uc010cdb.2	-	6	965	c.667G>A	c.(667-669)GTC>ATC	p.V223I	DOK4_uc002elu.1_Missense_Mutation_p.V223I|DOK4_uc002elv.3_Missense_Mutation_p.V223I	NM_018110	NP_060580	Q8TEW6	DOK4_HUMAN	docking protein 4	223	IRS-type PTB.						insulin receptor binding			skin(1)	1																		---	---	---	---
MMP15	4324	broad.mit.edu	37	16	58074522	58074522	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58074522T>C	uc002ena.2	+	5	1803	c.830T>C	c.(829-831)ATG>ACG	p.M277T		NM_002428	NP_002419	P51511	MMP15_HUMAN	matrix metalloproteinase 15 preproprotein	277	Extracellular (Potential).				protein modification process|proteolysis	extracellular matrix|integral to plasma membrane	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			central_nervous_system(2)|breast(1)	3																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58580381	58580381	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58580381C>A	uc002env.2	-	29	4143	c.3850G>T	c.(3850-3852)GAG>TAG	p.E1284*	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Nonsense_Mutation_p.E1279*|CNOT1_uc002enx.2_Nonsense_Mutation_p.E1284*|CNOT1_uc010vik.1_Nonsense_Mutation_p.E241*	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1284					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)														---	---	---	---
TK2	7084	broad.mit.edu	37	16	66545914	66545914	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66545914C>A	uc002eos.2	-	10	1106	c.881G>T	c.(880-882)CGG>CTG	p.R294L	TK2_uc010vip.1_Missense_Mutation_p.R155L|TK2_uc002eor.2_Missense_Mutation_p.R221L|TK2_uc010cdq.2_3'UTR|TK2_uc010cdr.2_Missense_Mutation_p.R203L|TK2_uc010viq.1_Missense_Mutation_p.R276L|TK2_uc010vir.1_Missense_Mutation_p.R269L	NM_004614	NP_004605	O00142	KITM_HUMAN	thymidine kinase 2, mitochondrial	252					pyrimidine base metabolic process|pyrimidine nucleoside salvage	mitochondrial matrix	ATP binding|phosphotransferase activity, alcohol group as acceptor|thymidine kinase activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0736)|Epithelial(162;0.237)														---	---	---	---
CMTM1	113540	broad.mit.edu	37	16	66600818	66600818	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66600818G>A	uc002epi.3	+						CMTM1_uc002epb.3_Intron|CMTM1_uc002epc.3_Intron|CMTM1_uc002epd.3_Intron|CMTM1_uc002epe.3_Intron|CMTM1_uc002epf.3_Intron|CMTM1_uc002epg.3_Intron|CMTM1_uc002eph.3_Intron|CMTM1_uc002epl.3_Intron|CMTM1_uc002epj.3_Intron|CMTM1_uc002epk.3_Intron|CMTM1_uc002epa.3_Intron|CMTM1_uc002epn.3_Silent_p.S134S|CMTM1_uc002epo.3_RNA|CMTM1_uc002epp.3_RNA|CMTM1_uc002epq.3_RNA|CMTM1_uc010cds.2_RNA|CMTM1_uc002epr.3_Silent_p.S134S|CMTM1_uc002epm.3_RNA|CMTM1_uc010cdt.1_Silent_p.S134S	NM_181269	NP_851786			chemokine-like factor superfamily 1 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)														---	---	---	---
RANBP10	57610	broad.mit.edu	37	16	67763726	67763726	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67763726C>T	uc002eud.2	-	9	1120	c.1004G>A	c.(1003-1005)CGG>CAG	p.R335Q	RANBP10_uc010ceo.2_Missense_Mutation_p.R106Q|RANBP10_uc010vju.1_Missense_Mutation_p.R279Q|RANBP10_uc010vjv.1_Missense_Mutation_p.R218Q|RANBP10_uc010vjw.1_5'UTR	NM_020850	NP_065901	Q6VN20	RBP10_HUMAN	RAN binding protein 10	335	CTLH.									ovary(1)	1		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)														---	---	---	---
CIRH1A	84916	broad.mit.edu	37	16	69184536	69184536	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69184536C>T	uc002ews.3	+	7	931	c.835C>T	c.(835-837)CGG>TGG	p.R279W	CIRH1A_uc002ewr.2_Missense_Mutation_p.R279W|CIRH1A_uc002ewt.3_Missense_Mutation_p.R196W|CIRH1A_uc010cfi.2_Missense_Mutation_p.R196W|CIRH1A_uc010cfj.1_Missense_Mutation_p.R98W	NM_032830	NP_116219	Q969X6	CIR1A_HUMAN	cirhin	279						nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)												OREG0023906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FUK	197258	broad.mit.edu	37	16	70503177	70503177	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70503177C>T	uc002eyy.2	+	10	964	c.906C>T	c.(904-906)AGC>AGT	p.S302S	FUK_uc010cft.2_Silent_p.S334S|FUK_uc002eyz.2_Intron	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase	302						cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
SF3B3	23450	broad.mit.edu	37	16	70578443	70578443	+	Intron	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70578443T>A	uc002ezf.2	+							NM_012426	NP_036558			splicing factor 3b, subunit 3						protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
ZNF23	7571	broad.mit.edu	37	16	71483393	71483393	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71483393A>G	uc002faf.2	-	6	1349	c.535T>C	c.(535-537)TGT>CGT	p.C179R	ZNF23_uc002fad.2_Missense_Mutation_p.C121R|ZNF23_uc002fae.2_Missense_Mutation_p.C121R|ZNF23_uc010vmf.1_Missense_Mutation_p.C121R|ZNF23_uc002fag.2_Missense_Mutation_p.C121R|ZNF23_uc002fah.2_Missense_Mutation_p.C179R|ZNF23_uc002fai.2_Missense_Mutation_p.C218R	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23	179	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)														---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71712666	71712666	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71712666C>A	uc002fax.2	-	7	1266	c.1260G>T	c.(1258-1260)GTG>GTT	p.V420V	PHLPP2_uc002fav.2_RNA|PHLPP2_uc010cgf.2_Silent_p.V420V|PHLPP2_uc002fay.1_Silent_p.V420V	NM_015020	NP_055835	Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein	420	LRR 8.					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CHST5	23563	broad.mit.edu	37	16	75563303	75563303	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75563303T>G	uc002fei.2	-	3	2375	c.980A>C	c.(979-981)AAC>ACC	p.N327T	CHST5_uc002fej.1_Missense_Mutation_p.N333T	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	327	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
BCMO1	53630	broad.mit.edu	37	16	81303868	81303868	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81303868C>T	uc002fgn.1	+	7	1166	c.948C>T	c.(946-948)GAC>GAT	p.D316D	BCMO1_uc010vnp.1_Silent_p.D247D	NM_017429	NP_059125	Q9HAY6	BCDO1_HUMAN	beta-carotene 15,15'-monooxygenase	316					retinoid metabolic process|steroid metabolic process	cytosol	beta-carotene 15,15'-monooxygenase activity|metal ion binding|monooxygenase activity				0																		---	---	---	---
KIAA1609	57707	broad.mit.edu	37	16	84520637	84520637	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84520637C>T	uc002fib.2	-	5	665	c.558G>A	c.(556-558)TGG>TGA	p.W186*	KIAA1609_uc010vod.1_Nonsense_Mutation_p.W159*|KIAA1609_uc002fic.2_RNA	NM_020947	NP_065998	Q6P9B6	K1609_HUMAN	hypothetical protein LOC57707	186							protein binding			ovary(2)	2																		---	---	---	---
ZDHHC7	55625	broad.mit.edu	37	16	85024236	85024236	+	5'UTR	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85024236C>T	uc002fiq.2	-	3					ZDHHC7_uc010voi.1_5'UTR|ZDHHC7_uc002fir.1_RNA	NM_017740	NP_060210			zinc finger, DHHC-type containing 7 isoform 2							integral to membrane	acyltransferase activity|protein binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
ZCCHC14	23174	broad.mit.edu	37	16	87446254	87446254	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87446254G>T	uc002fjz.1	-	12	1689	c.1662C>A	c.(1660-1662)AGC>AGA	p.S554R	ZCCHC14_uc002fka.1_RNA|ZCCHC14_uc002fkb.2_Missense_Mutation_p.S330R	NM_015144	NP_055959	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	554					cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)														---	---	---	---
C16orf7	9605	broad.mit.edu	37	16	89774889	89774889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89774889C>T	uc002fom.1	-	14	1873	c.1748G>A	c.(1747-1749)GGC>GAC	p.G583D	C16orf7_uc002fol.1_Missense_Mutation_p.G513D	NM_004913	NP_004904	Q9Y2B5	CP007_HUMAN	chromosome 16 open reading frame 7	583	VPS9.				ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
TUBB3	10381	broad.mit.edu	37	16	89986504	89986504	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89986504T>C	uc002fpf.2	+	1	1246	c.838T>C	c.(838-840)TTC>CTC	p.F280L	MC1R_uc002fpe.3_Missense_Mutation_p.F280L|TUBB3_uc010ciz.1_5'Flank	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4	Error:Variant_position_missing_in_Q13509_after_alignment					'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	725693	725693	+	Missense_Mutation	SNP	G	A	A	rs139124108		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:725693G>A	uc002fsa.2	-	4	709	c.617C>T	c.(616-618)CCG>CTG	p.P206L	NXN_uc002fsb.1_Missense_Mutation_p.P93L|NXN_uc010vqd.1_5'UTR|NXN_uc002frz.2_5'UTR|NXN_uc010vqe.1_Missense_Mutation_p.P98L	NM_022463	NP_071908	Q6DKJ4	NXN_HUMAN	nucleoredoxin	206	Thioredoxin.				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)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1581900	1581900	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1581900G>A	uc002fte.2	-	13	1880	c.1766C>T	c.(1765-1767)ACG>ATG	p.T589M		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	589						catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2203279	2203279	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2203279C>T	uc002fub.1	-	2	823	c.768G>A	c.(766-768)ACG>ACA	p.T256T	SMG6_uc002fud.1_Silent_p.T225T	NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	256	Interaction with telomeric DNA.				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
OR3A4	390756	broad.mit.edu	37	17	3214311	3214311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3214311G>A	uc002fvi.2	+	1	773	c.707G>A	c.(706-708)GGC>GAC	p.G236D		NR_024128				RecName: Full=Olfactory receptor 3A4; AltName: Full=Olfactory receptor 17-24;          Short=OR17-24;											ovary(1)	1																		---	---	---	---
GP1BA	2811	broad.mit.edu	37	17	4836563	4836563	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4836563C>A	uc010vsq.1	+	2	739	c.664C>A	c.(664-666)CCC>ACC	p.P222T	uc002fzn.1_RNA	NM_000173	NP_000164	P07359	GP1BA_HUMAN	platelet glycoprotein Ib alpha polypeptide	222											0																		---	---	---	---
AIPL1	23746	broad.mit.edu	37	17	6328975	6328975	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6328975C>T	uc002gcp.2	-	6	1055	c.960G>A	c.(958-960)CGG>CGA	p.R320R	AIPL1_uc002gcq.2_Silent_p.R260R|AIPL1_uc002gcr.2_Silent_p.R257R|AIPL1_uc010clk.2_Silent_p.R298R|AIPL1_uc010cll.2_Silent_p.R296R|AIPL1_uc002gcs.2_3'UTR	NM_014336	NP_055151	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting	320					protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
ASGR1	432	broad.mit.edu	37	17	7077743	7077743	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7077743A>G	uc002ges.3	-	6	802	c.392T>C	c.(391-393)GTG>GCG	p.V131A	ASGR1_uc010clx.1_Missense_Mutation_p.V30A	NM_001671	NP_001662	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	131	Extracellular (Probable).				receptor-mediated endocytosis	integral to plasma membrane	asialoglycoprotein receptor activity|metal ion binding|sugar binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
NEURL4	84461	broad.mit.edu	37	17	7230998	7230998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7230998C>T	uc002gga.1	-	2	495	c.488G>A	c.(487-489)CGC>CAC	p.R163H	NEURL4_uc002ggb.1_Missense_Mutation_p.R163H|NEURL4_uc002ggc.1_5'Flank	NM_032442	NP_115818	Q96JN8	NEUL4_HUMAN	neuralized homolog 4 isoform 1	163	NHR 1.						protein binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	A	A	rs121913343		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577121G>A	uc002gim.2	-	8	1011	c.817C>T	c.(817-819)CGT>TGT	p.R273C	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R273C|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R141C|TP53_uc010cng.1_Missense_Mutation_p.R141C|TP53_uc002gii.1_Missense_Mutation_p.R141C|TP53_uc010cnh.1_Missense_Mutation_p.R273C|TP53_uc010cni.1_Missense_Mutation_p.R273C|TP53_uc002gij.2_Missense_Mutation_p.R273C	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	273	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|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|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R273H(467)|p.R273C(396)|p.R273L(83)|p.R273P(24)|p.R273S(11)|p.R273G(9)|p.0?(7)|p.R273fs*72(3)|p.?(2)|p.R273fs*33(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273R(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		R273C(SH10TC_STOMACH)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(RH30_SOFT_TISSUE)|R273C(PANC0213_PANCREAS)|R273C(SJRH30_SOFT_TISSUE)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(TT2609C02_THYROID)|R273C(MFE319_ENDOMETRIUM)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(NCIH1048_LUNG)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
NTN1	9423	broad.mit.edu	37	17	9066235	9066235	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9066235C>T	uc002glw.3	+	3	1231	c.1124C>T	c.(1123-1125)ACC>ATC	p.T375I		NM_004822	NP_004813	O95631	NET1_HUMAN	netrin 1 precursor	375	Laminin EGF-like 2.				apoptosis|axon guidance		protein binding				0																		---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	16049688	16049688	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16049688A>G	uc002gpo.2	-	10	1322	c.1082_splice	c.e10+1	p.R361_splice	NCOR1_uc002gpn.2_Splice_Site_p.R361_splice|NCOR1_uc002gpp.1_Splice_Site_p.R252_splice|NCOR1_uc002gpr.2_Splice_Site_p.R252_splice|NCOR1_uc002gps.1_Splice_Site_p.R370_splice|NCOR1_uc010coz.1_Splice_Site_p.R177_splice|NCOR1_uc010cpb.1_Splice_Site_p.R370_splice|NCOR1_uc010cpa.1_Splice_Site_p.R361_splice	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17697546	17697546	+	Silent	SNP	G	A	A	rs113249215		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17697546G>A	uc002grm.2	+	3	1753	c.1284G>A	c.(1282-1284)TCG>TCA	p.S428S	RAI1_uc002grn.1_Silent_p.S428S	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	428						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)														---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17721064	17721064	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17721064G>A	uc002gru.1	-	7	1544	c.1350C>T	c.(1348-1350)AGC>AGT	p.S450S	SREBF1_uc002grp.1_Missense_Mutation_p.A20V|SREBF1_uc002grq.1_5'UTR|SREBF1_uc002grr.1_Silent_p.S196S|SREBF1_uc002grs.1_Silent_p.S426S|SREBF1_uc002grt.1_Silent_p.S480S|SREBF1_uc010cpp.1_Silent_p.S426S|SREBF1_uc010cpq.1_Silent_p.S450S	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	450	Gly/Pro/Ser-rich.|Cytoplasmic (Potential).|Interaction with LMNA (By similarity).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1																		---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17754256	17754256	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17754256G>A	uc002grz.3	-	13	1446	c.1289C>T	c.(1288-1290)GCG>GTG	p.A430V	TOM1L2_uc002gry.3_Missense_Mutation_p.A380V|TOM1L2_uc010vwy.1_Missense_Mutation_p.A406V|TOM1L2_uc010cpr.2_Missense_Mutation_p.A385V|TOM1L2_uc010vwz.1_Missense_Mutation_p.A311V|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc002grv.3_Missense_Mutation_p.A163V	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	430					intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20108736	20108736	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20108736T>C	uc002gwq.2	+	4	1519	c.1374T>C	c.(1372-1374)ACT>ACC	p.T458T	CYTSB_uc010cqx.2_Silent_p.T458T|CYTSB_uc002gwr.2_Silent_p.T458T|CYTSB_uc002gws.2_Silent_p.T458T|CYTSB_uc002gwv.2_Silent_p.T377T|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Silent_p.T234T|CYTSB_uc002gwt.2_Silent_p.T377T|CYTSB_uc002gwu.2_Silent_p.T377T	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b	458						nucleus					0																		---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21318878	21318878	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21318878G>A	uc002gyv.1	+	3	929	c.224G>A	c.(223-225)TGT>TAT	p.C75Y		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	75	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
SLC13A2	9058	broad.mit.edu	37	17	26821104	26821104	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26821104A>G	uc002hbh.2	+	8	1234	c.1167A>G	c.(1165-1167)CCA>CCG	p.P389P	SLC13A2_uc010wal.1_3'UTR|SLC13A2_uc010wam.1_Silent_p.P345P|SLC13A2_uc010wan.1_Silent_p.P438P|SLC13A2_uc010wao.1_Silent_p.P346P|SLC13A2_uc002hbi.2_Silent_p.P318P	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13, member 2 isoform b	389	Helical; (Potential).					integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)													---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27421841	27421841	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27421841T>C	uc002hdt.1	-	30	4695	c.4537A>G	c.(4537-4539)ACC>GCC	p.T1513A	MYO18A_uc010wbc.1_Missense_Mutation_p.T1055A|MYO18A_uc002hds.2_Missense_Mutation_p.T1055A|MYO18A_uc010csa.1_Missense_Mutation_p.T1513A|MYO18A_uc002hdu.1_Missense_Mutation_p.T1513A	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	1513	Potential.				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)															---	---	---	---
NF1	4763	broad.mit.edu	37	17	29677318	29677318	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29677318A>G	uc002hgg.2	+	50	7772	c.7439A>G	c.(7438-7440)CAT>CGT	p.H2480R	NF1_uc002hgh.2_Missense_Mutation_p.H2459R|NF1_uc010cso.2_Missense_Mutation_p.H668R|NF1_uc010wbt.1_Missense_Mutation_p.M11V|NF1_uc010wbu.1_RNA	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	2480					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)			---	---	---	---
CDK5R1	8851	broad.mit.edu	37	17	30815316	30815316	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30815316G>A	uc002hhn.2	+	2	899	c.678G>A	c.(676-678)CTG>CTA	p.L226L	CDK5R1_uc010wca.1_Silent_p.L226L|CDK5R1_uc010ctc.2_5'UTR	NM_003885	NP_003876	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1	226					axon guidance|axonal fasciculation|brain development|cell proliferation|embryo development|ionotropic glutamate receptor signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of transcription, DNA-dependent|neuron cell-cell adhesion|neuron migration|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of neuron apoptosis|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation	axon|contractile fiber|cyclin-dependent protein kinase 5 holoenzyme complex|cytosol|dendritic spine|growth cone|neuromuscular junction|neuronal cell body|perinuclear region of cytoplasm|plasma membrane	cadherin binding|calcium ion binding|protein kinase binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)															---	---	---	---
SPACA3	124912	broad.mit.edu	37	17	31324543	31324543	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31324543T>C	uc002hhs.1	+	4	656	c.581_splice	c.e4+2	p.W194_splice	SPACA3_uc010cte.1_Splice_Site	NM_173847	NP_776246			sperm acrosome associated 3						cell wall macromolecule catabolic process|defense response to Gram-positive bacterium|monocyte activation|peptidoglycan catabolic process|positive regulation of macrophage activation|positive regulation of phagocytosis|response to virus	acrosomal membrane|extracellular region|integral to membrane|lysosome	bacterial cell surface binding|lysozyme activity|protein binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.193)															---	---	---	---
LIG3	3980	broad.mit.edu	37	17	33313055	33313055	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33313055A>G	uc002hik.1	+	3	704	c.596A>G	c.(595-597)CAG>CGG	p.Q199R	LIG3_uc002hii.2_Missense_Mutation_p.Q199R|LIG3_uc002hij.2_Missense_Mutation_p.Q199R|LIG3_uc010cth.1_Missense_Mutation_p.Q208R	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	199					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					---	---	---	---
MMP28	79148	broad.mit.edu	37	17	34095306	34095306	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34095306G>A	uc002hjy.1	-	8	1202	c.943C>T	c.(943-945)CGC>TGC	p.R315C	MMP28_uc002hjw.1_RNA|MMP28_uc002hjz.1_RNA	NM_024302	NP_077278	Q9H239	MMP28_HUMAN	matrix metalloproteinase 28 isoform 1	315					proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
RPL23	9349	broad.mit.edu	37	17	37009243	37009243	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37009243A>G	uc002hqx.1	-						RPL23_uc002hqw.1_Intron|RPL23_uc002hqy.1_Intron|SNORA21_uc002hqz.1_RNA	NM_000978	NP_000969			ribosomal protein L23						endocrine pancreas development|ribosomal protein import into nucleus|translational elongation|translational termination|viral transcription	cytosol|ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37455302	37455302	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37455302C>T	uc010wed.1	-	5	491	c.270G>A	c.(268-270)GGG>GGA	p.G90G	FBXL20_uc002hrt.2_Silent_p.G90G|FBXL20_uc010cvu.2_Silent_p.G90G	NM_032875	NP_116264	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	90	LRR 1.					cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)															---	---	---	---
ZPBP2	124626	broad.mit.edu	37	17	38028518	38028518	+	Intron	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38028518T>A	uc002hte.2	+						ZPBP2_uc002htf.2_Intron	NM_199321	NP_955353			zona pellucida binding protein 2 isoform 2						binding of sperm to zona pellucida	extracellular region				ovary(1)	1	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
MED24	9862	broad.mit.edu	37	17	38191589	38191589	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38191589C>T	uc002htt.2	-	6	653	c.340G>A	c.(340-342)GCA>ACA	p.A114T	MED24_uc010wes.1_5'UTR|MED24_uc010wet.1_RNA|MED24_uc002hts.2_Missense_Mutation_p.A139T|MED24_uc002htu.2_Missense_Mutation_p.A101T|MED24_uc010cwn.2_Missense_Mutation_p.A101T|MED24_uc010weu.1_Missense_Mutation_p.A24T|MED24_uc010wev.1_Missense_Mutation_p.A64T|MED24_uc010wew.1_Missense_Mutation_p.A43T|MED24_uc010wex.1_Intron|MED24_uc010wez.1_5'Flank|MED24_uc010wfa.1_Missense_Mutation_p.A64T|MED24_uc010wfb.1_Missense_Mutation_p.A126T|MED24_uc010wfc.1_Missense_Mutation_p.A51T	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1	114					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)															OREG0024387	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
WIPF2	147179	broad.mit.edu	37	17	38433330	38433330	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38433330C>T	uc002hug.1	+						WIPF2_uc002huh.1_Intron|WIPF2_uc010cww.1_Intron|WIPF2_uc002hui.1_Intron|WIPF2_uc010cwx.1_Intron|WIPF2_uc010cwy.1_Intron	NM_133264	NP_573571			WIRE protein							cytoplasm|cytoskeleton	actin binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3															HNSCC(43;0.11)			---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38562635	38562635	+	Splice_Site	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38562635C>T	uc002huq.2	-	16	2079	c.1953_splice	c.e16+1	p.L651_splice		NM_001067	NP_001058			DNA topoisomerase II, alpha isozyme						apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)													---	---	---	---
GAST	2520	broad.mit.edu	37	17	39871806	39871806	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39871806A>G	uc002hxl.2	+	2	150	c.118A>G	c.(118-120)AGG>GGG	p.R40G	JUP_uc010wfs.1_Intron	NM_000805	NP_000796	P01350	GAST_HUMAN	gastrin preproprotein	40		Cleavage.				extracellular region	hormone activity				0		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
JUP	3728	broad.mit.edu	37	17	39925443	39925443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39925443G>A	uc002hxq.2	-	4	762	c.485C>T	c.(484-486)GCG>GTG	p.A162V	JUP_uc010wfs.1_Missense_Mutation_p.A162V|JUP_uc002hxr.2_Missense_Mutation_p.A162V|JUP_uc002hxs.2_Missense_Mutation_p.A162V	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	162	ARM 1.				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)														---	---	---	---
FKBP10	60681	broad.mit.edu	37	17	39975515	39975515	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39975515G>A	uc002hxv.2	+	5	1106	c.781G>A	c.(781-783)GTG>ATG	p.V261M	FKBP10_uc002hxw.1_Translation_Start_Site	NM_021939	NP_068758	Q96AY3	FKB10_HUMAN	FK506 binding protein 10 precursor	261	PPIase FKBP-type 2.				protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)														---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40359573	40359573	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40359573T>C	uc002hzh.2	-							NM_012448	NP_036580			signal transducer and activator of transcription						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)													---	---	---	---
COASY	80347	broad.mit.edu	37	17	40714445	40714445	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40714445C>T	uc002hzz.2	+						COASY_uc010cyj.2_Missense_Mutation_p.L6F|COASY_uc002iab.2_Intron|COASY_uc002iad.2_5'UTR|COASY_uc002iac.2_5'UTR|COASY_uc002iae.2_5'Flank	NM_001042529	NP_001035994			coenzyme A synthase isoform a						coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40849679	40849679	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40849679C>T	uc002iay.2	+	22	3892	c.3676C>T	c.(3676-3678)CGA>TGA	p.R1226*	CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	1226	Laminin G-like 4.|Extracellular (Potential).				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)														---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41570257	41570257	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41570257C>T	uc002idu.1	+	6	785	c.712C>T	c.(712-714)CGG>TGG	p.R238W	DHX8_uc010wif.1_Missense_Mutation_p.R147W|DHX8_uc010wig.1_Missense_Mutation_p.R238W	NM_004941	NP_004932	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	238						catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)														---	---	---	---
PYY	5697	broad.mit.edu	37	17	42030346	42030346	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42030346G>A	uc002ieq.2	-	7	813	c.272C>T	c.(271-273)TCG>TTG	p.S91L	PYY_uc002ier.1_3'UTR	NM_004160	NP_004151	P10082	PYY_HUMAN	peptide YY precursor	91					cell proliferation|cell-cell signaling|cellular component movement|cytoskeleton organization|digestion|G-protein coupled receptor protein signaling pathway	soluble fraction					0		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)														---	---	---	---
FMNL1	752	broad.mit.edu	37	17	43322710	43322710	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43322710T>C	uc002iin.2	+	22	3019	c.2819T>C	c.(2818-2820)ATG>ACG	p.M940T	FMNL1_uc002iiq.2_Missense_Mutation_p.M518T|FMNL1_uc010dag.2_RNA|LOC100133991_uc010dah.2_5'Flank	NM_005892	NP_005883	O95466	FMNL_HUMAN	formin-like 1	940	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			pancreas(1)	1																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45734321	45734321	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45734321G>A	uc002ilt.1	+	4	714	c.378G>A	c.(376-378)TGG>TGA	p.W126*	KPNB1_uc010wkw.1_5'UTR|KPNB1_uc010wkx.1_5'UTR	NM_002265	NP_002256	Q14974	IMB1_HUMAN	karyopherin beta 1	126	HEAT 1.				DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45741591	45741591	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45741591A>G	uc002ilt.1	+	8	1189	c.853A>G	c.(853-855)AAT>GAT	p.N285D	KPNB1_uc010wkw.1_Missense_Mutation_p.N140D|KPNB1_uc010wkx.1_Intron	NM_002265	NP_002256	Q14974	IMB1_HUMAN	karyopherin beta 1	285					DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
DLX3	1747	broad.mit.edu	37	17	48070879	48070879	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48070879G>A	uc002ipy.2	-	2	627	c.401C>T	c.(400-402)ACG>ATG	p.T134M		NM_005220	NP_005211	O60479	DLX3_HUMAN	distal-less homeobox 3	134	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
ITGA3	3675	broad.mit.edu	37	17	48151644	48151644	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48151644G>A	uc010dbl.2	+	9	1846	c.1382G>A	c.(1381-1383)CGG>CAG	p.R461Q	ITGA3_uc010dbm.2_Missense_Mutation_p.R461Q	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor	461	FG-GAP 7.|Extracellular (Potential).				blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MMD	23531	broad.mit.edu	37	17	53488653	53488653	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53488653T>C	uc002iui.2	-	3	519	c.234A>G	c.(232-234)GTA>GTG	p.V78V		NM_012329	NP_036461	Q15546	PAQRB_HUMAN	monocyte to macrophage	78	Helical; (Potential).				cytolysis	integral to plasma membrane|late endosome membrane|lysosomal membrane|membrane fraction	receptor activity				0																		---	---	---	---
TMEM100	55273	broad.mit.edu	37	17	53798072	53798072	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53798072C>A	uc002iuj.3	-	2	671	c.360G>T	c.(358-360)GAG>GAT	p.E120D	TMEM100_uc002iuk.3_Missense_Mutation_p.E120D	NM_018286	NP_060756	Q9NV29	TM100_HUMAN	transmembrane protein 100	120						integral to membrane					0																		---	---	---	---
MPO	4353	broad.mit.edu	37	17	56357012	56357012	+	Intron	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56357012C>A	uc002ivu.1	-							NM_000250	NP_000241			myeloperoxidase						anti-apoptosis|hydrogen peroxide catabolic process|low-density lipoprotein particle remodeling	extracellular space|lysosome|nucleus|stored secretory granule	chromatin binding|heme binding|heparin binding|peroxidase activity			ovary(2)|large_intestine(1)|pancreas(1)	4					Cefdinir(DB00535)													---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57093004	57093004	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57093004G>A	uc002iwy.3	-	21	2987	c.2543C>T	c.(2542-2544)GCG>GTG	p.A848V	TRIM37_uc002iwz.3_Missense_Mutation_p.A848V|TRIM37_uc002ixa.3_Missense_Mutation_p.A726V|TRIM37_uc010woc.1_Missense_Mutation_p.A814V	NM_001005207	NP_001005207	O94972	TRI37_HUMAN	tripartite motif-containing 37 protein	848						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				---	---	---	---
TBX2	6909	broad.mit.edu	37	17	59479301	59479301	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59479301A>G	uc010wox.1	+	2	933	c.652A>G	c.(652-654)AAG>GAG	p.K218E	TBX2_uc002ize.2_Missense_Mutation_p.K208E|TBX2_uc002izg.2_Missense_Mutation_p.K64E	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2	218	T-box.				cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0																		---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59989018	59989018	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59989018A>G	uc002izn.2	-	7	917	c.841T>C	c.(841-843)TTG>CTG	p.L281L	INTS2_uc002izm.2_Silent_p.L273L	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	281					snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
CSH1	1442	broad.mit.edu	37	17	61972426	61972426	+	Missense_Mutation	SNP	G	A	A	rs139446025	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61972426G>A	uc002jcs.1	-	5	726	c.610C>T	c.(610-612)CGC>TGC	p.R204C	CSH2_uc002jck.2_Intron|CSH1_uc002jcp.1_3'UTR|CSH1_uc002jcq.1_Missense_Mutation_p.R165C|CSH1_uc002jcr.1_3'UTR|CSH1_uc002jct.1_Missense_Mutation_p.R170C|CSH1_uc002jcu.1_3'UTR|CSH1_uc002jcv.1_Missense_Mutation_p.R109C|CSH1_uc002jcw.2_3'UTR	NM_001317	NP_001308	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 1 isoform 1	204					female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding			skin(1)	1														Russell-Silver_syndrome				---	---	---	---
SLC25A19	60386	broad.mit.edu	37	17	73269635	73269635	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73269635G>T	uc002jns.3	-	6	1770	c.860C>A	c.(859-861)CCC>CAC	p.P287H	SLC25A19_uc010dge.2_Missense_Mutation_p.P230H|SLC25A19_uc002jnv.3_Missense_Mutation_p.P287H|SLC25A19_uc002jnu.3_Missense_Mutation_p.P287H|SLC25A19_uc002jnw.3_Missense_Mutation_p.P287H|SLC25A19_uc002jnt.3_Missense_Mutation_p.P287H	NM_021734	NP_068380	Q9HC21	TPC_HUMAN	solute carrier family 25, member 19	287	Solcar 3.					integral to membrane|mitochondrial inner membrane	binding|deoxynucleotide transmembrane transporter activity			ovary(1)	1	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)															---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73836367	73836367	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73836367C>T	uc002jpp.2	-	10	1177	c.797G>A	c.(796-798)CGC>CAC	p.R266H	UNC13D_uc010wsk.1_Missense_Mutation_p.R266H|UNC13D_uc002jpq.1_5'UTR|UNC13D_uc010dgq.1_Missense_Mutation_p.R63H	NM_199242	NP_954712	Q70J99	UN13D_HUMAN	unc-13 homolog D	266	Interaction with RAB27A.				positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
Unknown	0	broad.mit.edu	37	17	76475713	76475713	+	IGR	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76475713C>T								DNAH17 (6857 upstream) : CYTH1 (194418 downstream)																																			---	---	---	---
USP36	57602	broad.mit.edu	37	17	76795011	76795011	+	Silent	SNP	G	A	A	rs148007252		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76795011G>A	uc002jvz.1	-	19	3544	c.3219C>T	c.(3217-3219)GAC>GAT	p.D1073D	USP36_uc002jwa.1_Silent_p.D1073D|USP36_uc002jvy.1_Silent_p.D133D	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	1071					ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
CCDC40	55036	broad.mit.edu	37	17	78013825	78013825	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78013825C>T	uc010dht.2	+	3	335	c.308C>T	c.(307-309)CCG>CTG	p.P103L	CCDC40_uc010wub.1_Missense_Mutation_p.P103L	NM_017950	NP_060420	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	103					axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78268635	78268635	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78268635G>A	uc002jyf.2	+	9	1731	c.1588G>A	c.(1588-1590)GCT>ACT	p.A530T	uc002jyg.1_Missense_Mutation_p.A261T	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
NPTX1	4884	broad.mit.edu	37	17	78447193	78447193	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78447193C>T	uc002jyp.1	-	3	862	c.704G>A	c.(703-705)CGG>CAG	p.R235Q		NM_002522	NP_002513	Q15818	NPTX1_HUMAN	neuronal pentraxin I precursor	235	Pentaxin.				central nervous system development|synaptic transmission|transport	transport vesicle	metal ion binding				0	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)															---	---	---	---
HGS	9146	broad.mit.edu	37	17	79667727	79667727	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79667727C>T	uc002kbg.2	+	20	2096	c.2019C>T	c.(2017-2019)AAC>AAT	p.N673N	MRPL12_uc002kbh.1_5'Flank|SLC25A10_uc010wut.1_5'Flank	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	673	Interaction with NF2.|Gln-rich.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)															---	---	---	---
PCYT2	5833	broad.mit.edu	37	17	79865653	79865653	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79865653C>G	uc002kcf.1	-	5	551	c.488G>C	c.(487-489)AGC>ACC	p.S163T	PCYT2_uc010wva.1_Missense_Mutation_p.S131T|PCYT2_uc010wvb.1_Missense_Mutation_p.S131T|PCYT2_uc002kce.1_Missense_Mutation_p.S85T|PCYT2_uc002kcg.1_Missense_Mutation_p.S174T|PCYT2_uc002kch.1_Missense_Mutation_p.S163T|PCYT2_uc002kci.1_Missense_Mutation_p.S104T|PCYT2_uc010dii.1_Missense_Mutation_p.S163T|PCYT2_uc010wvc.1_Missense_Mutation_p.S85T	NM_002861	NP_002852	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	163	Catalytic 1 (Potential).				phospholipid biosynthetic process		ethanolamine-phosphate cytidylyltransferase 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)															---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3215000	3215000	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3215000C>T	uc002klp.2	-	2	556	c.222G>A	c.(220-222)TCG>TCA	p.S74S	MYOM1_uc002klq.2_Silent_p.S74S	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	74						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20516850	20516850	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20516850C>A	uc002ktw.2	+	2	367	c.36C>A	c.(34-36)AAC>AAA	p.N12K	RBBP8_uc002kty.2_Missense_Mutation_p.N12K|RBBP8_uc002ktz.2_Missense_Mutation_p.N12K|RBBP8_uc002kua.2_Missense_Mutation_p.N12K|RBBP8_uc002ktx.1_Missense_Mutation_p.N12K	NM_002894	NP_002885	Q99708	COM1_HUMAN	retinoblastoma binding protein 8 isoform a	12					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					---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25532148	25532148	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25532148A>T	uc002kwg.2	-	16	3149	c.2690T>A	c.(2689-2691)CTT>CAT	p.L897H	CDH2_uc010xbn.1_Missense_Mutation_p.L866H	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	897	Cytoplasmic (Potential).				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																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31318982	31318982	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31318982A>C	uc010dmg.1	+	11	1669	c.1614A>C	c.(1612-1614)GAA>GAC	p.E538D	ASXL3_uc002kxq.2_Missense_Mutation_p.E245D	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	538					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34174854	34174854	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34174854G>A	uc002kzt.1	+	7	808	c.711G>A	c.(709-711)ACG>ACA	p.T237T	FHOD3_uc002kzr.1_Silent_p.T237T|FHOD3_uc002kzs.1_Silent_p.T237T|FHOD3_uc002kzu.1_Silent_p.T62T|FHOD3_uc010dmz.1_5'UTR	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	237	GBD/FH3.				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)																---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43497754	43497754	+	Silent	SNP	T	C	C	rs113333959		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43497754T>C	uc002lbm.2	-	17	3229	c.3129A>G	c.(3127-3129)CCA>CCG	p.P1043P	KIAA1632_uc002lbo.1_Silent_p.P1043P|KIAA1632_uc010xcq.1_5'Flank|KIAA1632_uc010xcr.1_5'Flank|KIAA1632_uc010xcs.1_5'Flank|KIAA1632_uc002lbn.2_5'UTR	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	1043					autophagy						0																		---	---	---	---
TCEB3B	51224	broad.mit.edu	37	18	44560001	44560001	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44560001G>A	uc002lcr.1	-	1	1988	c.1635C>T	c.(1633-1635)AGC>AGT	p.S545S	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	545	Activation domain (By similarity).				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																		---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47488638	47488638	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47488638T>C	uc002leb.2	-	12	1831	c.1543A>G	c.(1543-1545)AAG>GAG	p.K515E	MYO5B_uc002lec.1_Missense_Mutation_p.K514E	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	515	Myosin head-like.				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)														---	---	---	---
SKA1	220134	broad.mit.edu	37	18	47911643	47911643	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47911643C>A	uc002let.2	+	5	553	c.369C>A	c.(367-369)CCC>CCA	p.P123P	SKA1_uc002leu.2_Silent_p.P123P|SKA1_uc010xdl.1_Intron	NM_145060	NP_659497	Q96BD8	SKA1_HUMAN	spindle and KT associated 1	123					cell division|chromosome segregation|mitotic anaphase|mitotic prometaphase|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytosol|spindle microtubule	microtubule binding				0																		---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48190774	48190774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48190774A>G	uc002lev.2	+	2	1446	c.446A>G	c.(445-447)GAC>GGC	p.D149G	MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Missense_Mutation_p.D149G	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	149	Protein kinase.	Proton acceptor (By similarity).			cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50866217	50866217	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50866217C>A	uc002lfe.1	+	15	2886	c.2299C>A	c.(2299-2301)CCT>ACT	p.P767T	DCC_uc010xdr.1_Missense_Mutation_p.P615T|DCC_uc010dpf.1_Missense_Mutation_p.P422T	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	767	Extracellular (Potential).|Fibronectin type-III 4.				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)														---	---	---	---
C18orf54	162681	broad.mit.edu	37	18	51888064	51888064	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51888064G>C	uc002lfn.3	+	3	451	c.335G>C	c.(334-336)AGA>ACA	p.R112T	C18orf54_uc002lfo.3_Missense_Mutation_p.R112T	NM_173529	NP_775800	Q8IYD9	CR054_HUMAN	hypothetical protein LOC162681 precursor	112						extracellular region				ovary(1)|skin(1)	2				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)														---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55321212	55321212	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55321212C>T	uc002lgw.2	-						uc002lgu.1_Intron|uc002lgv.1_Intron	NM_005603	NP_005594			ATPase, class I, type 8B, member 1						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				---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56203863	56203863	+	Missense_Mutation	SNP	G	A	A	rs139032503		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56203863G>A	uc002lhj.3	-	5	3770	c.3556C>T	c.(3556-3558)CGC>TGC	p.R1186C	ALPK2_uc002lhk.1_Missense_Mutation_p.R517C	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1186							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																		---	---	---	---
MC4R	4160	broad.mit.edu	37	18	58038752	58038752	+	Silent	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58038752A>G	uc002lie.1	-	1	1250	c.831T>C	c.(829-831)TGT>TGC	p.C277C		NM_005912	NP_005903	P32245	MC4R_HUMAN	melanocortin 4 receptor	277	Extracellular (Potential).				feeding behavior|G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of bone resorption|positive regulation of cAMP biosynthetic process	integral to membrane|plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|ubiquitin protein ligase binding			lung(1)	1		Colorectal(73;0.0946)																---	---	---	---
PIGN	23556	broad.mit.edu	37	18	59742043	59742043	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59742043A>G	uc002lii.3	-	30	3036	c.2588T>C	c.(2587-2589)ATT>ACT	p.I863T	PIGN_uc002lij.3_Missense_Mutation_p.I863T	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	863	Helical; (Potential).				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)																---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72998236	72998236	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72998236C>T	uc002lly.2	+	2	1302	c.739C>T	c.(739-741)CGC>TGC	p.R247C		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	292						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)														---	---	---	---
SALL3	27164	broad.mit.edu	37	18	76757273	76757273	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76757273G>A	uc002lmt.2	+	3	3854	c.3854G>A	c.(3853-3855)CGC>CAC	p.R1285H	SALL3_uc010dra.2_Missense_Mutation_p.R820H	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	1285					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)														---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77805925	77805925	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77805925G>A	uc002lns.2	+	7	940	c.802G>A	c.(802-804)GTG>ATG	p.V268M	C18orf22_uc010drh.2_Silent_p.R239R|C18orf22_uc010dri.1_Intron|C18orf22_uc002lnt.2_Missense_Mutation_p.V101M|uc002lnu.2_5'Flank	NM_024805	NP_079081	Q8N0V3	RBFA_HUMAN	hypothetical protein LOC79863 precursor	268					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)														---	---	---	---
MED16	10025	broad.mit.edu	37	19	873579	873579	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:873579A>G	uc002lqd.1	-	11	1926	c.1775T>C	c.(1774-1776)ATT>ACT	p.I592T	MED16_uc010drw.1_Missense_Mutation_p.I417T|MED16_uc002lqe.2_Missense_Mutation_p.I581T|MED16_uc002lqf.2_Missense_Mutation_p.I581T|MED16_uc010xfv.1_RNA|MED16_uc010xfw.1_Missense_Mutation_p.I512T|MED16_uc010xfx.1_Missense_Mutation_p.I437T|MED16_uc010xfy.1_Missense_Mutation_p.I169T|MED16_uc010xfz.1_RNA	NM_005481	NP_005472	Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	592					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				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;9.42e-05)|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)														---	---	---	---
EFNA2	1943	broad.mit.edu	37	19	1298589	1298589	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1298589G>A	uc002lry.1	+	3	494	c.494G>A	c.(493-495)CGA>CAA	p.R165Q		NM_001405	NP_001396	O43921	EFNA2_HUMAN	ephrin-A2 precursor	165					cell-cell signaling	anchored to membrane|plasma membrane	ephrin receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1986617	1986617	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1986617A>G	uc002lup.1	-	9	1448	c.1448T>C	c.(1447-1449)CTG>CCG	p.L483P	BTBD2_uc002luo.1_Missense_Mutation_p.L162P	NM_017797	NP_060267	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	483						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	2422198	2422198	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2422198C>T	uc010xgx.1	+	13	2399	c.2399C>T	c.(2398-2400)ACG>ATG	p.T800M		NM_182973	NP_892018	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	800	Extracellular (Potential).				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)														---	---	---	---
DIRAS1	148252	broad.mit.edu	37	19	2717294	2717294	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2717294G>T	uc002lwf.3	-	2	669	c.511C>A	c.(511-513)CGG>AGG	p.R171R		NM_145173	NP_660156	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	171					small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity			ovary(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)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3028785	3028785	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3028785C>T	uc002lww.2	-	2	304	c.41G>A	c.(40-42)GGC>GAC	p.G14D	TLE2_uc010dth.2_Missense_Mutation_p.G14D|TLE2_uc010xhc.1_5'UTR|TLE2_uc010dti.2_Missense_Mutation_p.G27D|TLE2_uc010xhd.1_Missense_Mutation_p.G14D	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1	14	Gln-rich.				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)														---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3656399	3656399	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3656399G>A	uc002lyj.1	-						PIP5K1C_uc010xhq.1_Intron|PIP5K1C_uc010xhr.1_Intron	NM_012398	NP_036530			phosphatidylinositol-4-phosphate 5-kinase, type						axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
ATCAY	85300	broad.mit.edu	37	19	3907777	3907777	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3907777C>T	uc002lyy.3	+	5	834	c.404C>T	c.(403-405)GCG>GTG	p.A135V	ATCAY_uc010xhz.1_Missense_Mutation_p.A141V|ATCAY_uc010dts.2_5'Flank	NM_033064	NP_149053	Q86WG3	ATCAY_HUMAN	caytaxin	135					transport		protein binding			breast(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
SH3GL1	6455	broad.mit.edu	37	19	4365543	4365543	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4365543C>T	uc002maj.2	-	4	373	c.267G>A	c.(265-267)TCG>TCA	p.S89S	SH3GL1_uc002mak.2_Intron|SH3GL1_uc010xig.1_Intron	NM_003025	NP_003016	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	89	BAR.				central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)				T	MLL	AL								---	---	---	---
PLIN4	729359	broad.mit.edu	37	19	4512549	4512549	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4512549C>T	uc002mar.1	-	3	1381	c.1381G>A	c.(1381-1383)GGT>AGT	p.G461S	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	461	27 X 33 AA approximate tandem repeat.|12.					lipid particle|plasma membrane					0																		---	---	---	---
EMR1	2015	broad.mit.edu	37	19	6924780	6924780	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6924780G>A	uc002mfw.2	+	15	1921	c.1883G>A	c.(1882-1884)CGC>CAC	p.R628H	EMR1_uc010dvc.2_Intron|EMR1_uc010dvb.2_Missense_Mutation_p.R576H|EMR1_uc010xji.1_Missense_Mutation_p.R487H|EMR1_uc010xjj.1_Missense_Mutation_p.R451H	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	628	Cytoplasmic (Potential).				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)|lung(1)|skin(1)	5	all_hematologic(4;0.166)																	---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7585134	7585134	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7585134C>T	uc002mgn.2	+	2	1176	c.1006C>T	c.(1006-1008)CAC>TAC	p.H336Y	MCOLN1_uc010dvh.1_5'Flank|MCOLN1_uc002mgo.2_5'Flank|MCOLN1_uc002mgp.2_5'Flank	NM_018083	NP_060553	Q9NW07	ZN358_HUMAN	zinc finger protein 358	336	C2H2-type 7.				embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
FCER2	2208	broad.mit.edu	37	19	7755350	7755350	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7755350C>T	uc002mhn.2	-	9	747	c.563G>A	c.(562-564)CGG>CAG	p.R188Q	FCER2_uc010xjs.1_Missense_Mutation_p.R110Q|FCER2_uc010xjt.1_Missense_Mutation_p.R110Q|FCER2_uc002mhm.2_Missense_Mutation_p.R188Q	NM_002002	NP_001993	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor	188	C-type lectin.|Extracellular (Potential).				positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0																		---	---	---	---
LRRC8E	80131	broad.mit.edu	37	19	7965621	7965621	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7965621G>A	uc002mir.2	+	3	2315	c.2214G>A	c.(2212-2214)TCG>TCA	p.S738S		NM_025061	NP_079337	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member	738	LRR 10.					integral to membrane				lung(1)|pancreas(1)	2																		---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8550540	8550540	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8550540C>T	uc010dwe.2	+	14	1308	c.1228C>T	c.(1228-1230)CGC>TGC	p.R410C	HNRNPM_uc010xke.1_Missense_Mutation_p.R356C|HNRNPM_uc010dwd.2_Missense_Mutation_p.R371C|HNRNPM_uc002mka.2_Missense_Mutation_p.R275C|HNRNPM_uc002mkb.1_5'Flank	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	410	27 X 6 AA repeats of [GEVSTPAN]-[ILMV]- [DE]-[RH]-[MLVI]-[GAV].|2.				alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
MBD3L1	85509	broad.mit.edu	37	19	8953580	8953580	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8953580G>A	uc002mko.2	+	1	312	c.226G>A	c.(226-228)GCT>ACT	p.A76T		NM_145208	NP_660209	Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like	76	Transcription repressor.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9047875	9047875	+	Silent	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9047875A>C	uc002mkp.2	-	5	33960	c.33756T>G	c.(33754-33756)ACT>ACG	p.T11252T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11254	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	9061285	9061285	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9061285A>C	uc002mkp.2	-	3	26365	c.26161T>G	c.(26161-26163)TCA>GCA	p.S8721A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8723	Ser-rich.|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	9085145	9085145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9085145C>T	uc002mkp.2	-	1	6874	c.6670G>A	c.(6670-6672)GCA>ACA	p.A2224T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2224	Ser-rich.|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																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10071325	10071325	+	Splice_Site	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10071325A>G	uc002mmq.1	-	66	5177	c.5091_splice	c.e66+1	p.R1697_splice		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)															---	---	---	---
PPAN-P2RY11	692312	broad.mit.edu	37	19	10220665	10220665	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10220665C>A	uc002mna.2	+	7	667	c.667C>A	c.(667-669)CGC>AGC	p.R223S	PPAN-P2RY11_uc010xla.1_Missense_Mutation_p.R223S|P2RY11_uc002mnc.2_5'Flank|PPAN_uc002mmz.1_Missense_Mutation_p.R223S|PPAN_uc002mnb.1_Missense_Mutation_p.R170S	NM_001040664	NP_001035754	Q9NQ55	SSF1_HUMAN	PPAN-P2RY11 protein	223	Brix.				RNA splicing	nucleolus	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)															---	---	---	---
CDC37	11140	broad.mit.edu	37	19	10503997	10503997	+	Missense_Mutation	SNP	G	A	A	rs143134175		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10503997G>A	uc002mof.1	-	6	963	c.847C>T	c.(847-849)CGC>TGC	p.R283C	CDC37_uc002moe.1_Missense_Mutation_p.R238C|CDC37_uc010dxf.1_Missense_Mutation_p.R120C|CDC37_uc002mog.1_Intron|CDC37_uc002moh.2_Missense_Mutation_p.R283C	NM_007065	NP_008996	Q16543	CDC37_HUMAN	cell division cycle 37 protein	283					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)														---	---	---	---
SLC44A2	57153	broad.mit.edu	37	19	10738420	10738420	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10738420T>C	uc002mpf.2	+	3	248	c.109T>C	c.(109-111)TGT>CGT	p.C37R	SLC44A2_uc002mpe.3_Missense_Mutation_p.C35R	NM_020428	NP_065161	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 1	37	Helical; (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)													---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11577547	11577547	+	Silent	SNP	G	A	A	rs144461011		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11577547G>A	uc002mry.1	-	2	485	c.105C>T	c.(103-105)GAC>GAT	p.D35D	ELAVL3_uc002mrx.1_Silent_p.D35D	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1	35					cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ZNF44	51710	broad.mit.edu	37	19	12384634	12384634	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12384634A>G	uc010xmj.1	-	5	785	c.580T>C	c.(580-582)TGT>CGT	p.C194R	ZNF44_uc002mtl.2_Intron|ZNF44_uc010dyr.1_Intron|ZNF44_uc010xmi.1_RNA|ZNF44_uc002mtn.3_RNA|ZNF44_uc010dys.2_Missense_Mutation_p.C146R	NM_001164276	NP_001157748	P15621	ZNF44_HUMAN	zinc finger protein 44 isoform 1	194	C2H2-type 1; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)														---	---	---	---
ZNF490	57474	broad.mit.edu	37	19	12721453	12721453	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12721453G>T	uc002mtz.2	-	1	171	c.42C>A	c.(40-42)CCC>CCA	p.P14P	ZNF791_uc002mua.2_5'Flank|ZNF791_uc010xml.1_5'Flank|ZNF791_uc010dyu.1_5'Flank|ZNF791_uc010xmm.1_5'Flank	NM_020714	NP_065765	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	14					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ASNA1	439	broad.mit.edu	37	19	12856282	12856282	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12856282A>C	uc002muv.2	+	3	415	c.401A>C	c.(400-402)GAG>GCG	p.E134A	ASNA1_uc002muw.2_Missense_Mutation_p.E133A	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	134					response to arsenic-containing substance	endoplasmic reticulum|nucleolus|soluble fraction	arsenite-transporting ATPase activity|ATP binding|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)													---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12984646	12984646	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12984646G>A	uc002mvm.2	+	26	3803	c.3675G>A	c.(3673-3675)ACG>ACA	p.T1225T		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1225					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
EMR2	30817	broad.mit.edu	37	19	14863294	14863294	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14863294G>A	uc002mzp.1	-	15	2091	c.1635C>T	c.(1633-1635)AGC>AGT	p.S545S	EMR2_uc010dzs.1_Silent_p.S4S|EMR2_uc010xnw.1_Silent_p.S487S|EMR2_uc002mzo.1_Silent_p.S534S|EMR2_uc002mzq.1_Silent_p.S485S|EMR2_uc002mzr.1_Silent_p.S496S|EMR2_uc002mzs.1_Silent_p.S403S|EMR2_uc002mzt.1_Silent_p.S441S|EMR2_uc002mzu.1_Silent_p.S452S|EMR2_uc010xnx.1_RNA|EMR2_uc010xny.1_RNA	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	545	Helical; Name=1; (Potential).				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																		---	---	---	---
EMR2	30817	broad.mit.edu	37	19	14876537	14876537	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14876537G>A	uc002mzp.1	-	8	1170	c.714C>T	c.(712-714)TGC>TGT	p.C238C	EMR2_uc010dzs.1_5'Flank|EMR2_uc010xnw.1_Silent_p.C238C|EMR2_uc002mzo.1_Silent_p.C238C|EMR2_uc002mzq.1_Silent_p.C189C|EMR2_uc002mzr.1_Silent_p.C189C|EMR2_uc002mzs.1_Intron|EMR2_uc002mzt.1_Silent_p.C145C|EMR2_uc002mzu.1_Silent_p.C145C|EMR2_uc010xnx.1_RNA|EMR2_uc010xny.1_RNA	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	238	EGF-like 5; calcium-binding (Potential).|Extracellular (Potential).				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	p.C238S(1)		lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
OR10H1	26539	broad.mit.edu	37	19	15918305	15918305	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15918305C>T	uc002nbq.2	-	1	632	c.543G>A	c.(541-543)GTG>GTA	p.V181V		NM_013940	NP_039228	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
USE1	55850	broad.mit.edu	37	19	17327060	17327060	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17327060C>T	uc002nfo.2	+	4	374	c.314C>T	c.(313-315)GCC>GTC	p.A105V	USE1_uc002nfn.2_Missense_Mutation_p.A105V|USE1_uc010eal.1_Missense_Mutation_p.A105V	NM_018467	NP_060937	Q9NZ43	USE1_HUMAN	unconventional SNARE in the ER 1 homolog	105	Cytoplasmic (Potential).				lysosomal transport|protein catabolic process|protein transport|secretion by cell|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	protein binding				0																		---	---	---	---
GTPBP3	84705	broad.mit.edu	37	19	17450245	17450245	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17450245C>T	uc010eas.2	+	7	876	c.811C>T	c.(811-813)CGG>TGG	p.R271W	GTPBP3_uc010xpo.1_Missense_Mutation_p.R293W|GTPBP3_uc010ear.1_RNA|GTPBP3_uc002ngh.3_Missense_Mutation_p.R271W|GTPBP3_uc002ngg.3_Missense_Mutation_p.R303W|GTPBP3_uc002ngi.3_5'UTR	NM_032620	NP_116009	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial) isoform V	271					tRNA modification	mitochondrion	GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
KCNN1	3780	broad.mit.edu	37	19	18085948	18085948	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18085948G>A	uc002nht.2	+	4	760	c.450G>A	c.(448-450)ACG>ACA	p.T150T	KCNN1_uc010xqa.1_Silent_p.T150T	NM_002248	NP_002239	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance	150	Helical; Name=Segment S2; (Potential).				synaptic transmission	voltage-gated potassium channel complex	calmodulin binding|small conductance calcium-activated potassium channel activity				0																		---	---	---	---
MAST3	23031	broad.mit.edu	37	19	18242839	18242839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18242839G>A	uc002nhz.3	+	14	1466	c.1466G>A	c.(1465-1467)CGT>CAT	p.R489H		NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase	489	Protein kinase.						ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18876319	18876319	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18876319C>A	uc002nkb.3	+	9	1080	c.992C>A	c.(991-993)CCG>CAG	p.P331Q	CRTC1_uc010ebv.2_Missense_Mutation_p.P347Q|CRTC1_uc010ebw.2_Missense_Mutation_p.P196Q|CRTC1_uc002nkc.3_Missense_Mutation_p.P196Q	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform	331	Ser-rich.				interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519																		---	---	---	---
SFRS14	10147	broad.mit.edu	37	19	19136411	19136411	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19136411T>A	uc002nkx.2	-	3	892	c.746A>T	c.(745-747)AAT>ATT	p.N249I	SFRS14_uc002nkz.1_Missense_Mutation_p.N263I|SFRS14_uc002nla.1_Missense_Mutation_p.N249I|SFRS14_uc002nlb.2_Missense_Mutation_p.N249I|SFRS14_uc010xqk.1_Intron	NM_014884	NP_055699	Q8IX01	SUGP2_HUMAN	splicing factor, arginine/serine-rich 14	249					mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)															---	---	---	---
NCAN	1463	broad.mit.edu	37	19	19329855	19329855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19329855G>A	uc002nlz.2	+	3	304	c.205G>A	c.(205-207)GCA>ACA	p.A69T		NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	69	Ig-like V-type.				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)															---	---	---	---
ZNF101	94039	broad.mit.edu	37	19	19790896	19790896	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19790896T>C	uc002nni.1	+	4	1208	c.1098T>C	c.(1096-1098)TAT>TAC	p.Y366Y	ZNF101_uc010ecg.1_Silent_p.Y246Y|ZNF101_uc002nnj.1_Silent_p.Y246Y	NM_033204	NP_149981	Q8IZC7	ZN101_HUMAN	zinc finger protein 101	366	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33535190	33535190	+	Silent	SNP	G	A	A	rs140849987		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33535190G>A	uc002nuf.2	-	2	216	c.150C>T	c.(148-150)GCC>GCT	p.A50A	RHPN2_uc010xro.1_5'UTR	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	50	REM.|Interaction with Rho.				signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33585180	33585180	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33585180G>A	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
GPI	2821	broad.mit.edu	37	19	34868778	34868778	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34868778G>A	uc002nvg.1	+	6	728	c.625G>A	c.(625-627)GCC>ACC	p.A209T	GPI_uc002nvf.2_Missense_Mutation_p.A248T|GPI_uc010xrv.1_Missense_Mutation_p.A220T|GPI_uc010xrw.1_Missense_Mutation_p.A181T|GPI_uc010edl.1_Missense_Mutation_p.A209T	NM_000175	NP_000166	P06744	G6PI_HUMAN	glucose phosphate isomerase	209					angiogenesis|gluconeogenesis|glycolysis|hemostasis|humoral immune response	cytosol|extracellular space|nucleus|plasma membrane	cytokine activity|glucose-6-phosphate isomerase activity|growth factor activity			ovary(1)|kidney(1)	2	Esophageal squamous(110;0.162)																	---	---	---	---
ZNF599	148103	broad.mit.edu	37	19	35251100	35251100	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35251100C>T	uc010edn.1	-	4	994	c.606G>A	c.(604-606)ACG>ACA	p.T202T	ZNF599_uc010edm.1_Silent_p.T165T	NM_001007248	NP_001007249	Q96NL3	ZN599_HUMAN	zinc finger protein 599	202	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38939370	38939370	+	Missense_Mutation	SNP	G	A	A	rs138647682		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38939370G>A	uc002oit.2	+	11	1169	c.1039G>A	c.(1039-1041)GTG>ATG	p.V347M	RYR1_uc002oiu.2_Missense_Mutation_p.V347M	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	347	Cytoplasmic.|MIR 5.				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)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38948733	38948733	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38948733G>A	uc002oit.2	+	18	2098	c.1968G>A	c.(1966-1968)ACG>ACA	p.T656T	RYR1_uc002oiu.2_Silent_p.T656T	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	656	Cytoplasmic.|B30.2/SPRY 1.				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)													---	---	---	---
LGALS7B	653499	broad.mit.edu	37	19	39281340	39281340	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39281340A>C	uc002ojf.3	+	3	124	c.107A>C	c.(106-108)AAC>ACC	p.N36T		NM_001042507	NP_001035972	P47929	LEG7_HUMAN	galectin-7B	36	Galectin.				apoptosis|heterophilic cell-cell adhesion	cytoplasm|extracellular space|nucleus	sugar binding				0																		---	---	---	---
IL28A	282616	broad.mit.edu	37	19	39760138	39760138	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39760138G>A	uc002oku.1	+	4	333	c.281G>A	c.(280-282)CGC>CAC	p.R94H		NM_172138	NP_742150	Q8IZJ0	IL28A_HUMAN	interleukin 28A precursor	94					response to virus	extracellular space	cytokine activity			ovary(1)|skin(1)	2	all_cancers(60;1.85e-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;5.39e-26)|all cancers(26;4.1e-23)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)															---	---	---	---
TIMM50	92609	broad.mit.edu	37	19	39976416	39976416	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39976416T>C	uc002olu.1	+	6	903	c.770T>C	c.(769-771)CTC>CCC	p.L257P	TIMM50_uc002olt.1_RNA|TIMM50_uc002olv.1_5'UTR	NM_001001563	NP_001001563	Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50	154	Mitochondrial intermembrane (Potential).|FCP1 homology.				mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport	integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck	interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding			ovary(1)	1	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)															---	---	---	---
ZNF780B	163131	broad.mit.edu	37	19	40542152	40542152	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40542152T>C	uc002omu.2	-	5	679	c.614A>G	c.(613-615)CAC>CGC	p.H205R	ZNF780B_uc002omv.2_Missense_Mutation_p.H57R	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	205	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)																	---	---	---	---
LTBP4	8425	broad.mit.edu	37	19	41111033	41111033	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41111033T>C	uc002ooh.1	+	5	544	c.544T>C	c.(544-546)TTG>CTG	p.L182L	LTBP4_uc002oog.1_Silent_p.L145L|LTBP4_uc002ooi.1_Silent_p.L115L	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding	182					growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41916646	41916646	+	Silent	SNP	C	T	T	rs138025447	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41916646C>T	uc002oqq.2	+	2	242	c.213C>T	c.(211-213)AAC>AAT	p.N71N	CYP2F1_uc010xvw.1_Intron|BCKDHA_uc002oqm.3_Silent_p.N105N|BCKDHA_uc002oqp.1_Translation_Start_Site|BCKDHA_uc002oqr.2_Silent_p.N71N|BCKDHA_uc010xvz.1_Silent_p.N49N	NM_000709	NP_000700	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha	71					branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
ZNF574	64763	broad.mit.edu	37	19	42585199	42585199	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42585199G>A	uc002osm.3	+	2	2610	c.2441G>A	c.(2440-2442)CGC>CAC	p.R814H	ZNF574_uc002osk.3_Missense_Mutation_p.R904H	NM_022752	NP_073589	Q6ZN55	ZN574_HUMAN	zinc finger protein 574	814	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.059)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43375919	43375919	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43375919G>T	uc002ovb.2	-	3	847	c.709C>A	c.(709-711)CCG>ACG	p.P237T	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.P237T|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Missense_Mutation_p.P237T|PSG1_uc010eio.1_Missense_Mutation_p.P237T|PSG1_uc002oux.1_Missense_Mutation_p.P166T|PSG1_uc002ouy.1_Missense_Mutation_p.H237N|PSG1_uc002ouz.1_Missense_Mutation_p.P237T|PSG1_uc002ova.1_Intron|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Missense_Mutation_p.P237T	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	237					female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
XRCC1	7515	broad.mit.edu	37	19	44058886	44058886	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44058886C>T	uc002owt.2	-	4	446	c.326G>A	c.(325-327)CGC>CAC	p.R109H	XRCC1_uc010xwp.1_Missense_Mutation_p.R78H	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1	109					base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)											Other_BER_factors					---	---	---	---
SPACA4	171169	broad.mit.edu	37	19	49110225	49110225	+	5'UTR	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49110225G>A	uc002pjo.2	+	1					FAM83E_uc002pjn.2_Intron	NM_133498	NP_598005			sperm acrosomal membrane protein 14 precursor						cell adhesion	acrosomal vesicle|anchored to membrane|plasma membrane				central_nervous_system(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;9.98e-05)|all cancers(93;0.000112)|GBM - Glioblastoma multiforme(486;0.00615)|Epithelial(262;0.0155)														---	---	---	---
DHDH	27294	broad.mit.edu	37	19	49442913	49442913	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49442913C>T	uc002ple.1	+	4	614	c.574C>T	c.(574-576)CAG>TAG	p.Q192*		NM_014475	NP_055290	Q9UQ10	DHDH_HUMAN	dimeric dihydrodiol dehydrogenase	192					carbohydrate metabolic process		binding|D-xylose 1-dehydrogenase (NADP+) activity|electron carrier activity|NAD(P)+ transhydrogenase activity|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity				0		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)														---	---	---	---
VRK3	51231	broad.mit.edu	37	19	50482394	50482394	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50482394C>T	uc002prg.2	-	14	1480	c.1382G>A	c.(1381-1383)CGT>CAT	p.R461H	VRK3_uc002prh.1_Missense_Mutation_p.R461H|VRK3_uc002pri.1_Missense_Mutation_p.R411H|VRK3_uc010ens.2_Missense_Mutation_p.R461H|VRK3_uc010ybl.1_Missense_Mutation_p.R411H|VRK3_uc010ybm.1_Missense_Mutation_p.R230H	NM_016440	NP_057524	Q8IV63	VRK3_HUMAN	vaccinia related kinase 3 isoform 1	461						nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)														---	---	---	---
NAPSA	9476	broad.mit.edu	37	19	50861861	50861861	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50861861G>A	uc002prx.2	-	9	1265	c.1212C>T	c.(1210-1212)CGC>CGT	p.R404R	NR1H2_uc002prv.3_Intron	NM_004851	NP_004842	O96009	NAPSA_HUMAN	napsin A preproprotein	404					proteolysis	extracellular region	aspartic-type endopeptidase activity				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0183)														---	---	---	---
KLK4	9622	broad.mit.edu	37	19	51410327	51410327	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51410327G>C	uc002pua.1	-	5	628	c.628C>G	c.(628-630)CCC>GCC	p.P210A	KLK4_uc002pty.1_3'UTR|KLK4_uc002ptz.1_RNA|KLK4_uc002pub.1_Missense_Mutation_p.P115A|KLK4_uc002puc.1_RNA	NM_004917	NP_004908	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4 preproprotein	210	Peptidase S1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)														---	---	---	---
KLK8	11202	broad.mit.edu	37	19	51503767	51503767	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51503767G>A	uc002pur.1	-	3	322	c.143C>T	c.(142-144)GCG>GTG	p.A48V	KLK9_uc002puw.1_RNA|KLK8_uc002puq.1_Missense_Mutation_p.A93V|KLK8_uc002pus.1_Intron|KLK8_uc002put.1_Intron|KLK8_uc002puu.1_Missense_Mutation_p.A48V|KLK9_uc002puv.1_Intron	NM_007196	NP_009127	O60259	KLK8_HUMAN	kallikrein 8 isoform 1 preproprotein	48	Peptidase S1.				cell death|keratinocyte proliferation|memory|negative regulation of axon regeneration|negative regulation of myelination|neuron projection morphogenesis|proteolysis|regulation of synapse organization|response to wounding	cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)														---	---	---	---
KLK8	11202	broad.mit.edu	37	19	51503984	51503984	+	Intron	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51503984G>A	uc002pur.1	-						KLK9_uc002puw.1_Intron|KLK8_uc002puq.1_Intron|KLK8_uc002pus.1_Intron|KLK8_uc002put.1_Intron|KLK8_uc002puu.1_Intron|KLK9_uc002puv.1_Intron	NM_007196	NP_009127			kallikrein 8 isoform 1 preproprotein						cell death|keratinocyte proliferation|memory|negative regulation of axon regeneration|negative regulation of myelination|neuron projection morphogenesis|proteolysis|regulation of synapse organization|response to wounding	cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)														---	---	---	---
FPR1	2357	broad.mit.edu	37	19	52249649	52249649	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52249649A>G	uc002pxq.2	-	2	694	c.599T>C	c.(598-600)GTG>GCG	p.V200A		NM_002029	NP_002020	P21462	FPR1_HUMAN	formyl peptide receptor 1	200	Extracellular (Potential).				activation of MAPK activity|cellular component movement|chemotaxis|G-protein signaling, coupled to cAMP nucleotide second messenger|nitric oxide mediated signal transduction	endosome|integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)|lung(1)|skin(1)	3		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)													---	---	---	---
ZNF808	388558	broad.mit.edu	37	19	53056872	53056872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53056872G>A	uc010epq.1	+	5	880	c.703G>A	c.(703-705)GAG>AAG	p.E235K	ZNF808_uc002pzq.2_RNA|ZNF808_uc010epr.1_5'Flank	NM_001039886	NP_001034975	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	235	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)														---	---	---	---
ZNF701	55762	broad.mit.edu	37	19	53085780	53085780	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53085780C>A	uc002pzs.1	+	4	595	c.468C>A	c.(466-468)CCC>CCA	p.P156P	ZNF701_uc010ydn.1_Silent_p.P222P	NM_018260	NP_060730	Q9NV72	ZN701_HUMAN	zinc finger protein 701	156					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)														---	---	---	---
ZNF611	81856	broad.mit.edu	37	19	53217351	53217351	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53217351G>A	uc002pzz.2	-	6	424	c.107C>T	c.(106-108)GCA>GTA	p.A36V	ZNF611_uc010eqc.2_5'UTR|ZNF611_uc010ydo.1_Intron|ZNF611_uc010ydr.1_Intron|ZNF611_uc010ydp.1_Missense_Mutation_p.A36V|ZNF611_uc010ydq.1_Missense_Mutation_p.A36V|ZNF611_uc002qaa.3_5'UTR	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	36	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)														---	---	---	---
VN1R2	317701	broad.mit.edu	37	19	53762612	53762612	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53762612C>T	uc002qbi.2	+	1	1068	c.984C>T	c.(982-984)TAC>TAT	p.Y328Y		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	328	Helical; Name=6; (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)														---	---	---	---
VN1R2	317701	broad.mit.edu	37	19	53762736	53762736	+	Missense_Mutation	SNP	C	A	A	rs141012802	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53762736C>A	uc002qbi.2	+	1	1192	c.1108C>A	c.(1108-1110)CGT>AGT	p.R370S		NM_173856	NP_776255	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	370	Cytoplasmic (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity				0				GBM - Glioblastoma multiforme(134;0.00301)														---	---	---	---
LILRB5	10990	broad.mit.edu	37	19	54758702	54758702	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54758702G>A	uc002qex.2	-	6	1262	c.1151C>T	c.(1150-1152)CCT>CTT	p.P384L	LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.P375L|LILRB5_uc002qey.2_Missense_Mutation_p.P384L|LILRB5_uc002qez.2_Missense_Mutation_p.P284L|LILRB5_uc002qfa.1_Missense_Mutation_p.P274L|LILRB5_uc010yes.1_RNA	NM_006840	NP_006831	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor,	384	Ig-like C2-type 4.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity			ovary(1)|pancreas(1)	2	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
LAIR2	3904	broad.mit.edu	37	19	55019409	55019409	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55019409T>C	uc002qgc.2	+						LAIR2_uc002qgd.2_Intron|LAIR2_uc010erl.2_Intron	NM_002288	NP_002279			leukocyte-associated immunoglobulin-like							extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55253679	55253679	+	Silent	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55253679C>A	uc002qgv.2	+	3	342	c.324C>A	c.(322-324)CCC>CCA	p.P108P	KIR2DL3_uc002qgx.2_Silent_p.P108P|KIR2DL3_uc002qgy.2_Silent_p.P108P|KIR2DL3_uc010erw.1_Silent_p.P108P|KIR2DL1_uc002qgz.1_Silent_p.P18P|KIR2DL3_uc002qha.1_RNA	NM_015868	NP_056952	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two	108	Extracellular (Potential).				immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55489190	55489190	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55489190A>C	uc002qij.2	+	4	482	c.396A>C	c.(394-396)CAA>CAC	p.Q132H	NLRP2_uc010yfp.1_Missense_Mutation_p.Q109H|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Missense_Mutation_p.Q132H|NLRP2_uc010esp.2_Missense_Mutation_p.Q132H	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	132					apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)														---	---	---	---
TMEM190	147744	broad.mit.edu	37	19	55889219	55889219	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55889219C>T	uc002qkt.1	+	4	288	c.270C>T	c.(268-270)GGC>GGT	p.G90G		NM_139172	NP_631911	Q8WZ59	TM190_HUMAN	transmembrane protein 190 precursor	90	Helical; (Potential).					integral to membrane					0	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)														---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56244332	56244332	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56244332G>A	uc002qly.2	-	2	893	c.865C>T	c.(865-867)CAT>TAT	p.H289Y		NM_176820	NP_789790	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	289	NACHT.					cytoplasm	ATP binding			skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)														---	---	---	---
ZNF667	63934	broad.mit.edu	37	19	56953331	56953331	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56953331G>T	uc002qnd.2	-	5	1195	c.1033C>A	c.(1033-1035)CTG>ATG	p.L345M	ZNF667_uc010etl.2_Missense_Mutation_p.L127M|ZNF667_uc002qne.2_Missense_Mutation_p.L345M|ZNF667_uc010etm.2_Missense_Mutation_p.L288M	NM_022103	NP_071386	Q5HYK9	ZN667_HUMAN	zinc finger protein 667	345	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)														---	---	---	---
ZNF548	147694	broad.mit.edu	37	19	57910578	57910578	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57910578C>T	uc002qom.2	+	3	1173	c.923C>T	c.(922-924)CCG>CTG	p.P308L	ZNF547_uc002qpm.3_Intron|ZNF548_uc002qon.2_Missense_Mutation_p.P311L	NM_152909	NP_690873	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	308					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58723003	58723003	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58723003C>T	uc002qrq.1	+	9	1389	c.930C>T	c.(928-930)ACC>ACT	p.T310T	ZNF274_uc002qrr.1_Silent_p.T278T|ZNF274_uc002qrs.1_Silent_p.T205T|ZNF274_uc010eum.1_Silent_p.T69T	NM_133502	NP_598009	Q96GC6	ZN274_HUMAN	zinc finger protein 274 isoform c	310	KRAB 2.				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)														---	---	---	---
ZSCAN22	342945	broad.mit.edu	37	19	58850019	58850019	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58850019C>A	uc002qsc.2	+	3	950	c.803C>A	c.(802-804)TCC>TAC	p.S268Y	ZSCAN22_uc010yhz.1_Missense_Mutation_p.P263T	NM_181846	NP_862829	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	268	C2H2-type 1.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)														---	---	---	---
ZNF324	25799	broad.mit.edu	37	19	58980632	58980632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58980632G>A	uc002qsw.1	+	2	174	c.80G>A	c.(79-81)CGC>CAC	p.R27H	ZNF324_uc002qsx.1_5'Flank	NM_014347	NP_055162	O75467	Z324A_HUMAN	zinc finger protein 324	27	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
PDYN	5173	broad.mit.edu	37	20	1961558	1961558	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1961558C>A	uc010gaj.2	-	3	418	c.176G>T	c.(175-177)TGG>TTG	p.W59L	uc002wfu.1_Intron|PDYN_uc002wfv.2_Missense_Mutation_p.W59L|PDYN_uc010zpt.1_Intron	NM_024411	NP_077722	P01213	PDYN_HUMAN	beta-neoendorphin-dynorphin preproprotein	59					cell death|neuropeptide signaling pathway|synaptic transmission	extracellular region|plasma membrane	opioid peptide activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2593878	2593878	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2593878G>A	uc002wgf.1	+	14	1797	c.1782G>A	c.(1780-1782)ACG>ACA	p.T594T	TMC2_uc002wgg.1_Silent_p.T578T|TMC2_uc010zpw.1_Silent_p.T426T|TMC2_uc010zpx.1_Silent_p.T425T	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	594	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3																		---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13071839	13071839	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13071839C>A	uc002wod.1	+	5	1005	c.716C>A	c.(715-717)CCA>CAA	p.P239Q		NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base	239					sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13273089	13273089	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13273089G>A	uc010gce.1	+	5	862	c.856G>A	c.(856-858)GCC>ACC	p.A286T	TASP1_uc010zri.1_Intron	NM_080826	NP_543016	B1AKI9	ISM1_HUMAN	isthmin 1 homolog precursor	286						extracellular region					0																		---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13971151	13971151	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13971151T>C	uc010gcf.2	-	1	112	c.30A>G	c.(28-30)ATA>ATG	p.I10M	SEL1L2_uc002woq.3_Translation_Start_Site|SEL1L2_uc010zrl.1_Missense_Mutation_p.I10M|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 precursor	10						integral to membrane	binding			ovary(2)	2																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	13976403	13976403	+	Translation_Start_Site	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13976403C>T	uc002wou.2	+	1	258	c.-6C>T	c.(-8--4)CACGG>CATGG		MACROD2_uc002wot.2_Translation_Start_Site|SEL1L2_uc002wor.2_5'Flank|MACROD2_uc002wos.2_RNA	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17434530	17434530	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17434530C>T	uc002wpm.2	+	9	1349	c.1029C>T	c.(1027-1029)TAC>TAT	p.Y343Y	PCSK2_uc002wpl.2_Silent_p.Y324Y|PCSK2_uc010zrm.1_Silent_p.Y308Y	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	343	Catalytic.				enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity	p.Y343Y(1)		ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17462302	17462302	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17462302C>T	uc002wpm.2	+	12	1824	c.1504C>T	c.(1504-1506)CGC>TGC	p.R502C	PCSK2_uc002wpl.2_Missense_Mutation_p.R483C|PCSK2_uc010zrm.1_Missense_Mutation_p.R467C|PCSK2_uc002wpn.2_Missense_Mutation_p.R156C	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	502					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
SNX5	27131	broad.mit.edu	37	20	17937586	17937586	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17937586C>T	uc002wqc.2	-	2	233	c.147G>A	c.(145-147)GTG>GTA	p.V49V	SNX5_uc002wqb.2_RNA|SNX5_uc002wqd.2_Silent_p.V49V|SNX5_uc002wqe.2_5'UTR|SNX5_uc010zrt.1_Silent_p.V49V	NM_014426	NP_055241	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	49	PX.				cell communication|pinocytosis|protein transport	cytoplasmic vesicle membrane|early endosome membrane|extrinsic to endosome membrane|extrinsic to internal side of plasma membrane|macropinocytic cup|phagocytic cup|ruffle	phosphatidylinositol binding			large_intestine(1)	1																		---	---	---	---
C20orf72	92667	broad.mit.edu	37	20	17956339	17956339	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17956339A>G	uc002wqh.2	+	3	606	c.524A>G	c.(523-525)CAA>CGA	p.Q175R	C20orf72_uc010gco.2_Intron|C20orf72_uc010gcp.2_RNA	NM_052865	NP_443097	Q9BQP7	CT072_HUMAN	hypothetical protein LOC92667	175											0																		---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18529376	18529376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18529376C>T	uc002wqz.1	+	16	2310	c.1867C>T	c.(1867-1869)CCC>TCC	p.P623S	SEC23B_uc002wra.1_Missense_Mutation_p.P623S|SEC23B_uc002wrb.1_Missense_Mutation_p.P623S|SEC23B_uc010zsb.1_Missense_Mutation_p.P605S|SEC23B_uc002wrc.1_Missense_Mutation_p.P623S	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B	623					ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20493316	20493316	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20493316C>T	uc002wrz.2	-	32	4840	c.4697G>A	c.(4696-4698)CGC>CAC	p.R1566H	RALGAPA2_uc010gcx.2_Missense_Mutation_p.R1270H|RALGAPA2_uc010zsg.1_Missense_Mutation_p.R1014H|RALGAPA2_uc002wsa.1_Missense_Mutation_p.R338H	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1566					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
GGTLC1	92086	broad.mit.edu	37	20	23965921	23965921	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23965921C>T	uc002wts.2	-	6	743	c.610G>A	c.(610-612)GTC>ATC	p.V204I	GGTLC1_uc002wtu.2_Missense_Mutation_p.V204I	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	204							gamma-glutamyltransferase activity			ovary(1)	1																		---	---	---	---
HM13	81502	broad.mit.edu	37	20	30155873	30155873	+	Intron	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30155873T>A	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwf.2_Intron|HM13_uc010gdu.2_Intron	NM_030789	NP_110416			minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
HCK	3055	broad.mit.edu	37	20	30659469	30659469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30659469G>A	uc002wxh.2	+	2	238	c.67G>A	c.(67-69)GGG>AGG	p.G23R	HCK_uc010gdy.2_Missense_Mutation_p.G2R|HCK_uc002wxi.2_Missense_Mutation_p.G2R	NM_002110	NP_002101	P08631	HCK_HUMAN	hemopoietic cell kinase isoform p61HCK	23				G->A: Myristoylation and palmitoylation are abolished, cytoplasmic and no calveolar localization; in isoform p59- HCK.	interspecies interaction between organisms|mesoderm development|regulation of defense response to virus by virus|viral reproduction	caveola|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1)	9			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
CDK5RAP1	51654	broad.mit.edu	37	20	31984872	31984872	+	5'UTR	SNP	G	T	T	rs150574173	by1000genomes	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31984872G>T	uc010gek.2	-	2					CDK5RAP1_uc002wyy.2_Intron|CDK5RAP1_uc002wyz.2_5'UTR|CDK5RAP1_uc002wza.2_5'UTR|CDK5RAP1_uc010gel.2_Intron|CDK5RAP1_uc010gem.2_5'UTR|CDK5RAP1_uc002wzc.1_5'UTR|CDK5RAP1_uc010gen.2_5'UTR	NM_016408	NP_057492			CDK5 regulatory subunit associated protein 1						brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
KIAA0406	9675	broad.mit.edu	37	20	36640099	36640099	+	Missense_Mutation	SNP	C	T	T	rs141770247	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36640099C>T	uc002xhl.2	-	3	2329	c.2120G>A	c.(2119-2121)CGT>CAT	p.R707H	KIAA0406_uc002xhm.2_Missense_Mutation_p.R707H	NM_014657	NP_055472	O43156	TTI1_HUMAN	hypothetical protein LOC9675	707							binding				0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
TOP1	7150	broad.mit.edu	37	20	39706287	39706287	+	Intron	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39706287T>C	uc002xjl.2	+						TOP1_uc010gge.1_Intron	NM_003286	NP_003277			DNA topoisomerase I						DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(3)|ovary(2)|central_nervous_system(1)|kidney(1)	7		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)			T	NUP98	AML*								---	---	---	---
TOP1	7150	broad.mit.edu	37	20	39744023	39744023	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39744023C>A	uc002xjl.2	+	16	1897	c.1651C>A	c.(1651-1653)CTA>ATA	p.L551I	uc002xjn.1_Intron	NM_003286	NP_003277	P11387	TOP1_HUMAN	DNA topoisomerase I	551					DNA topological change|interspecies interaction between organisms|phosphorylation|programmed cell death|response to drug	chromosome|nucleolus|nucleoplasm	ATP binding|chromatin DNA binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA topoisomerase type I activity|protein binding			breast(3)|ovary(2)|central_nervous_system(1)|kidney(1)	7		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Topotecan(DB01030)			T	NUP98	AML*								---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39986566	39986566	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39986566T>C	uc002xjx.2	+	17	2175	c.2084T>C	c.(2083-2085)ATG>ACG	p.M695T	LPIN3_uc010ggh.2_Missense_Mutation_p.M696T|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	695	C-LIP.				fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40033290	40033290	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40033290T>C	uc002xka.1	-	37	8269	c.8091A>G	c.(8089-8091)GAA>GAG	p.E2697E	CHD6_uc002xjz.1_Silent_p.E234E	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2697					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)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40727077	40727077	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40727077T>A	uc002xkg.2	-	27	4014	c.3830A>T	c.(3829-3831)GAG>GTG	p.E1277V	PTPRT_uc010ggj.2_Missense_Mutation_p.E1296V|PTPRT_uc010ggi.2_Missense_Mutation_p.E480V	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1277	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				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	40735471	40735471	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40735471G>A	uc002xkg.2	-	24	3529	c.3345C>T	c.(3343-3345)TGC>TGT	p.C1115C	PTPRT_uc010ggj.2_Silent_p.C1134C|PTPRT_uc010ggi.2_Silent_p.C318C	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1115	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				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)																---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43138579	43138579	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43138579G>A	uc002xme.2	-	5	700	c.566C>T	c.(565-567)TCA>TTA	p.S189L	SERINC3_uc002xmf.1_Missense_Mutation_p.S189L|SERINC3_uc010ggs.1_Missense_Mutation_p.S182L|SERINC3_uc010zwp.1_Missense_Mutation_p.S134L	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	189	Cytoplasmic (Potential).					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)															---	---	---	---
ADA	100	broad.mit.edu	37	20	43248966	43248966	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43248966T>C	uc002xmj.2	-	11	1180	c.1052A>G	c.(1051-1053)TAT>TGT	p.Y351C	ADA_uc010ggt.2_RNA	NM_000022	NP_000013	P00813	ADA_HUMAN	adenosine deaminase	351					adenosine catabolic process|cell adhesion|hypoxanthine salvage|inosine biosynthetic process|negative regulation of adenosine receptor signaling pathway|purine nucleotide salvage|purine ribonucleoside monophosphate biosynthetic process|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation	cell junction|cytoplasmic membrane-bounded vesicle lumen|cytosol|external side of plasma membrane|lysosome	adenosine deaminase activity|protein binding|zinc ion binding			pancreas(2)|ovary(1)	3		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Cladribine(DB00242)|Dipyridamole(DB00975)|Erythromycin(DB00199)|Fludarabine(DB01073)|Idoxuridine(DB00249)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)									Adenosine_Deaminase_Deficiency				---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	45003869	45003869	+	Intron	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45003869A>G	uc002xrt.1	-						ELMO2_uc010zxq.1_Intron|ELMO2_uc002xrs.1_Intron|ELMO2_uc002xru.1_Intron|ELMO2_uc010zxr.1_Intron|ELMO2_uc010zxs.1_Intron|ELMO2_uc002xrv.1_Intron|ELMO2_uc002xrw.2_Intron	NM_133171	NP_573403			engulfment and cell motility 2						apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47266542	47266542	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47266542G>A	uc002xtw.1	-	24	3043	c.3020C>T	c.(3019-3021)CCG>CTG	p.P1007L	PREX1_uc002xtv.1_Missense_Mutation_p.P304L	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1007					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47879934	47879934	+	Silent	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47879934T>C	uc002xui.2	-	6	2485	c.2238A>G	c.(2236-2238)GAA>GAG	p.E746E		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	746							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
SPATA2	9825	broad.mit.edu	37	20	48523040	48523040	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48523040G>A	uc010gie.2	-	3	1029	c.679C>T	c.(679-681)CGA>TGA	p.R227*	SPATA2_uc002xuw.2_Nonsense_Mutation_p.R227*|SPATA2_uc010zyn.1_Nonsense_Mutation_p.R90*	NM_001135773	NP_001129245	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	227					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus				central_nervous_system(1)|skin(1)	2	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)															---	---	---	---
SNAI1	6615	broad.mit.edu	37	20	48600381	48600381	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48600381T>A	uc002xuz.2	+	2	173	c.103T>A	c.(103-105)TAC>AAC	p.Y35N		NM_005985	NP_005976	O95863	SNAI1_HUMAN	snail 1 homolog	35					epithelial to mesenchymal transition|mesoderm formation|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|zinc ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)															---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49219090	49219090	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49219090C>T	uc002xvm.2	-	13	1484	c.1166G>A	c.(1165-1167)CGG>CAG	p.R389Q	FAM65C_uc010zyt.1_Missense_Mutation_p.R393Q|FAM65C_uc010zyu.1_RNA|FAM65C_uc002xvn.1_Missense_Mutation_p.R389Q	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	389										ovary(2)	2																		---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50133334	50133334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50133334G>A	uc002xwd.2	-	3	1541	c.1321C>T	c.(1321-1323)CCT>TCT	p.P441S	NFATC2_uc002xwc.2_Missense_Mutation_p.P441S|NFATC2_uc010zyv.1_Missense_Mutation_p.P222S|NFATC2_uc010zyw.1_Missense_Mutation_p.P222S|NFATC2_uc010zyx.1_Missense_Mutation_p.P421S|NFATC2_uc010zyy.1_Missense_Mutation_p.P222S|NFATC2_uc010zyz.1_Missense_Mutation_p.P222S|NFATC2_uc002xwe.2_Missense_Mutation_p.P421S	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	441	RHD.				B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58567530	58567530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58567530G>A	uc002ybe.2	+	10	1681	c.1381G>A	c.(1381-1383)GTA>ATA	p.V461I	CDH26_uc002ybf.1_Missense_Mutation_p.V41I|CDH26_uc010zzy.1_RNA|CDH26_uc002ybg.2_5'Flank	NM_177980	NP_817089	Q8IXH8	CAD26_HUMAN	cadherin-like 26 isoform a	461	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60448951	60448951	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60448951C>T	uc002ybn.1	+	7	1059	c.1045C>T	c.(1045-1047)CGA>TGA	p.R349*	CDH4_uc002ybp.1_Nonsense_Mutation_p.R275*	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	349	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60888776	60888776	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60888776C>T	uc002ycq.2	-	63	8654	c.8587G>A	c.(8587-8589)GCA>ACA	p.A2863T		NM_005560	NP_005551	O15230	LAMA5_HUMAN	laminin alpha 5 precursor	2863	Laminin G-like 1.				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60892086	60892086	+	Intron	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60892086C>T	uc002ycq.2	-							NM_005560	NP_005551			laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
C20orf195	79025	broad.mit.edu	37	20	62187305	62187305	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62187305A>G	uc002yfj.2	+	2	381	c.289A>G	c.(289-291)AGC>GGC	p.S97G	C20orf195_uc002yfk.2_Missense_Mutation_p.S97G	NM_024059	NP_076964	Q9BVV2	CT195_HUMAN	hypothetical protein LOC79025	97											0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)															---	---	---	---
ZNF512B	57473	broad.mit.edu	37	20	62595544	62595544	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62595544G>A	uc002yhl.1	-	8	1414	c.1360C>T	c.(1360-1362)CGA>TGA	p.R454*		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	454					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)																	---	---	---	---
LIPI	149998	broad.mit.edu	37	21	15561475	15561475	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15561475T>G	uc002yjm.2	-	2	385	c.375A>C	c.(373-375)GAA>GAC	p.E125D	LIPI_uc010gkw.1_Missense_Mutation_p.E58D	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	104					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)														---	---	---	---
TMPRSS15	5651	broad.mit.edu	37	21	19770545	19770545	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19770545T>C	uc002ykw.2	-	2	278	c.247A>G	c.(247-249)AAA>GAA	p.K83E		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	83	Extracellular (Potential).|SEA.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30329691	30329691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30329691C>T	uc002ymr.2	-	15	3006	c.2993G>A	c.(2992-2994)AGT>AAT	p.S998N		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	952							ligase activity|zinc ion binding				0																		---	---	---	---
CLDN17	26285	broad.mit.edu	37	21	31538770	31538770	+	Nonsense_Mutation	SNP	G	A	A	rs148594408		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31538770G>A	uc011acv.1	-	1	166	c.166C>T	c.(166-168)CGA>TGA	p.R56*		NM_012131	NP_036263	P56750	CLD17_HUMAN	claudin 17	56	Extracellular (Potential).				calcium-independent cell-cell adhesion|tight junction assembly	Golgi apparatus|integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
KRTAP19-1	337882	broad.mit.edu	37	21	31852407	31852407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31852407C>T	uc011acx.1	-	1	230	c.230G>A	c.(229-231)CGC>CAC	p.R77H		NM_181607	NP_853638	Q8IUB9	KR191_HUMAN	keratin associated protein 19-1	77	26 X 2 AA repeats of G-[YCGS].					intermediate filament					0																		---	---	---	---
IFNGR2	3460	broad.mit.edu	37	21	34809262	34809262	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34809262C>T	uc002yrp.3	+	7	1655	c.1007C>T	c.(1006-1008)ACG>ATG	p.T336M	IFNGR2_uc002yrq.3_Missense_Mutation_p.T355M|IFNGR2_uc010gma.2_Missense_Mutation_p.T257M|IFNGR2_uc002yrr.3_Missense_Mutation_p.T257M|TMEM50B_uc002yrs.1_Intron	NM_005534	NP_005525	P38484	INGR2_HUMAN	interferon gamma receptor 2 precursor	336	Cytoplasmic (Potential).				regulation of interferon-gamma-mediated signaling pathway|response to virus	endoplasmic reticulum|integral to plasma membrane	interferon-gamma receptor activity				0					Interferon gamma-1b(DB00033)													---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36171728	36171728	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36171728C>T	uc002yuh.2	-	5	2334	c.756G>A	c.(754-756)TGG>TGA	p.W252*	RUNX1_uc002yui.2_Nonsense_Mutation_p.W188*|RUNX1_uc010gmu.2_Nonsense_Mutation_p.W279*|RUNX1_uc010gmv.2_Nonsense_Mutation_p.W279*|RUNX1_uc002yuj.3_Nonsense_Mutation_p.W147*|RUNX1_uc002yuk.3_Nonsense_Mutation_p.W279*|RUNX1_uc002yul.1_Nonsense_Mutation_p.W44*|RUNX1_uc002yum.1_Nonsense_Mutation_p.W83*	NM_001001890	NP_001001890	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform	252	Pro/Ser/Thr-rich.			Missing: No DNA-binding.	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				---	---	---	---
CHAF1B	8208	broad.mit.edu	37	21	37763965	37763965	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37763965C>T	uc002yvj.2	+	4	514	c.376C>T	c.(376-378)CGG>TGG	p.R126W		NM_005441	NP_005432	Q13112	CAF1B_HUMAN	chromatin assembly factor 1 subunit B	126					cell cycle|DNA repair|DNA replication|DNA replication-dependent nucleosome assembly|protein complex assembly|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|cytoplasm	chromatin binding|histone binding|unfolded protein binding			ovary(1)|skin(1)	2																		---	---	---	---
FAM3B	54097	broad.mit.edu	37	21	42694964	42694964	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42694964G>A	uc002yzb.1	+	2	280	c.134G>A	c.(133-135)CGC>CAC	p.R45H	FAM3B_uc002yza.2_RNA|FAM3B_uc002yzc.1_Intron|FAM3B_uc002yzd.1_Missense_Mutation_p.R68H|FAM3B_uc011aeq.1_Missense_Mutation_p.R59H	NM_058186	NP_478066	P58499	FAM3B_HUMAN	family with sequence similarity 3, member B	45					apoptosis|insulin secretion	extracellular space	cytokine activity				0		Prostate(19;1.57e-07)|all_epithelial(19;0.0404)																---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43161902	43161902	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43161902C>T	uc002yzn.1	-	8	1499	c.1451G>A	c.(1450-1452)CGG>CAG	p.R484Q		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	484						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
ZNF295	49854	broad.mit.edu	37	21	43411221	43411221	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43411221T>C	uc002zab.3	-	3	3198	c.2984A>G	c.(2983-2985)AAG>AGG	p.K995R	ZNF295_uc002yzz.3_Missense_Mutation_p.K794R|ZNF295_uc002yzy.3_Missense_Mutation_p.K995R|ZNF295_uc002zaa.3_Missense_Mutation_p.K995R	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	995					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	43504209	43504209	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43504209G>T	uc002zaf.1	+	3	335	c.335G>T	c.(334-336)GGG>GTG	p.G112V	UMODL1_uc002zad.1_Missense_Mutation_p.G40V|UMODL1_uc002zae.1_Missense_Mutation_p.G40V|UMODL1_uc002zag.1_Missense_Mutation_p.G112V|UMODL1_uc010gow.1_5'Flank|UMODL1_uc002zai.1_5'Flank|UMODL1_uc010gox.1_5'Flank|UMODL1_uc010goy.1_5'Flank|UMODL1_uc002zaj.1_5'Flank|UMODL1_uc010goz.1_5'Flank	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	112	Extracellular (Potential).					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
UBASH3A	53347	broad.mit.edu	37	21	43854998	43854998	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43854998G>T	uc002zbe.2	+	10	1363	c.1327G>T	c.(1327-1329)GGG>TGG	p.G443W	UBASH3A_uc002zbf.2_Missense_Mutation_p.G405W|UBASH3A_uc010gpc.2_RNA|UBASH3A_uc010gpd.2_RNA|UBASH3A_uc010gpe.2_Missense_Mutation_p.G405W	NM_018961	NP_061834	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing,	443	Phosphatase-like.					cytosol|nucleus				ovary(3)	3																		---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46326963	46326963	+	Silent	SNP	C	T	T	rs149429459	byFrequency	TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46326963C>T	uc002zgd.2	-	3	239	c.195G>A	c.(193-195)CGG>CGA	p.R65R	ITGB2_uc002zge.2_Silent_p.R65R|ITGB2_uc002zgf.3_Silent_p.R65R|ITGB2_uc011afl.1_5'UTR|ITGB2_uc010gpw.2_Silent_p.R65R|ITGB2_uc002zgg.2_Silent_p.R65R	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	65	Extracellular (Potential).				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	46888205	46888205	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46888205G>A	uc011afs.1	+	2	1422	c.1401G>A	c.(1399-1401)CCG>CCA	p.P467P	COL18A1_uc002zhg.2_Silent_p.P52P|COL18A1_uc002zhi.2_Silent_p.P232P	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	467	TSP N-terminal.				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)														---	---	---	---
MCM3AP	8888	broad.mit.edu	37	21	47680751	47680751	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47680751G>A	uc002zir.1	-	15	3573	c.3537C>T	c.(3535-3537)CGC>CGT	p.R1179R	MCM3AP_uc002zip.1_5'Flank|MCM3AP_uc002ziq.1_Silent_p.R106R	NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	1179					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)																	---	---	---	---
CCT8L2	150160	broad.mit.edu	37	22	17073106	17073106	+	Missense_Mutation	SNP	G	A	A	rs147878859		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17073106G>A	uc002zlp.1	-	1	595	c.335C>T	c.(334-336)ACG>ATG	p.T112M		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	112					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)																---	---	---	---
TSSK2	23617	broad.mit.edu	37	22	19119321	19119321	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19119321C>T	uc002zow.2	+	1	1001	c.409C>T	c.(409-411)CTC>TTC	p.L137F	DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA	NM_053006	NP_443732	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	137	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)	1	Colorectal(54;0.0993)																	---	---	---	---
SMARCB1	6598	broad.mit.edu	37	22	24135750	24135750	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24135750C>T	uc002zyb.2	+	3	444	c.237C>T	c.(235-237)CAC>CAT	p.H79H	SMARCB1_uc002zyg.2_Silent_p.H79H|SMARCB1_uc011ajb.1_Silent_p.H70H|SMARCB1_uc002zya.2_Silent_p.H79H|SMARCB1_uc002zyc.2_Silent_p.H70H|SMARCB1_uc002zyd.2_Silent_p.H70H|SMARCB1_uc002zye.1_Silent_p.H42H|SMARCB1_uc002zyf.1_RNA|SMARCB1_uc010gue.1_Intron	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	79					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	p.?(2)		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				---	---	---	---
SMARCB1	6598	broad.mit.edu	37	22	24145518	24145518	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24145518C>T	uc002zyb.2	+	5	744	c.537C>T	c.(535-537)AAC>AAT	p.N179N	SMARCB1_uc002zya.2_Silent_p.N179N|SMARCB1_uc002zyc.2_Silent_p.N170N|SMARCB1_uc002zyd.2_Silent_p.N188N|SMARCB1_uc002zye.1_Silent_p.N105N|SMARCB1_uc002zyf.1_RNA|SMARCB1_uc010gue.1_RNA	NM_003073	NP_003064	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin	179	DNA-binding (Potential).				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	p.?(5)		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				---	---	---	---
PIWIL3	440822	broad.mit.edu	37	22	25151789	25151789	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25151789C>T	uc003abd.1	-	6	1071	c.654G>A	c.(652-654)TCG>TCA	p.S218S	PIWIL3_uc011ajx.1_Silent_p.S109S|PIWIL3_uc011ajy.1_Silent_p.S109S|PIWIL3_uc010gut.1_Silent_p.S218S	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3	218					cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
MN1	4330	broad.mit.edu	37	22	28193441	28193441	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28193441C>T	uc003adj.2	-	1	4046	c.3091G>A	c.(3091-3093)GGG>AGG	p.G1031R		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	1031							binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10								T	ETV6	AML|meningioma								---	---	---	---
MTMR3	8897	broad.mit.edu	37	22	30418067	30418067	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30418067G>A	uc003agv.3	+	18	3603	c.3275G>A	c.(3274-3276)CGC>CAC	p.R1092H	MTMR3_uc003agu.3_Intron|MTMR3_uc003agw.3_Intron	NM_021090	NP_066576	Q13615	MTMR3_HUMAN	myotubularin-related protein 3 isoform c	1092					phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)															---	---	---	---
SMTN	6525	broad.mit.edu	37	22	31495882	31495882	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31495882A>G	uc003ajl.1	+	19	2821	c.2603A>G	c.(2602-2604)GAG>GGG	p.E868G	SMTN_uc003ajk.1_Missense_Mutation_p.E868G|SMTN_uc003ajm.1_Missense_Mutation_p.E868G|SMTN_uc011ale.1_Missense_Mutation_p.E953G|SMTN_uc011alf.1_Missense_Mutation_p.E924G|SMTN_uc003ajn.1_Missense_Mutation_p.E891G|SMTN_uc011alg.1_Missense_Mutation_p.E324G|SMTN_uc003ajo.1_Missense_Mutation_p.E391G|SMTN_uc010gwe.1_Missense_Mutation_p.E248G|SMTN_uc003ajp.1_5'Flank	NM_006932	NP_008863	P53814	SMTN_HUMAN	smoothelin isoform c	868	CH.				muscle organ development|smooth muscle contraction	actin cytoskeleton|cytoplasm	actin binding|structural constituent of muscle			large_intestine(2)|pancreas(1)	3																		---	---	---	---
C1QTNF6	114904	broad.mit.edu	37	22	37578581	37578581	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37578581T>C	uc003aqw.1	-	2	932	c.427A>G	c.(427-429)ACG>GCG	p.T143A	C1QTNF6_uc003aqx.1_Missense_Mutation_p.T162A|C1QTNF6_uc003aqy.1_Missense_Mutation_p.T162A|C1QTNF6_uc003aqz.1_RNA	NM_182486	NP_872292	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	143	C1q.					collagen					0																		---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37769859	37769859	+	Silent	SNP	G	A	A	rs138855230		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37769859G>A	uc003asq.3	-	3	2502	c.1716C>T	c.(1714-1716)CCC>CCT	p.P572P		NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	572	Cytoplasmic (Potential).					cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38119208	38119208	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38119208C>T	uc003atr.2	+	7	916	c.645C>T	c.(643-645)GGC>GGT	p.G215G	TRIOBP_uc003atu.2_Silent_p.G43G|TRIOBP_uc003atq.1_Silent_p.G215G|TRIOBP_uc003ats.1_Silent_p.G43G	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	215					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38122069	38122069	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38122069G>A	uc003atr.2	+	7	3777	c.3506G>A	c.(3505-3507)CGG>CAG	p.R1169Q	TRIOBP_uc003atu.2_Missense_Mutation_p.R997Q|TRIOBP_uc003atq.1_Missense_Mutation_p.R1169Q|TRIOBP_uc003ats.1_Missense_Mutation_p.R997Q	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1169					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
GCAT	23464	broad.mit.edu	37	22	38211178	38211178	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38211178G>A	uc003atz.2	+	5	642	c.622G>A	c.(622-624)GAT>AAT	p.D208N	GCAT_uc003aua.1_Missense_Mutation_p.D234N	NM_014291	NP_055106	O75600	KBL_HUMAN	glycine C-acetyltransferase precursor	208					biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
MCHR1	2847	broad.mit.edu	37	22	41076969	41076969	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41076969G>A	uc003ayz.2	+	2	574	c.306G>A	c.(304-306)ACG>ACA	p.T102T	MCHR1_uc003aza.2_5'UTR	NM_005297	NP_005288	Q99705	MCHR1_HUMAN	G protein-coupled receptor 24	102	Extracellular (Potential).				elevation of cytosolic calcium ion concentration|feeding behavior|generation of precursor metabolites and energy|inhibition of adenylate cyclase activity by G-protein signaling pathway	integral to plasma membrane|nonmotile primary cilium	neuropeptide receptor activity				0																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41527639	41527639	+	Splice_Site	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41527639T>C	uc003azl.3	+	6	1923	c.1528_splice	c.e6+2	p.S510_splice		NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
SREBF2	6721	broad.mit.edu	37	22	42276824	42276824	+	Silent	SNP	C	T	T	rs141892188		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42276824C>T	uc003bbi.2	+	10	2035	c.1866C>T	c.(1864-1866)AAC>AAT	p.N622N	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.2_RNA	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	622	Cytoplasmic (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
RRP7A	27341	broad.mit.edu	37	22	42910211	42910211	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42910211C>T	uc003bcq.2	-	6	674	c.658G>A	c.(658-660)GCA>ACA	p.A220T	SERHL_uc011apm.1_Intron|RRP7A_uc003bcp.2_Missense_Mutation_p.A243T	NM_015703	NP_056518	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A	220							nucleotide binding|RNA binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44028036	44028036	+	Silent	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44028036G>T	uc003bdy.1	-	19	2396	c.2181C>A	c.(2179-2181)ACC>ACA	p.T727T	EFCAB6_uc003bdz.1_Silent_p.T575T|EFCAB6_uc010gzi.1_Silent_p.T575T|EFCAB6_uc010gzj.1_Silent_p.T25T|EFCAB6_uc010gzk.1_RNA	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	727					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)																---	---	---	---
ALG12	79087	broad.mit.edu	37	22	50301525	50301525	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50301525A>G	uc003biy.2	-	7	1110	c.836T>C	c.(835-837)ATC>ACC	p.I279T		NM_024105	NP_077010	Q9BV10	ALG12_HUMAN	alpha-1,6-mannosyltransferase ALG12	279	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane					0		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
CPT1B	1375	broad.mit.edu	37	22	51015369	51015369	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51015369G>C	uc003bmk.3	-	3	538	c.376C>G	c.(376-378)CAA>GAA	p.Q126E	CPT1B_uc003bml.2_Missense_Mutation_p.Q126E|CPT1B_uc003bmm.2_Missense_Mutation_p.Q126E|CPT1B_uc003bmo.2_Missense_Mutation_p.Q126E|CPT1B_uc011asa.1_Missense_Mutation_p.Q126E|CPT1B_uc003bmn.2_Missense_Mutation_p.Q126E|CPT1B_uc011asb.1_Missense_Mutation_p.Q126E|CHKB-CPT1B_uc003bmp.2_5'UTR	NM_001145137	NP_001138609	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B isoform a	126	Cytoplasmic (Potential).				carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)												OREG0026685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CSF2RA	1438	broad.mit.edu	37	X	1401634	1401634	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1401634T>C	uc010nct.2	+	4	360	c.38T>C	c.(37-39)TTA>TCA	p.L13S	CSF2RA_uc011mhb.1_Missense_Mutation_p.L13S|CSF2RA_uc004cpq.2_Missense_Mutation_p.L13S|CSF2RA_uc004cpn.2_Missense_Mutation_p.L13S|CSF2RA_uc004cpo.2_Missense_Mutation_p.L13S|CSF2RA_uc010ncu.2_RNA|CSF2RA_uc011mhc.1_5'UTR|CSF2RA_uc004cpp.2_Missense_Mutation_p.L13S|CSF2RA_uc010ncv.2_Missense_Mutation_p.L13S|CSF2RA_uc004cpr.2_Missense_Mutation_p.L13S	NM_001161529	NP_001155001	P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor alpha chain	13						extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		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)			Sargramostim(DB00020)													---	---	---	---
ZRSR2	8233	broad.mit.edu	37	X	15822297	15822297	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15822297C>T	uc004cxg.3	+	5	421	c.376C>T	c.(376-378)CGA>TGA	p.R126*		NM_005089	NP_005080	Q15696	U2AFM_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 2	126					spliceosome assembly	U12-type spliceosomal complex	nucleotide binding|pre-mRNA 3'-splice site binding|protein binding|zinc ion binding			breast(3)	3	Hepatocellular(33;0.183)																	---	---	---	---
FAM48B2	170067	broad.mit.edu	37	X	24332236	24332236	+	5'Flank	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24332236G>A	uc011mjw.1	-							NM_001136233	NP_001129705			family with sequence similarity 48, member B2												0																		---	---	---	---
USP9X	8239	broad.mit.edu	37	X	41029259	41029259	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41029259G>C	uc004dfb.2	+	19	3281	c.2648G>C	c.(2647-2649)GGT>GCT	p.G883A	USP9X_uc004dfc.2_Missense_Mutation_p.G883A	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	883					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6																		---	---	---	---
DUSP21	63904	broad.mit.edu	37	X	44703423	44703423	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44703423G>A	uc004dgd.2	+	1	175	c.45G>A	c.(43-45)CAG>CAA	p.Q15Q		NM_022076	NP_071359	Q9H596	DUS21_HUMAN	dual specificity phosphatase 21	15						cytoplasm|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity			large_intestine(1)|lung(1)	2																		---	---	---	---
ARAF	369	broad.mit.edu	37	X	47424708	47424708	+	Silent	SNP	G	A	A	rs56202823		TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47424708G>A	uc011mlq.1	+	6	649	c.516G>A	c.(514-516)TCG>TCA	p.S172S	ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Silent_p.S38S|ARAF_uc011mlp.1_Silent_p.S172S|ARAF_uc004dic.1_5'UTR	NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	172					intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(2)|ovary(1)|skin(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
PPP1R3F	89801	broad.mit.edu	37	X	49143388	49143388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49143388G>A	uc004dnh.1	+	4	2252	c.2236G>A	c.(2236-2238)GCA>ACA	p.A746T	PPP1R3F_uc011mnd.1_Missense_Mutation_p.A417T|PPP1R3F_uc004dni.2_Missense_Mutation_p.A400T|PPP1R3F_uc004dnj.1_Missense_Mutation_p.A400T	NM_033215	NP_149992	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory (inhibitor)	746	Extracellular (Potential).					integral to membrane				ovary(2)|skin(1)	3	Ovarian(276;0.236)																	---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74651314	74651314	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74651314G>A	uc004ecg.2	-	5	899	c.421C>T	c.(421-423)CGC>TGC	p.R141C	ZDHHC15_uc004ech.2_Missense_Mutation_p.R132C|ZDHHC15_uc011mqo.1_RNA	NM_144969	NP_659406	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15 isoform 1	141	DHHC-type.					integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
HDX	139324	broad.mit.edu	37	X	83616610	83616610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83616610C>T	uc004eek.1	-	5	1425	c.1316G>A	c.(1315-1317)CGC>CAC	p.R439H	HDX_uc011mqv.1_Missense_Mutation_p.R439H|HDX_uc004eel.1_Missense_Mutation_p.R381H	NM_144657	NP_653258	Q7Z353	HDX_HUMAN	highly divergent homeobox	439	Homeobox 2.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
KLHL4	56062	broad.mit.edu	37	X	86919768	86919768	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86919768G>T	uc004efb.2	+	10	2112	c.1930G>T	c.(1930-1932)GAT>TAT	p.D644Y	KLHL4_uc004efa.2_Missense_Mutation_p.D644Y	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	644	Kelch 5.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
PCDH11X	27328	broad.mit.edu	37	X	91132491	91132491	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:91132491C>A	uc004efk.1	+	2	2097	c.1252C>A	c.(1252-1254)CTG>ATG	p.L418M	PCDH11X_uc004efl.1_Missense_Mutation_p.L418M|PCDH11X_uc004efo.1_Missense_Mutation_p.L418M|PCDH11X_uc010nmv.1_Missense_Mutation_p.L418M|PCDH11X_uc004efm.1_Missense_Mutation_p.L418M|PCDH11X_uc004efn.1_Missense_Mutation_p.L418M|PCDH11X_uc004efh.1_Missense_Mutation_p.L418M|PCDH11X_uc004efj.1_Missense_Mutation_p.L418M	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	418	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2																		---	---	---	---
ZMAT1	84460	broad.mit.edu	37	X	101139336	101139336	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101139336T>A	uc004eim.2	-	2	4048	c.550A>T	c.(550-552)AGA>TGA	p.R184*	ZMAT1_uc011mrl.1_Nonsense_Mutation_p.R355*|ZMAT1_uc004ein.2_Nonsense_Mutation_p.R184*|ZMAT1_uc011mrm.1_Nonsense_Mutation_p.R184*	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	184						nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
GPRASP1	9737	broad.mit.edu	37	X	101911911	101911911	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101911911G>A	uc004ejj.3	+	5	3871	c.3070G>A	c.(3070-3072)GCC>ACC	p.A1024T	GPRASP1_uc004eji.3_Missense_Mutation_p.A1024T|GPRASP1_uc010nod.2_Missense_Mutation_p.A1024T	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	1024	OPRD1-binding.					cytoplasm	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
MORC4	79710	broad.mit.edu	37	X	106185215	106185215	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106185215C>T	uc004emu.3	-	16	2856	c.2613G>A	c.(2611-2613)CAG>CAA	p.Q871Q	MORC4_uc004emp.3_Intron|MORC4_uc004emv.3_Silent_p.Q871Q|MORC4_uc004emw.3_Silent_p.Q619Q	NM_024657	NP_078933	Q8TE76	MORC4_HUMAN	zinc finger, CW type with coiled-coil domain 2	871	Potential.						ATP binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CHRDL1	91851	broad.mit.edu	37	X	109931837	109931837	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109931837C>T	uc004eou.3	-	9	1322	c.973G>A	c.(973-975)GGT>AGT	p.G325S	CHRDL1_uc004eov.2_Missense_Mutation_p.E319K|CHRDL1_uc004eow.2_Missense_Mutation_p.G324S|CHRDL1_uc010nps.2_Missense_Mutation_p.G324S|CHRDL1_uc004eot.2_Missense_Mutation_p.G245S|CHRDL1_uc011mss.1_Missense_Mutation_p.G239S	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	318					BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0																		---	---	---	---
CHRDL1	91851	broad.mit.edu	37	X	110005996	110005996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110005996C>T	uc004eou.3	-	3	483	c.134G>A	c.(133-135)AGA>AAA	p.R45K	CHRDL1_uc004eov.2_Missense_Mutation_p.R39K|CHRDL1_uc004eow.2_Missense_Mutation_p.R45K|CHRDL1_uc010nps.2_Missense_Mutation_p.R45K|CHRDL1_uc004eot.2_Missense_Mutation_p.R45K|CHRDL1_uc011mss.1_Missense_Mutation_p.R39K|CHRDL1_uc004eox.3_Missense_Mutation_p.R39K	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	39	VWFC 1.				BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0																		---	---	---	---
HTR2C	3358	broad.mit.edu	37	X	114141456	114141456	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114141456C>T	uc004epu.1	+	6	1583	c.855C>T	c.(853-855)AAC>AAT	p.N285N	HTR2C_uc010nqc.1_Silent_p.N285N|HTR2C_uc004epv.1_3'UTR	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	285	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)													---	---	---	---
ZCCHC12	170261	broad.mit.edu	37	X	117960020	117960020	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117960020C>T	uc004equ.2	+	4	1286	c.813C>T	c.(811-813)GAC>GAT	p.D271D		NM_173798	NP_776159	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	271					regulation of transcription, DNA-dependent|transcription, DNA-dependent		nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
OCRL	4952	broad.mit.edu	37	X	128724180	128724180	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128724180C>A	uc004euq.2	+	24	2804	c.2639C>A	c.(2638-2640)ACT>AAT	p.T880N	OCRL_uc004eur.2_Missense_Mutation_p.T872N|OCRL_uc010nrb.2_RNA	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	880	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4																		---	---	---	---
RBMX2	51634	broad.mit.edu	37	X	129546425	129546425	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129546425G>A	uc004evt.2	+	6	636	c.572G>A	c.(571-573)CGC>CAC	p.R191H		NM_016024	NP_057108	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	191	Lys-rich.						nucleotide binding|RNA binding			breast(3)|ovary(1)	4																		---	---	---	---
IGSF1	3547	broad.mit.edu	37	X	130408789	130408789	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130408789T>C	uc004ewd.2	-	18	3773	c.3535A>G	c.(3535-3537)ATC>GTC	p.I1179V	IGSF1_uc004ewe.3_Missense_Mutation_p.I1173V|IGSF1_uc004ewf.2_Missense_Mutation_p.I1159V	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	1179	Extracellular (Potential).|Ig-like C2-type 12.				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
MAGEC1	9947	broad.mit.edu	37	X	140995387	140995387	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140995387G>T	uc004fbt.2	+	4	2483	c.2197G>T	c.(2197-2199)GGG>TGG	p.G733W	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	733							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)														HNSCC(15;0.026)			---	---	---	---
SLITRK2	84631	broad.mit.edu	37	X	144904763	144904763	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144904763A>G	uc004fcd.2	+	5	1810	c.820A>G	c.(820-822)AGG>GGG	p.R274G	SLITRK2_uc010nsp.2_Missense_Mutation_p.R274G|SLITRK2_uc010nso.2_Missense_Mutation_p.R274G|SLITRK2_uc011mwq.1_Missense_Mutation_p.R274G|SLITRK2_uc011mwr.1_Missense_Mutation_p.R274G|SLITRK2_uc011mws.1_Missense_Mutation_p.R274G|SLITRK2_uc004fcg.2_Missense_Mutation_p.R274G|SLITRK2_uc011mwt.1_Missense_Mutation_p.R274G	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	274	Extracellular (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
GABRA3	2556	broad.mit.edu	37	X	151376568	151376568	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151376568T>G	uc010ntk.1	-	7	923	c.683A>C	c.(682-684)AAC>ACC	p.N228T		NM_000808	NP_000799	P34903	GBRA3_HUMAN	gamma-aminobutyric acid A receptor, alpha 3	228	Extracellular (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(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)				Alprazolam(DB00404)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)													---	---	---	---
NSDHL	50814	broad.mit.edu	37	X	152037483	152037483	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152037483T>A	uc004fgt.1	+	9	1206	c.945T>A	c.(943-945)AGT>AGA	p.S315R	NSDHL_uc004fgs.1_Missense_Mutation_p.S315R	NM_001129765	NP_001123237	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	315	Helical; (Potential).				cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity				0	Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)													---	---	---	---
IDH3G	3421	broad.mit.edu	37	X	153053045	153053045	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153053045G>A	uc004fip.2	-	8	734	c.548C>T	c.(547-549)GCG>GTG	p.A183V	IDH3G_uc004fio.2_Missense_Mutation_p.A125V|IDH3G_uc004fiq.2_Missense_Mutation_p.A183V|IDH3G_uc010num.2_Missense_Mutation_p.A125V|IDH3G_uc004fir.2_Missense_Mutation_p.A125V|IDH3G_uc004fit.1_Missense_Mutation_p.A183V|IDH3G_uc004fis.2_Missense_Mutation_p.A125V|IDH3G_uc004fiu.2_5'UTR	NM_004135	NP_004126	P51553	IDH3G_HUMAN	isocitrate dehydrogenase 3 (NAD+) gamma isoform	183					carbohydrate metabolic process|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleolus	ATP binding|isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0	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)				NADH(DB00157)													---	---	---	---
DNASE1L1	1774	broad.mit.edu	37	X	153631964	153631964	+	Splice_Site	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153631964C>T	uc004fks.1	-	5	503	c.312_splice	c.e5-1	p.R104_splice	RPL10_uc004fkq.1_RNA|RPL10_uc004fkr.1_3'UTR|DNASE1L1_uc004fkt.1_Splice_Site_p.R104_splice|DNASE1L1_uc004fku.1_Splice_Site_p.R104_splice|DNASE1L1_uc004fkv.1_Splice_Site_p.R104_splice|DNASE1L1_uc004fkw.1_Splice_Site_p.R104_splice	NM_006730	NP_006721			deoxyribonuclease I-like 1 precursor						DNA catabolic process	endoplasmic reticulum	DNA binding|endodeoxyribonuclease activity, producing 5'-phosphomonoesters				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)																	---	---	---	---
TAZ	6901	broad.mit.edu	37	X	153648592	153648592	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153648592C>A	uc004fkx.2	+	9	992	c.688C>A	c.(688-690)CGC>AGC	p.R230S	TAZ_uc004fky.2_Missense_Mutation_p.R216S|TAZ_uc004fkz.2_RNA|TAZ_uc004fla.2_Missense_Mutation_p.R200S|TAZ_uc004flb.2_Missense_Mutation_p.R186S|TAZ_uc010nuy.2_Missense_Mutation_p.R234S|TAZ_uc004flc.3_Missense_Mutation_p.R200S	NM_000116	NP_000107	Q16635	TAZ_HUMAN	tafazzin isoform 1	230					cardiac muscle contraction|cardiac muscle tissue development|cardiolipin biosynthetic process|cristae formation|hemopoiesis|mitochondrial ATP synthesis coupled electron transport|mitochondrial respiratory chain complex I assembly|skeletal muscle tissue development	integral to membrane|mitochondrion	1-acylglycerophosphocholine O-acyltransferase activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)																	---	---	---	---
IL9R	3581	broad.mit.edu	37	X	155232611	155232611	+	Silent	SNP	C	T	T			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155232611C>T	uc004fnv.1	+	2	248	c.69C>T	c.(67-69)GGC>GGT	p.G23G	IL9R_uc010nvn.2_Silent_p.G2G|IL9R_uc004fnu.1_Silent_p.G70G	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	23					cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				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)																	---	---	---	---
IL9R	3581	broad.mit.edu	37	X	155235812	155235812	+	Silent	SNP	G	A	A			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155235812G>A	uc004fnv.1	+	7	1025	c.846G>A	c.(844-846)CTG>CTA	p.L282L	IL9R_uc010nvn.2_Silent_p.L261L|IL9R_uc004fnu.1_Silent_p.L317L	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	282	Helical; (Potential).				cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				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)																	---	---	---	---
NLGN4Y	22829	broad.mit.edu	37	Y	16953056	16953056	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4256-01A-01D-1126-08	TCGA-BR-4256-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:16953056A>G	uc004ftg.2	+	6	2617	c.2365A>G	c.(2365-2367)ATG>GTG	p.M789V	NLGN4Y_uc004fte.2_Missense_Mutation_p.M621V|NLGN4Y_uc011nas.1_Missense_Mutation_p.M809V|NLGN4Y_uc004ftf.2_Missense_Mutation_p.M482V|NLGN4Y_uc004fth.2_Missense_Mutation_p.M789V	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked isoform 1	789	Cytoplasmic (Potential).				brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|integral to plasma membrane|synapse	neurexin binding|receptor activity				0																		---	---	---	---
