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sample_2_vep_snps.txt
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#Uploaded_variation Location Allele Consequence IMPACT SYMBOL Gene Feature_type Feature BIOTYPE EXON INTRON HGVSc HGVSp cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation REF_ALLELE UPLOADED_ALLELE DISTANCE STRAND FLAGS SYMBOL_SOURCE HGNC_ID MANE_SELECT MANE_PLUS_CLINICAL TSL APPRIS SIFT PolyPhen HGVS_OFFSET AF CLIN_SIG SOMATIC PHENO PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE TRANSCRIPTION_FACTORS
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000320856.5 protein_coding - 12/20 ENST00000320856.5:c.2365+7184C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000378738.3 protein_coding - 14/14 ENST00000378738.3:c.2737+3639C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A upstream_gene_variant MODIFIER RNY4P13 ENSG00000207011 Transcript ENST00000384284.1 misc_RNA - - - - - - - - - - T T/A 4193 -1 - HGNC 34063 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000394832.2 protein_coding - 14/14 ENST00000394832.2:c.2737+3639C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000394835.3 protein_coding - 14/22 ENST00000394835.3:c.2737+3639C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000419434.1 protein_coding - 9/17 ENST00000419434.1:c.1783+7184C>A - - - - - - - T T/A - 1 cds_start_NF HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant,NMD_transcript_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000423598.2 nonsense_mediated_decay - 12/13 ENST00000423598.2:c.*1576+5450C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant,NMD_transcript_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000440741.3 nonsense_mediated_decay - 14/15 ENST00000440741.3:c.2737+3639C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000536908.2 protein_coding - 13/14 ENST00000536908.2:c.2412+5450C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000541045.1 protein_coding - 12/13 ENST00000541045.1:c.1551+5450C>A - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A downstream_gene_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000581617.1 retained_intron - - - - - - - - - - T T/A 3457 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant,non_coding_transcript_variant MODIFIER AC104984.4 ENSG00000265289 Transcript ENST00000583250.1 antisense - 1/1 ENST00000583250.1:n.44+2294G>T - - - - - - - T T/A - -1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000588978.1 protein_coding - 11/11 ENST00000588978.1:c.2132+3639C>A - - - - - - - T T/A - 1 cds_start_NF HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390358-28390358 A upstream_gene_variant MODIFIER RNY4P13 ENSG00000267482 Transcript ENST00000590718.1 unprocessed_pseudogene - - - - - - - - - - T T/A 4193 -1 - Clone_based_vega_gene 34063 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000320856.5 protein_coding - 12/20 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000378738.3 protein_coding - 14/14 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A upstream_gene_variant MODIFIER RNY4P13 ENSG00000207011 Transcript ENST00000384284.1 misc_RNA - - - - - - - - - - T T/A 4196 -1 - HGNC 34063 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000394832.2 protein_coding - 14/14 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000394835.3 protein_coding - 14/22 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000419434.1 protein_coding - 9/17 - - - - - - - - T T/A - 1 cds_start_NF HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant,NMD_transcript_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000423598.2 nonsense_mediated_decay - 12/13 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant,NMD_transcript_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000440741.3 nonsense_mediated_decay - 14/15 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000536908.2 protein_coding - 13/14 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000541045.1 protein_coding - 12/13 - - - - - - - - T T/A - 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A downstream_gene_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000581617.1 retained_intron - - - - - - - - - - T T/A 3460 1 - HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant,non_coding_transcript_variant MODIFIER AC104984.4 ENSG00000265289 Transcript ENST00000583250.1 antisense - 1/1 - - - - - - - - T T/A - -1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A intron_variant MODIFIER EFCAB5 ENSG00000176927 Transcript ENST00000588978.1 protein_coding - 11/11 - - - - - - - - T T/A - 1 cds_start_NF HGNC 24801 - - - - - - - - - - - - - - - - -
. 17:28390361-28390361 A upstream_gene_variant MODIFIER RNY4P13 ENSG00000267482 Transcript ENST00000590718.1 unprocessed_pseudogene - - - - - - - - - - T T/A 4196 -1 - Clone_based_vega_gene 34063 - - - - - - - - - - - - - - - - -
. 17:30870867-30870867 T intron_variant MODIFIER MYO1D ENSG00000176658 Transcript ENST00000318217.5 protein_coding - 21/21 ENST00000318217.5:c.2865-48934T>A - - - - - - - G G/T - -1 - HGNC 7598 - - - - - - - - - - - - - - - - -
. 17:30870867-30870867 T intron_variant MODIFIER MYO1D ENSG00000176658 Transcript ENST00000394649.4 protein_coding - 23/23 ENST00000394649.4:c.2601-48934T>A - - - - - - - G G/T - -1 - HGNC 7598 - - - - - - - - - - - - - - - - -
. 17:30870867-30870867 T intron_variant,non_coding_transcript_variant MODIFIER MYO1D ENSG00000176658 Transcript ENST00000577352.1 retained_intron - 5/5 ENST00000577352.1:n.812-48934T>A - - - - - - - G G/T - -1 - HGNC 7598 - - - - - - - - - - - - - - - - -
. 17:33880141-33880141 T synonymous_variant LOW SLFN14 ENSG00000236320 Transcript ENST00000415846.3 protein_coding 3/4 - ENST00000415846.3:c.1512G>A ENSP00000391101.2:p.Gly504%3D 1548 1512 504 G ggG/ggA COSV104711259 C C/T - -1 - HGNC 32689 - - - - - - - - - 1 1 - - - - - -
. 17:33880141-33880141 T upstream_gene_variant MODIFIER RP11-1094M14.12 ENSG00000267359 Transcript ENST00000588445.1 antisense - - - - - - - - - COSV104711259 C C/T 83 1 - Clone_based_vega_gene - - - - - - - - - - 1 1 - - - - - -
. 17:33880162-33880162 T missense_variant MODERATE SLFN14 ENSG00000236320 Transcript ENST00000415846.3 protein_coding 3/4 - - ENSP00000391101.2:p.His497Gln 1527 1491 497 H/Q caT/caA - A A/T - -1 - HGNC 32689 - - - - - - - - - - - - - - - - -
. 17:33880162-33880162 T upstream_gene_variant MODIFIER RP11-1094M14.12 ENSG00000267359 Transcript ENST00000588445.1 antisense - - - - - - - - - - A A/T 62 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:33880168-33880168 A missense_variant MODERATE SLFN14 ENSG00000236320 Transcript ENST00000415846.3 protein_coding 3/4 - ENST00000415846.3:c.1485A>T ENSP00000391101.2:p.Lys495Asn 1521 1485 495 K/N aaA/aaT - T T/A - -1 - HGNC 32689 - - - - deleterious(0.04) possibly_damaging(0.617) - - - - - - - - - - -
. 17:33880168-33880168 A upstream_gene_variant MODIFIER RP11-1094M14.12 ENSG00000267359 Transcript ENST00000588445.1 antisense - - - - - - - - - - T T/A 56 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000309486.4 protein_coding - 18/21 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000346315.3 protein_coding - 15/18 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000351666.3 protein_coding - 15/18 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000352993.3 protein_coding - 18/21 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000354071.3 protein_coding - 14/17 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000357654.3 protein_coding - 19/22 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant,NMD_transcript_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000461221.1 nonsense_mediated_decay - 19/22 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000468300.1 protein_coding - 19/21 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000471181.2 protein_coding - 20/23 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000491747.2 protein_coding - 19/22 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000493795.1 protein_coding - 18/21 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000586385.1 protein_coding - 4/7 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591534.1 protein_coding - 7/10 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208709-41208709 A intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591849.1 protein_coding - 1/4 - - - - - - - - G G/A - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000309486.4 protein_coding - 18/21 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000346315.3 protein_coding - 15/18 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000351666.3 protein_coding - 15/18 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000352993.3 protein_coding - 18/21 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000354071.3 protein_coding - 14/17 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000357654.3 protein_coding - 19/22 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant,NMD_transcript_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000461221.1 nonsense_mediated_decay - 19/22 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000468300.1 protein_coding - 19/21 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000471181.2 protein_coding - 20/23 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000491747.2 protein_coding - 19/22 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000493795.1 protein_coding - 18/21 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000586385.1 protein_coding - 4/7 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591534.1 protein_coding - 7/10 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208712-41208712 G intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591849.1 protein_coding - 1/4 - - - - - - - - T T/G - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000309486.4 protein_coding - 18/21 ENST00000309486.4:c.4389+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000346315.3 protein_coding - 15/18 ENST00000346315.3:c.4560+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000351666.3 protein_coding - 15/18 ENST00000351666.3:c.1728+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000352993.3 protein_coding - 18/21 ENST00000352993.3:c.1851+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000354071.3 protein_coding - 14/17 ENST00000354071.3:c.4482+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000357654.3 protein_coding - 19/22 ENST00000357654.3:c.5277+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant,NMD_transcript_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000461221.1 nonsense_mediated_decay - 19/22 ENST00000461221.1:c.*5060+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000468300.1 protein_coding - 19/21 ENST00000468300.1:c.1965+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000471181.2 protein_coding - 20/23 ENST00000471181.2:c.5340+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000491747.2 protein_coding - 19/22 ENST00000491747.2:c.1965+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000493795.1 protein_coding - 18/21 ENST00000493795.1:c.5136+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000586385.1 protein_coding - 4/7 ENST00000586385.1:c.207+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591534.1 protein_coding - 7/10 ENST00000591534.1:c.750+351T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208718-41208718 C intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591849.1 protein_coding - 1/4 ENST00000591849.1:c.-98-6511T>G - - - - - - - T T/C - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000309486.4 protein_coding - 18/21 ENST00000309486.4:c.4389+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000346315.3 protein_coding - 15/18 ENST00000346315.3:c.4560+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000351666.3 protein_coding - 15/18 ENST00000351666.3:c.1728+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000352993.3 protein_coding - 18/21 ENST00000352993.3:c.1851+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000354071.3 protein_coding - 14/17 ENST00000354071.3:c.4482+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000357654.3 protein_coding - 19/22 ENST00000357654.3:c.5277+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant,NMD_transcript_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000461221.1 nonsense_mediated_decay - 19/22 ENST00000461221.1:c.*5060+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000468300.1 protein_coding - 19/21 ENST00000468300.1:c.1965+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000471181.2 protein_coding - 20/23 ENST00000471181.2:c.5340+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000491747.2 protein_coding - 19/22 ENST00000491747.2:c.1965+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000493795.1 protein_coding - 18/21 ENST00000493795.1:c.5136+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000586385.1 protein_coding - 4/7 ENST00000586385.1:c.207+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591534.1 protein_coding - 7/10 ENST00000591534.1:c.750+340T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:41208729-41208729 T intron_variant MODIFIER BRCA1 ENSG00000012048 Transcript ENST00000591849.1 protein_coding - 1/4 ENST00000591849.1:c.-98-6522T>A - - - - - - - C C/T - -1 - HGNC 1100 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000268893.6 protein_coding - 2/30 ENST00000268893.6:c.441+96C>A - - - - - - - C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000343736.4 protein_coding - 2/31 ENST00000343736.4:c.441+96C>A - - - - - - - C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000355701.3 protein_coding - 2/30 ENST00000355701.3:c.441+96C>A - - - - - - - C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000384835.1 miRNA - - - - - - - - - - C C/T 4645 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000578334.1 antisense - - - - - - - - - - C C/T 2428 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000579003.1 antisense - - - - - - - - - - C C/T 4297 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T intron_variant,non_coding_transcript_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000579527.1 antisense - 1/4 ENST00000579527.1:n.279+859G>T - - - - - - - C C/T - 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580515.1 antisense - - - - - - - - - - C C/T 2351 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580633.1 antisense - - - - - - - - - - C C/T 3018 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403948-56403948 T upstream_gene_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000583624.1 retained_intron - - - - - - - - - - C C/T 3866 -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000268893.6 protein_coding - 2/30 ENST00000268893.6:c.441+90T>G - - - - - - - T T/C - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000343736.4 protein_coding - 2/31 ENST00000343736.4:c.441+90T>G - - - - - - - T T/C - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000355701.3 protein_coding - 2/30 ENST00000355701.3:c.441+90T>G - - - - - - - T T/C - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000384835.1 miRNA - - - - - - - - - - T T/C 4639 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000578334.1 antisense - - - - - - - - - - T T/C 2422 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000579003.1 antisense - - - - - - - - - - T T/C 4291 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C intron_variant,non_coding_transcript_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000579527.1 antisense - 1/4 ENST00000579527.1:n.279+865A>C - - - - - - - T T/C - 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580515.1 antisense - - - - - - - - - - T T/C 2345 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580633.1 antisense - - - - - - - - - - T T/C 3012 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403954-56403954 C upstream_gene_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000583624.1 retained_intron - - - - - - - - - - T T/C 3872 -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000268893.6 protein_coding - 2/30 ENST00000268893.6:c.441+75G>A - - - - - - rs1271520756 C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000343736.4 protein_coding - 2/31 ENST00000343736.4:c.441+75G>A - - - - - - rs1271520756 C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000355701.3 protein_coding - 2/30 ENST00000355701.3:c.441+75G>A - - - - - - rs1271520756 C C/T - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000384835.1 miRNA - - - - - - - - - rs1271520756 C C/T 4624 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000578334.1 antisense - - - - - - - - - rs1271520756 C C/T 2407 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000579003.1 antisense - - - - - - - - - rs1271520756 C C/T 4276 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T intron_variant,non_coding_transcript_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000579527.1 antisense - 1/4 ENST00000579527.1:n.279+880C>T - - - - - - rs1271520756 C C/T - 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580515.1 antisense - - - - - - - - - rs1271520756 C C/T 2330 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580633.1 antisense - - - - - - - - - rs1271520756 C C/T 2997 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403969-56403969 T upstream_gene_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000583624.1 retained_intron - - - - - - - - - rs1271520756 C C/T 3887 -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000268893.6 protein_coding - 2/30 - - - - - - - - A A/G - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000343736.4 protein_coding - 2/31 - - - - - - - - A A/G - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G intron_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000355701.3 protein_coding - 2/30 - - - - - - - - A A/G - -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000384835.1 miRNA - - - - - - - - - - A A/G 4618 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000578334.1 antisense - - - - - - - - - - A A/G 2401 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G downstream_gene_variant MODIFIER MIR142 ENSG00000265206 Transcript ENST00000579003.1 antisense - - - - - - - - - - A A/G 4270 -1 - HGNC 31529 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G intron_variant,non_coding_transcript_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000579527.1 antisense - 1/4 - - - - - - - - A A/G - 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580515.1 antisense - - - - - - - - - - A A/G 2324 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G upstream_gene_variant MODIFIER BZRAP1-AS1 ENSG00000265148 Transcript ENST00000580633.1 antisense - - - - - - - - - - A A/G 2991 1 - HGNC 44148 - - - - - - - - - - - - - - - - -
. 17:56403975-56403975 G upstream_gene_variant MODIFIER BZRAP1 ENSG00000005379 Transcript ENST00000583624.1 retained_intron - - - - - - - - - - A A/G 3893 -1 - HGNC 16831 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A intron_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000303375.5 protein_coding - 13/29 ENST00000303375.5:c.2196-480C>A - - - - - - - G G/A - 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A upstream_gene_variant MODIFIER RNU6-446P ENSG00000199697 Transcript ENST00000362827.1 snRNA - - - - - - - - - - G G/A 4585 1 - HGNC 47409 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000446119.2 protein_coding - - - - - - - - - - G G/A 2138 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000579432.1 protein_coding - - - - - - - - - - G G/A 2133 1 cds_end_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000583597.1 retained_intron - - - - - - - - - - G G/A 1311 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A downstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584265.1 retained_intron - - - - - - - - - - G G/A 2716 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756681-60756681 A intron_variant,NMD_transcript_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584682.1 nonsense_mediated_decay - 3/4 ENST00000584682.1:c.471-480C>A - - - - - - - G G/A - 1 cds_start_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G intron_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000303375.5 protein_coding - 13/29 ENST00000303375.5:c.2196-474A>G - - - - - - - A A/G - 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G upstream_gene_variant MODIFIER RNU6-446P ENSG00000199697 Transcript ENST00000362827.1 snRNA - - - - - - - - - - A A/G 4579 1 - HGNC 47409 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000446119.2 protein_coding - - - - - - - - - - A A/G 2132 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000579432.1 protein_coding - - - - - - - - - - A A/G 2127 1 cds_end_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000583597.1 retained_intron - - - - - - - - - - A A/G 1305 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G downstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584265.1 retained_intron - - - - - - - - - - A A/G 2722 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756687-60756687 G intron_variant,NMD_transcript_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584682.1 nonsense_mediated_decay - 3/4 ENST00000584682.1:c.471-474A>G - - - - - - - A A/G - 1 cds_start_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A intron_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000303375.5 protein_coding - 13/29 ENST00000303375.5:c.2196-470T>A - - - - - - - T T/A - 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A upstream_gene_variant MODIFIER RNU6-446P ENSG00000199697 Transcript ENST00000362827.1 snRNA - - - - - - - - - - T T/A 4575 1 - HGNC 47409 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000446119.2 protein_coding - - - - - - - - - - T T/A 2128 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000579432.1 protein_coding - - - - - - - - - - T T/A 2123 1 cds_end_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A upstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000583597.1 retained_intron - - - - - - - - - - T T/A 1301 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A downstream_gene_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584265.1 retained_intron - - - - - - - - - - T T/A 2726 1 - HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:60756691-60756691 A intron_variant,NMD_transcript_variant MODIFIER MRC2 ENSG00000011028 Transcript ENST00000584682.1 nonsense_mediated_decay - 3/4 ENST00000584682.1:c.471-470T>A - - - - - - - T T/A - 1 cds_start_NF HGNC 16875 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T intron_variant MODIFIER SDK2 ENSG00000069188 Transcript ENST00000388726.3 protein_coding - 38/43 - - - - - - - - C C/T - -1 - HGNC 19308 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T intron_variant MODIFIER SDK2 ENSG00000069188 Transcript ENST00000392650.3 protein_coding - 39/44 - - - - - - - - C C/T - -1 - HGNC 19308 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T intron_variant,non_coding_transcript_variant MODIFIER SDK2 ENSG00000069188 Transcript ENST00000410094.1 processed_transcript - 4/9 - - - - - - - - C C/T - -1 - HGNC 19308 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T intron_variant MODIFIER SDK2 ENSG00000069188 Transcript ENST00000424778.1 protein_coding - 21/26 - - - - - - - - C C/T - -1 cds_start_NF HGNC 19308 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T intron_variant,non_coding_transcript_variant MODIFIER SDK2 ENSG00000069188 Transcript ENST00000479356.1 retained_intron - 32/32 - - - - - - - - C C/T - -1 - HGNC 19308 - - - - - - - - - - - - - - - - -
. 17:71357147-71357147 T regulatory_region_variant MODIFIER - - RegulatoryFeature ENSR00001599425 enhancer - - - - - - - - - - C C/T - - - - - - - - - - - - - - - - - - - - - -
. 17:76606596-76606596 T intergenic_variant MODIFIER - - - - - - - - - - - - - - - C C/T - - - - - - - - - - - - - - - - - - - - - -
. 17:76606606-76606606 G regulatory_region_variant MODIFIER - - RegulatoryFeature ENSR00001897318 enhancer - - - - - - - - - - A A/G - - - - - - - - - - - - - - - - - - - - - -
. 17:76606606-76606606 G intergenic_variant MODIFIER - - - - - - - - - - - - - - - A A/G - - - - - - - - - - - - - - - - - - - - - -
. 17:81155155-81155155 T upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - C C/T 4610 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:81155161-81155161 T upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - C C/T 4604 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:81155164-81155164 G upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - A A/G 4601 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:81155175-81155175 A upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - T T/A 4590 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:81155177-81155177 T upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - G G/T 4588 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -
. 17:81155179-81155179 A upstream_gene_variant MODIFIER AC139099.6 ENSG00000262952 Transcript ENST00000572850.1 lincRNA - - - - - - - - - - C C/A 4586 1 - Clone_based_vega_gene - - - - - - - - - - - - - - - - - -