{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Tian Y"],"funding":["NCI NIH HHS","National Institutes of Health","NIH HHS"],"pagination":["1610-1621"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9122641"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["31(10)"],"pubmed_abstract":["Although previous studies identified numerous single nucleotide polymorphisms (SNPs) and their target genes predisposed to prostate cancer (PrCa) risks, SNP-related splicing associations are rarely reported. In this study, we applied distance-based sQTL analysis (sQTLseekeR) using RNA-seq and SNP genotype data from benign prostate tissue (n = 467) and identified significant associations in 3344 SNP-transcript pairs (P ≤ 0.05) at PrCa risk loci. We characterized a common SNP (rs7247241) and its target gene (PPP1R14A) located in chr19q13, an sQTL with risk allele T associated with upregulation of long isoform (P = 9.99E-7). We confirmed the associations in both TCGA (P = 2.42E-24) and GTEX prostate cohorts (P = 9.08E-78). To functionally characterize this SNP, we performed chromatin immunopr"],"journal":["Human molecular genetics"],"pubmed_title":["Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation."],"pmcid":["PMC9122641"],"funding_grant_id":["R01CA212097","R01 CA212097","R01 CA250018","R01CA250018","P30 CA076292"],"pubmed_authors":["Huang CC","Wu L","Park JY","Soupir A","Tian Y","Liu Q","Wang L"],"additional_accession":[]},"is_claimable":false,"name":"Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation.","description":"Although previous studies identified numerous single nucleotide polymorphisms (SNPs) and their target genes predisposed to prostate cancer (PrCa) risks, SNP-related splicing associations are rarely reported. In this study, we applied distance-based sQTL analysis (sQTLseekeR) using RNA-seq and SNP genotype data from benign prostate tissue (n = 467) and identified significant associations in 3344 SNP-transcript pairs (P ≤ 0.05) at PrCa risk loci. We characterized a common SNP (rs7247241) and its target gene (PPP1R14A) located in chr19q13, an sQTL with risk allele T associated with upregulation of long isoform (P = 9.99E-7). We confirmed the associations in both TCGA (P = 2.42E-24) and GTEX prostate cohorts (P = 9.08E-78). To functionally characterize this SNP, we performed chromatin immunopr","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 May","modification":"2026-07-14T17:37:24.367Z","creation":"2024-11-21T01:22:40.863Z"},"accession":"S-EPMC9122641","cross_references":{"pubmed":["34849858"],"doi":["10.1093/hmg/ddab347"]}}