biostudies-literatureGriesemer DHoward Hughes Medical InstituteNIAID NIH HHSNHGRINHGRI NIH HHSNIHBroad InstituteNIGMS NIH HHSNational Science Foundation5247-5260.e19https://www.ebi.ac.uk/biostudies/studies/S-EPMC8487971biostudies-literatureUnknown184(20)3' untranslated region (3'UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the massively parallel reporter assay for 3'UTRs (MPRAu) to sensitively assay 12,173 3'UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide association studies (GWAS) and human evolutionary adaptation. MPRAu expands our understanding of 3'UTR function, suggesting that simple sequences predominately explain 3'UTR regulatory activity. We adapt MPRAu to uncover diverse molecular mechanisms at base pair resolution, including an adenylate-uridylate (AU)-rich element of LEPR linked to potential metabolic evolutionary adaptations in East Asians. We nominate hundreds of 3'UTR causal variants with genetically fine-mapped phenotype associations. Using endogenous allelic replacements, we characterize one variant that disrupts a miRNA site regulating the viral defense gene TRIM14 and one that alters PILRB abundance, nominating a causal variant underlying transcriptional changes in age-related macular degeneration.CellGenome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution.PMC8487971F32HG00922UM1HG009435F32 HG009226DEB-1401237R37 AI147868K99HG010669F30GM114940F30 GM114940R00 HG008179R37AI147868UM1 HG009435R00HG008179K99 HG010669Finucane HKDavis JRUlirsch JCLuban JMontgomery SBYang DKXue JRButts JCKukreja KGuney MHReilly SKKanai MNovina CDGriesemer DTewhey RSabeti PCfalseGenome-wide functional screen of 3'UTR variants uncovers causal variants for human disease and evolution.3' untranslated region (3'UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the massively parallel reporter assay for 3'UTRs (MPRAu) to sensitively assay 12,173 3'UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide association studies (GWAS) and human evolutionary adaptation. MPRAu expands our understanding of 3'UTR function, suggesting that simple sequences predominately explain 3'UTR regulatory activity. We adapt MPRAu to uncover diverse molecular mechanisms at base pair resolution, including an adenylate-uridylate (AU)-rich element of LEPR linked to potential metabolic evolutionary adaptations in East Asians. We nominate hundreds of 3'UTR causal variants with genetically fine-mapped phenotype associations. Using endogenous allelic replacements, we characterize one variant that disrupts a miRNA site regulating the viral defense gene TRIM14 and one that alters PILRB abundance, nominating a causal variant underlying transcriptional changes in age-related macular degeneration.2021-01-01T00:00:00Z2021 Sep2026-05-08T01:48:13.993Z2025-05-18T12:50:25.884ZS-EPMC84879713453444510.1016/j.cell.2021.08.025