{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:24:19Z","timestamp":1783038259884,"version":"3.54.6"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T00:00:00Z","timestamp":1629849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA193466"],"award-info":[{"award-number":["R01CA193466"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Genome-wide association studies (GWAS) have identified thousands of non-coding single-nucleotide polymorphisms (SNPs) associated with human traits and diseases. However, functional interpretation of these SNPs remains a significant challenge. Our recent study established the concept of 3\u2032 untranslated region (3\u2032UTR) alternative polyadenylation (APA) quantitative trait loci (3\u2032aQTLs), which can be used to interpret \u223c16.1% of GWAS SNPs and are distinct from gene expression QTLs and splicing QTLs. Despite the growing interest in 3\u2032aQTLs, there is no comprehensive database for users to search and visualize them across human normal tissues. In the 3\u2032aQTL-atlas (https:\/\/wlcb.oit.uci.edu\/3aQTLatlas), we provide a comprehensive list of 3\u2032aQTLs containing \u223c1.49 million SNPs associated with APA of target genes, based on 15,201 RNA-seq samples across 49 human Genotype-Tissue Expression (GTEx v8) tissues isolated from 838 individuals. The 3\u2032aQTL-atlas provides a \u223c2-fold increase in sample size compared with our published study. It also includes 3\u2032aQTL searches by Gene\/SNP across tissues, a 3\u2032aQTL genome browser, 3\u2032aQTL boxplots, and GWAS-3\u2032aQTL colocalization event visualization. The 3\u2032aQTL-atlas aims to establish APA as an emerging molecular phenotype to explain a large fraction of GWAS risk SNPs, leading to significant novel insights into the genetic basis of APA and APA-linked susceptibility genes in human traits and diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkab740","type":"journal-article","created":{"date-parts":[[2021,8,14]],"date-time":"2021-08-14T03:55:19Z","timestamp":1628913319000},"page":"D39-D45","source":"Crossref","is-referenced-by-count":33,"title":["3\u2032aQTL-atlas: an atlas of 3\u2032UTR alternative polyadenylation quantitative trait loci across human normal tissues"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1574-0928","authenticated-orcid":false,"given":"Ya","family":"Cui","sequence":"first","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8818-3785","authenticated-orcid":false,"given":"Fanglue","family":"Peng","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yumei","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason Sheng","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9931-5990","authenticated-orcid":false,"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,25]]},"reference":[{"key":"2022010507351326500_B1","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","author":"GTEx Consortium","year":"2017","journal-title":"Nature"},{"key":"2022010507351326500_B2","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1126\/science.aaz1776","article-title":"The GTEx Consortium atlas of genetic regulatory effects across human tissues","volume":"369","author":"GTEx Consortium","year":"2020","journal-title":"Science"},{"key":"2022010507351326500_B3","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1016\/j.cell.2016.10.026","article-title":"Genetic drivers of epigenetic and transcriptional variation in human immune cells","volume":"167","author":"Chen","year":"2016","journal-title":"Cell"},{"key":"2022010507351326500_B4","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1126\/science.aad6970","article-title":"Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases","volume":"353","author":"Franzen","year":"2016","journal-title":"Science"},{"key":"2022010507351326500_B5","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1038\/s41588-018-0154-4","article-title":"Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation","volume":"50","author":"Gamazon","year":"2018","journal-title":"Nat. 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