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3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues
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′ untranslat...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728222/ https://www.ncbi.nlm.nih.gov/pubmed/34432052 http://dx.doi.org/10.1093/nar/gkab740 |
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author | Cui, Ya Peng, Fanglue Wang, Dan Li, Yumei Li, Jason Sheng Li, Lei Li, Wei |
author_facet | Cui, Ya Peng, Fanglue Wang, Dan Li, Yumei Li, Jason Sheng Li, Lei Li, Wei |
author_sort | Cui, Ya |
collection | PubMed |
description | 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′ untranslated region (3′UTR) alternative polyadenylation (APA) quantitative trait loci (3′aQTLs), which can be used to interpret ∼16.1% of GWAS SNPs and are distinct from gene expression QTLs and splicing QTLs. Despite the growing interest in 3′aQTLs, there is no comprehensive database for users to search and visualize them across human normal tissues. In the 3′aQTL-atlas (https://wlcb.oit.uci.edu/3aQTLatlas), we provide a comprehensive list of 3′aQTLs containing ∼1.49 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′aQTL-atlas provides a ∼2-fold increase in sample size compared with our published study. It also includes 3′aQTL searches by Gene/SNP across tissues, a 3′aQTL genome browser, 3′aQTL boxplots, and GWAS-3′aQTL colocalization event visualization. The 3′aQTL-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. |
format | Online Article Text |
id | pubmed-8728222 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87282222022-01-05 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues Cui, Ya Peng, Fanglue Wang, Dan Li, Yumei Li, Jason Sheng Li, Lei Li, Wei Nucleic Acids Res Database Issue 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′ untranslated region (3′UTR) alternative polyadenylation (APA) quantitative trait loci (3′aQTLs), which can be used to interpret ∼16.1% of GWAS SNPs and are distinct from gene expression QTLs and splicing QTLs. Despite the growing interest in 3′aQTLs, there is no comprehensive database for users to search and visualize them across human normal tissues. In the 3′aQTL-atlas (https://wlcb.oit.uci.edu/3aQTLatlas), we provide a comprehensive list of 3′aQTLs containing ∼1.49 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′aQTL-atlas provides a ∼2-fold increase in sample size compared with our published study. It also includes 3′aQTL searches by Gene/SNP across tissues, a 3′aQTL genome browser, 3′aQTL boxplots, and GWAS-3′aQTL colocalization event visualization. The 3′aQTL-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. Oxford University Press 2021-08-25 /pmc/articles/PMC8728222/ /pubmed/34432052 http://dx.doi.org/10.1093/nar/gkab740 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Cui, Ya Peng, Fanglue Wang, Dan Li, Yumei Li, Jason Sheng Li, Lei Li, Wei 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title | 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title_full | 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title_fullStr | 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title_full_unstemmed | 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title_short | 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues |
title_sort | 3′aqtl-atlas: an atlas of 3′utr alternative polyadenylation quantitative trait loci across human normal tissues |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728222/ https://www.ncbi.nlm.nih.gov/pubmed/34432052 http://dx.doi.org/10.1093/nar/gkab740 |
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