3'aQTL-atlas: an atlas of 3'UTR alternative polyadenylation quantitative trait loci across human normal tissues.
3' Untranslated Regions
/ genetics
Alternative Splicing
/ genetics
Gene Expression Regulation
/ genetics
Genome-Wide Association Study
Humans
Organ Specificity
/ genetics
Polyadenylation
/ genetics
Quantitative Trait Loci
/ genetics
RNA 3' Polyadenylation Signals
/ genetics
RNA, Messenger
/ genetics
Software
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
07 01 2022
07 01 2022
Historique:
accepted:
13
08
2021
revised:
10
08
2021
received:
31
07
2021
pubmed:
26
8
2021
medline:
24
2
2022
entrez:
25
8
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34432052
pii: 6357732
doi: 10.1093/nar/gkab740
pmc: PMC8728222
doi:
Substances chimiques
3' Untranslated Regions
0
RNA, Messenger
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
D39-D45Subventions
Organisme : NCI NIH HHS
ID : R01 CA193466
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
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