TargetGene: a comprehensive database of cell-type-specific target genes for genetic variants

Abstract Annotating genetic variants to their target genes is of great importance in unraveling the causal variants and genetic mechanisms that underlie complex diseases. However, disease-associated genetic variants are often located in non-coding regions and manifest context-specific effects, makin...

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Published in:Nucleic acids research 2024-01, Vol.52 (D1), p.D1072-D1081
Main Authors: Lin, Shiqi, Wu, Song, Zhao, Wei, Fang, Zhanjie, Kang, Hongen, Liu, Xinxuan, Pan, Siyu, Yu, Fudong, Bao, Yiming, Jia, Peilin
Format: Article
Language:English
Subjects:
Chromatin - genetics
Databases, Factual
Genome-Wide Association Study - methods
Humans
Polymorphism, Single Nucleotide
Quantitative Trait Loci - genetics
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Summary:Abstract Annotating genetic variants to their target genes is of great importance in unraveling the causal variants and genetic mechanisms that underlie complex diseases. However, disease-associated genetic variants are often located in non-coding regions and manifest context-specific effects, making it challenging to accurately identify the target genes and regulatory mechanisms. Here, we present TargetGene (https://ngdc.cncb.ac.cn/targetgene/), a comprehensive database reporting target genes for human genetic variants from various aspects. Specifically, we collected a comprehensive catalog of multi-omics data at the single-cell and bulk levels and from various human tissues, cell types and developmental stages. To facilitate the identification of Single Nucleotide Polymorphism (SNP)-to-gene connections, we have implemented multiple analytical tools based on chromatin co-accessibility, 3D interaction, enhancer activities and quantitative trait loci, among others. We applied the pipeline to evaluate variants from nearly 1300 Genome-wide association studies (GWAS) and assembled a comprehensive atlas of multiscale regulation of genetic variants. TargetGene is equipped with user-friendly web interfaces that enable intuitive searching, navigation and browsing through the results. Overall, TargetGene provides a unique resource to empower researchers to study the regulatory mechanisms of genetic variants in complex human traits. Graphical Abstract Graphical Abstract
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad901