GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

Nucleic Acids Research
Dandan HuangMulin Jun Li

Abstract

Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab.tmu.edu.cn/gwas4d or http://mulinlab.org/gwas4d), that systematically evaluates GWAS signals and identifies context-specific regulatory variants. The updated web server includes six major features: (i) updates the regulatory variant prioritization method with our new algorithm; (ii) incorporates 127 tissue/cell type-specific epigenomes data; (iii) integrates motifs of 1480 transcriptional regulators from 13 public resources; (iv) uniformly processes Hi-C data and generates significant interactions at 5 kb resolution across 60 tissues/cell types; (v) adds comprehensive non-coding variant functional annotations; (vi) equips a highly interactive visualization function for SNP-target intera...Continue Reading

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Aug 19, 2016·Nature·Monkol LekUNKNOWN Exome Aggregation Consortium
Dec 1, 2017·Nature Communications·Kyoko WatanabeDanielle Posthuma

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Citations

Nov 8, 2018·Database : the Journal of Biological Databases and Curation·Ruifeng HuZhongming Zhao
Nov 18, 2018·Nucleic Acids Research·Xianfeng LiFengbiao Mao
Sep 4, 2019·Nature Communications·Somsakul Pop WongpaleeSteven E Jacobsen
Dec 8, 2019·Scientific Reports·S Akila Parvathy DharshiniM Michael Gromiha
Jun 12, 2020·Frontiers in Cell and Developmental Biology·Hecun ZouHong-Hao Zhou
Mar 2, 2019·Nature Genetics·Brian W KunkleUNKNOWN Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium (
Jul 17, 2020·Computational and Structural Biotechnology Journal·Alexandria Lau, Hon-Cheong So
Nov 20, 2020·Computational and Structural Biotechnology Journal·Xuanshi LiuWei Li
Apr 6, 2021·Frontiers in Genetics·S Akila Parvathy DharshiniM Michael Gromiha
Aug 13, 2021·Advanced Science·Siyu WeiYongshuai Jiang
Apr 27, 2021·The Journal of Investigative Dermatology·Maria K SobczykUNKNOWN eQTLGen Consortium, BIOS Consortium, GoDMC

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