GWAS3D specifications

Information


Unique identifier OMICS_08579
Name GWAS3D
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Junwen Wang <>

Publication for GWAS3D

GWAS3D in publications

 (7)
PMCID: 5792005
PMID: 29385209
DOI: 10.1371/journal.pone.0192105

[…] factor enrichment analysis using snp2tfbs (http://ccg.vital-it.ch/snp2tfbs/) tool which selects and visualizes user defined variants that affect single or multiple transcription factors., gwas3d (http://jjwanglab.org/gwas3d) systematically calculates the probability of gwas-associated snps which affect regulatory pathways and underlie disease associations by integrating functional […]

PMCID: 5253231
PMID: 27899403
DOI: 10.1161/CIRCRESAHA.116.308765

[…] loci identified were extracted from the 1000 genomes data and then entered into pupasuite v3.1. in addition, all known (novel and previously identified) aaa-associated snps were entered into the gwas3d (bioinformatics tool detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions, and histone modifications) web-portal […]

PMCID: 5378805
PMID: 28044063
DOI: 10.1038/mp.2016.241

[…] funcisnp http://bioconductor.org/packages/2.12/bioc/html/funcisnp.html., transfac http://www.gene-regulation.com/index2., mapper2 http://genome.ufl.edu/mapperdb., gwas3d http://jjwanglab.org/gwas3d/., deepsea http://deepsea.princeton.edu/job/analysis/create/., nrcistrome http://www.cistrome.org/cistrome/cistrome_project.html., gwava […]

PMCID: 5120913
PMID: 27861356
DOI: 10.1097/MD.0000000000005300

[…] sites and identification of variants that disrupt enhancers, repressors, and promoters. complementary annotations were performed using cadd,[] regulomedb,[] haploreg v4,[] snipa,[] and rvarbase.[] gwas3d was used to predict genetic variants or variants in linkage disequilibrium (ld) affecting regulatory pathways and essential disease/trait associations by integrating functional genomics, […]

PMCID: 4773152
PMID: 26930606
DOI: 10.1371/journal.pone.0150070

[…] organisms. string was used to generate risk gene (protein) network., interpreting disease associated non-coding snps is an indispensable step to understand molecular mechanism of complex diseases. gwas3d (http://jjwanglab.org/gwas3d) systematically computes the probability of gwas associated snps affecting regulatory pathways and underlying disease associations by integrating chromatin state, […]


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GWAS3D institution(s)
Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
GWAS3D funding source(s)
Research Grants Council [781511M] of Hong Kong and National Science Foundation [91229105] of China

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