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Number of citations per year for the bioinformatics software tool GWAS3D

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GWAS3D specifications


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


  • Primates
    • Homo sapiens


  • person_outline Junwen Wang

Publication for GWAS3D

GWAS3D citations


Integrative analysis of super enhancer SNPs for type 2 diabetes

PLoS One
PMCID: 5792005
PMID: 29385209
DOI: 10.1371/journal.pone.0192105

[…] affinity (), including 76 SNPs have direct effect by GWAS leading SNPs and 29 variants have indirect effect by high LD of GWAS leading SNPs. Interestingly, among the 105 functional SNPs identified by GWAS3D, 96 SNPs were also confirmed by HaploReg regulatory prediction results ( & ). […]


RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses

PLoS One
PMCID: 5404774
PMID: 28441463
DOI: 10.1371/journal.pone.0175957

[…] associated with continuous phenotypic traits. For examining whether the identified SNPs are in long range LD [], the pipeline could be supplemented with other methods or tools such as GLIDERS [] and GWAS3D []. Furthermore, the pipeline has not been tested whether it is able to detect the rare variants. Instead, other approaches such as those proposed by Hoffmann et al. [], sequence kernel associa […]


Meta Analysis of Genome Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease Specific Risk Loci

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

[…] a key role in the development of AAA.The other novel AAA loci identified here contain LINC00540, ERG, and SMYD2. LINC00540 is a long noncoding RNA with no currently known function; however, both our GWAS3D and eQTL analyses independently suggested an association with FGF9, which was also differentially expressed within AAA tissue. ERG encodes a TF that is normally present in hematopoietic and end […]


A childhood acute lymphoblastic leukemia genome wide association study identifies novel sex specific risk variants

PMCID: 5120913
PMID: 27861356
DOI: 10.1097/MD.0000000000005300
call_split See protocol

[…] ng 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, chroma […]


Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome Wide Association Studies

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

[…] SNPs rs1463104, rs4729260 and rs2887571 were detected as significant SNPs by GWAS3D based on the CEU population and all cell types listed in GWAS3D (). SNP rs1463104, located on the downstream of MEPE intronic region of DECR1 in chromosome 4, has two long-range interaction sig […]


High density genotyping of immune related loci identifies new SLE risk variants in individuals with Asian ancestry

Nat Genet
PMCID: 4767573
PMID: 26808113
DOI: 10.1038/ng.3496

[…] is shown in , and we report eQTL results in .We annotated epigenetic regulatory features for all independent lead SNPs (and their correlated variants r2>0.8) in our novel regions using the Haploreg, GWAS3D, and rSNPBase online tools. Haploreg provides functional annotations for binding motifs and epigenetic marks. GWAS3D aggregates epigenetic data from 16 cell types from multiple databases, inclu […]

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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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