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Protocols

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 citations

 (12)
library_books

Integrative analysis of super enhancer SNPs for type 2 diabetes

2018
PLoS One
PMCID: 5792005
PMID: 29385209
DOI: 10.1371/journal.pone.0192105

[…] GWAS3D was used to identify T2D super enhancer SNPs which have a long-range interaction signal with their distal regulatory elements. Finally, we detected 82 SNPs (Fisher’s combined p-value < 1×E-5) a […]

library_books

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

2017
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 […]

library_books

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

2017
Circ Res
PMCID: 5253231
PMID: 27899403
DOI: 10.1161/CIRCRESAHA.116.308765

[…] Annotation did not identify any nonsynonymous variants in high linkage disequilibrium (R2>0.5) with the lead SNPs at the AAA risk loci (Online Tables XIV and XV). Based on GWAS3D analysis, all 9 lead SNPs were associated with TF-binding site affinity variants (Online Tables XVI and XVII). Eight SNPs had potential long-range interactions with distal genomic regions (Figu […]

call_split

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

2016
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 […]

library_books

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

2016
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 […]

library_books

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

2016
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 […]

Citations

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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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