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. 2008 Dec 15;24(24):2938-9.
doi: 10.1093/bioinformatics/btn564. Epub 2008 Oct 30.

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

Andrew D Johnson  1 , Robert E Handsaker, Sara L Pulit, Marcia M Nizzari, Christopher J O'Donnell, Paul I W de Bakker
Affiliations

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

Andrew D Johnson et al. Bioinformatics. .

Abstract

Summary: The interpretation of genome-wide association results is confounded by linkage disequilibrium between nearby alleles. We have developed a flexible bioinformatics query tool for single-nucleotide polymorphisms (SNPs) to identify and to annotate nearby SNPs in linkage disequilibrium (proxies) based on HapMap. By offering functionality to generate graphical plots for these data, the SNAP server will facilitate interpretation and comparison of genome-wide association study results, and the design of fine-mapping experiments (by delineating genomic regions harboring associated variants and their proxies).

Availability: SNAP server is available at http://www.broad.mit.edu/mpg/snap/.

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Figures

Fig. 1.
Fig. 1.
Regional LD plot for SNPs rs10757278 and rs10811661 at 9p21.3, associated with coronary artery disease and type 2 diabetes, respectively.
See this image and copyright information in PMC

References

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