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

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

SUBMITTER: Johnson AD

PROVIDER: S-EPMC2720775 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

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

Johnson Andrew D AD Handsaker Robert E RE Pulit Sara L SL Nizzari Marcia M MM O'Donnell Christopher J CJ de Bakker Paul I W PI

Bioinformatics (Oxford, England) 20081030 24

<h4>Summary</h4>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, a ...[more]

PMID: 18974171

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