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SNPsnap: a Web-based tool for identification and annotation of matched SNPs.

ABSTRACT: An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co-localization of GWAS signals to gene-dense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density.SNPsnap server is available at http://www.broadinstitute.org/mpg/snpsnap/.joelh@broadinstitute.orgSupplementary data are available at Bioinformatics online.

SUBMITTER: Pers TH

PROVIDER: S-EPMC4308663 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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SNPsnap: a Web-based tool for identification and annotation of matched SNPs.

Pers Tune H TH Timshel Pascal P Hirschhorn Joel N JN

Bioinformatics (Oxford, England) 20141013 3

<h4>Summary</h4>An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co-localization of GWAS signals to gene-dense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analy ...[more]

PMID: 25316677

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