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

Tune Hannes Pers, Pascal Timshel, Joel N. Hirschhorn

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Summary: 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.
    Availability and implementation: SNPsnap server is available at http://www.broadinstitute.org/mpg/snpsnap/. Contact: joelh@broadinstitute.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Original languageEnglish
    JournalBioinformatics
    Volume31
    Issue number3
    Pages (from-to)418-420
    Number of pages3
    ISSN1367-4803
    DOIs
    Publication statusPublished - 2015

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