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

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

¹The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health and Boston University School of Medicine, Framingham, MA 01702, USA
²Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
³Division of Genetics, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School-Partners HealthCare Center for Genetics and Genomics, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
⁴Cardiology Division, Massachusetts General Hospital, Boston, MA 02114, USA

Received on August 13, 2008; revised on October 16, 2008; accepted on October 24, 2008; Advance Access publication October 30, 2008

Associate Editor: Alex Bateman

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

Contact: [email protected]

^*To whom correspondence should be addressed.

^†The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Bioinformatics 24(24):p 2938-2939, December 15, 2008.

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).