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Bioinformatics Advance Access published online on October 30, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn564
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Andrew D. Johnson 1,{dagger}, Robert E. Handsaker 2,{dagger}, Sara L. Pulit 3, Marcia M. Nizzari 2, Christopher J. O’Donnell 1,4 and Paul I. W. de Bakker 2,3,*

1The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health and Boston University School of Medicine (supported by Contract No. N01-HC-25195), 73 Mt. Wayte Ave, Suite 2, Framingham, MA 01702
2Broad Institute of MIT and Harvard, Cambridge, MA 02142
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
4Cardiology Division, Massachusetts General Hospital, Boston, MA 02114

*To whom correspondence should be addressed. Paul I. W. de Bakker, E-mail: debakker{at}broad.mit.edu


  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: http://www.broad.mit.edu/mpg/snap/

Contact:johnsonad2{at}nhlbi.nih.gov, handsake{at}broad.mit.edu, debakker{at}broad.mit.edu

Associate Editor: Dr. Alex Bateman

{dagger}These authors contributed equally to this work

Received on August 13, 2008; revised on October 16, 2008; accepted on October 24, 2008

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