SNP LD database from Broad Institute

 Link: http://www.broadinstitute.org/mpg/snap/ldsearchpw.php

SNAP finds proxy SNPs based on linkage disequilibrium, physical distance and/or membership in selected commercial genotyping arrays. Pair-wise linkage disequilibrium is pre-calculated based on phased genotype data from the International HapMap Project. Information about the genotyping arrays is based on data published by the vendors.

SNAP can also generate linkage disequilibrium plots, like the one shown at the right. To generate plots, click on the Plots tab above and select plotting options.

Data from 1000 Genomes Pilot 1 is now available by selecting 1000 Genomes Pilot 1 as the SNP data set. For details see SNP Data Set.

Links

To get started with SNAP, use the links below:

• SNAP Proxy Search
• Frequently Asked Questions
• SNAP Documentation
• Release Notes October 25, 2012

Citation

Johnson, A. D., Handsaker, R. E., Pulit, S., Nizzari, M. M., O'Donnell, C. J., de Bakker, P. I. W.
SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap
Bioinformatics, 2008 24(24):2938-2939