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.


To get started with SNAP, use the links below:


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


The SNAP server was developed and implemented by Bob Handsaker based on a concept design specified by Andrew Johnson. Sara Pulit contributed R code for generating plots. Greg Rushton developed the web interface for version 2.0. Douglas Voet added support for HapMap III release 2.

The regional association plots are based on a concept developed by Paul de Bakker for the genome-wide association study by the Diabetes Genetics Initiative (Science, 2007).

Computing resources for SNAP are provided by the Genomics Platform at the Broad Institute.
SNAP relies on data from the International HapMap Project.
The SNP annotations used in SNAP are from Gene Cruiser.

SNAP development is funded, in part, by the NHLBI CARe (Candidate Gene Resource) grant (N01-HC-65226), to REH, and by NHLBI's Framingham Heart Study (N01-HC-25195) and the Intramural training program of the NHLBI to ADJ.