The SNP Consortium database

http://snp.cshl.org

Thorisson, G. A., Stein, L. D.

Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor 11724 New York USA

Database Description

The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or SNP keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the DCC website (http://snp.cshl.org) are open source.

Recent Developments

GMOD genome browser showing SNPs in context of genes and other features on the genome assembly. Gene keyword search. SNP allele frequency and genotype data, from a number of human populations (asian, african-american, african,caucasian).

REFERENCES

Sachidanandam, R., Weissman, D., Schmidt, S., Kakol, J., Stein, L., Marth, G., Sherry, S., Mullikin, J., Mortimore, B., Willey, D., Hunt, S., Cole, C., Coggill, P., Rice, C., Ning, Z., Rogers, J., Bentley, D., Kwok, P., Mardis, E., Yeh, R., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R., McPherson, J., Gilman, B., Schaffner, S., Van Etten, W., Reich, D., Higgins, J., Daly, M., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M., Linton, L., Lander, E., and Altshuler, D. ; The International SNP Map Working Group.(2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928-933.