Here we describe a comprehensive web server designed to select SNPs for genetic association studies. In designing this application we provide 3 pipelines for SNP selection with options to combine all three pipelines. The candidate gene pipeline uses both a user-provided list of candidate genes and disease-specific GWAS data [readily available from dbGaP (www.ncbi.nlm.nih.gov/sites/entrez?db=gap) and elsewhere] to select SNPs that are predicted to have functional consequences and that are in high LD with a small P-value GWAS SNP. For genes where a large proportion of the SNPs were not in LD with any GWAS SNP and thus are uninvestigated in the GWAS, the web application can pick LD tag SNPs to evaluate the untagged SNPs. The second, genomic pipeline selects SNPs with likely functional consequences from SNPs with small P-value in a GWAS and from SNPs in high LD with such SNPs. The third, linkage pipeline uses a user-provided list of linkage regions to select small P-value GWAS SNPs for each linkage region. The web application has information on all SNPs in HapMap and dbSNP and automatically constructs ethnic-specific LD
