In addition to the three pipelines the server provides three additional tools. The first of these ‘TagSNP’ allows a user to combine the SNP lists selected from different pipelines and eliminate redundant SNPs based on LD relationships and SNPs with low SNP design scores. It also allows the user to mandate inclusion of SNPs of special interest, or exclusion of undesired SNPs. This same tool may be used as a stand-alone tool to find and list SNPs, choose LD tag SNPs, and produce high quality LD or genotype figures for individual genes or chromosome regions. A second stand-alone tool, ‘FuncPred’ allows a user to query functional prediction results and ethnic group allele frequencies for all of the SNPs in a gene or chromosomal region, or for a list of input SNPs. The final tool ‘SNPseq’ allows a user to visualize SNP related information and CpG regions in DNA sequence context for an individual SNP, gene, or region of a chromosome. This is particularly useful for PCR primer design.
