Enlis.com is by far the best publicly-available tool for SNP and whole-genome analysis. Promethease is based off of SNPedia, which is a wiki SNP database and much less complete than the professional databases like dbSNP. Other tools, like GeneticGenie, exist in a gray area of pseudoscience-derived speculation and extrapolations from the alternative health community. Nothing wrong with that per se, but if you want reliable peer-reviewed data be careful with GeneticGenie.
In addition to being one of the only science-based genome analysis tools, Enlis offers a whole range of search and query-functions. For example, you can search for SNPs with predicted deleterious effects to mRNA or protein folding, and filter by genes that are conserved across mammalian lineages: