SNP databases
I am just beginning to understand the world of online SNP databases. Known SNPs have unique ids (often called dbSNP ids) that start with rs — the PRNP D178N SNP is rs74315403 — and if you google one of them, you’ll find tens of websites that collect information about SNPs. Most notable and widely used are dbSNP by NCBI (page on rs74315403) searchable either by SNP id or by search term such as ‘ffi’, and 1000 genomes (page on rs74315403), searchable by things like SNP id, gene name, etc. but not as much by search terms. The prevalence of a particular SNP among indivudals in dbSNP and 1000 genomes are often used to estimate minor allele frequency. (Both databases appear to have zero individuals carrying rs74315403).
Perhaps more surprising, but not that surprising when you think about it, is the existence of OpenSNP, a project which someone somewhere has surely labeled “the social genome”. It’s a site which “allows customers of direct-to-customer genetic tests to publish their test results, find others with similar genetic variations, learn more about their results, find the latest primary literature on their variations and help scientists to find new associations”. People put their names and pictures on it and add phenotypic details such as whether they drink coffee. The site is super clean and they are dead serious about openness with data: if you click on “Genotypes”, right front and center is a link to download all the genotypes and phenotypes in one file. No one on the site has D178N, but for SNPs that are present you can get info and a list of people with the SNP, for instance for rs11954652.