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I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of phenotypic effects with some additional metadata. Thank you in advance.

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  • $\begingroup$ Any type of disease, or just a subset? $\endgroup$ – mdperry Jun 27 '15 at 17:13
  • $\begingroup$ @mdperry any Mendelian disease will do. $\endgroup$ – Eli Korvigo Jun 27 '15 at 17:27
  • $\begingroup$ @EliKorvigo Did you not find the desired information in the GWAS databases that I mentioned below? $\endgroup$ – WYSIWYG Jun 28 '15 at 9:16
  • $\begingroup$ @WYSIWYG I'm struggling to find true negatives. I've already found plenty of true positives though. Thank you for your answer. I'll wait a couple of days before accepting it in case someone else comes up with a valid way to find true negatives. $\endgroup$ – Eli Korvigo Jun 28 '15 at 9:44
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    $\begingroup$ @EliKorvigo - Be wary of the statistics for GWAS studies. Clinically we don't get too excited about them because the cost-effectiveness of doing a study has surpassed the ability for appropriate statistical analysis - the sample sizes are almost always much too small - too much noise to signal - there are several reviews to discuss this, e.g. [ncbi.nlm.nih.gov/pubmed/18464043] (review) $\endgroup$ – Vance L Albaugh Jun 28 '15 at 14:16
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You can search by traits (mostly diseases) for genome wide association, in these databases:

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Just to make this post a tiny bit more useful, I must add that there are several additional sources I've found:

  • UniProt has an open dataset called humsavar
  • ClinVar database
  • HGMD database
  • OMIM
  • A paper with a manually collected database based on recent publications in Nature Genetics.

Different datasets intersect to some extent, but all in all you get over 200k somewhat validated SNPs.

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