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I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm not looking for databases that contain additional information (pathogenicity etc.) on SNPs that are already in dbSNP, instead I want to know if there are any other databases that contain SNPs that aren't found in dbSNP.

I've been searching online and so far the only databases I can find are either deprecated or integrated into dbSNP, so any suggestions would be great.

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I'm pretty sure there are no public databases of variants that aren't included in dbSNP. That is the variant database so that's the one you want to use.

While there are various other databases around, they tend to use dbSNP rsIDs as well so any variants in those will also be in dbSNP. So while dbSNP is nowhere near complete, of course, it's still the most complete one you're likely to find.

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  • $\begingroup$ Fair enough, just thought I'd check. Thanks! $\endgroup$
    – JSneathThompson
    Commented Apr 30, 2018 at 18:10
  • $\begingroup$ Just adding to that, some of the more specialised databases (including OpenSNP) can be found for example here: biokeanos.com/search?q=SNPs+snp+%2Bhuman. $\endgroup$
    – ellimilial
    Commented Feb 5, 2021 at 13:09

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