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OpenSNP and SNP position information

I have emailed the folks at OpenSNP for some clarification, but I figure those here may know, and certainly if I get any information back from OpenSNP I will post it up in this thread.

I have recently starting doing some research using OpenSNP.

Does anyone know if the information on there is from GRCh37 or GRCh38?

I ask because for example, SNP rs1000016 is position 235690982 in GRCh37 and 234782338 in GRCh38.

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1000016

Yet in the OpenSNP database, when I pull up the SNP, It shows "Human GrCh37/hg19" in the Genome Browser Window, but the position given for the SNP is from GRCh38. https://opensnp.org/snps/rs1000016

When you get a aDNA report from 23andMe or Ancestry, it uses GRCh37. So in trying to do analysis of these reports against data on OpenSNP I run into issues. I have also seen that SNPedia has the same location as OpenSNP (GRCh38).

Just trying to figure out the best way to handle this and do my analysis.

Brian

opensnp
• 3,158 views • link
updated by Ram Ram • written by bfeeny • bfeeny

Here is a response I got from OpenSNP:

Hi Brian,

Thanks for getting in touch. So all SNP data which you can see on the website or get through the API is GRCh38. I'm not 100% sure why the genome browser is still showing the 37 right now (@Philipp: iirc you did the lift over, did you switch the DAS track there as well?).

For the downloads: I think by now 23andMe also switched to 38, but I'm not sure, in any case the Problem will remain the same, as we don't mess with the raw files as they are uploaded. So there will be NCBI36 to GRCh38 versions present. The easiest way to deal with those differences is to stick to the Rs-IDs which are pretty stable.

Hope that helps!

Cheers,
Bastian

• 0 views • link
updated by Ram Ram • written by bfeeny • bfeeny

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