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Can't locate dbSNP 131 anymore?

Hello,

I have some microarray data from a few years ago, and the rs identifier in the file was from dbSNP 131. In order to do some analysis on this old data, I will need to know the positions of the microarray SNPs, and thus would like to download dbSNP131.

However, on UCSC Table Browser, I can no long find this database. I tried: assembly: hg19, group: Variations - then there is no dbSNP131 under tracks.

Does anyone know any other places to access dbSNP131 please? Or, is it save to just use dbSNP 138? The microarray chip was HumanOmni2.5-8v1 from Illumina.

Thank you

dbsnp
• 2,626 views • link
updated by Ram Ram • written by DVA DVA

Hrmm... the dbSNP site doesn't appear to archive older data after poking around a bit. Sorry, that's not much help. Deleting my original answer.

• 0 views • link
updated by Ram Ram • written by Chris Miller Chris Miller

Don't worry about it. I found one from ANNOVAR. Thank you very much for your reply.

• 0 views • link
written by DVA DVA

2 answers

Okay after some digging, I found that you can downloading all old version of dbSNP databases from ANNOVAR.

Command:

annotate_variation.pl -buildver hg19 -downdb -webfrom annovar snp131 humandb/

The format is exactly the same with the dbSNP table from UCSC: https://genome.ucsc.edu/cgi-bin/hgTables

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

Go right to the source:

https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?view+summary=view+summary&build_id=131

ftp://ftp.ncbi.nlm.nih.gov/snp/

• 0 views • link
updated by Ram Ram • written by Chris Miller Chris Miller

Thank you Chris, but I must missed something important here - I tried ftp://ftp.ncbi.nlm.nih.gov/snp/, and clicked all the folders, but still don't see a link to dbSNP. Sorry if my question sounds very silly. I would really appreciate your help.

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updated by Ram Ram • written by DVA DVA

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