Question: Can't locate dbSNP 131 anymore?
1
gravatar for DVA
3.5 years ago by
DVA530
United States
DVA530 wrote:

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 • 1.1k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by DVA530

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.

ADD REPLYlink written 3.5 years ago by Chris Miller21k

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

ADD REPLYlink written 3.5 years ago by DVA530
2
gravatar for DVA
3.5 years ago by
DVA530
United States
DVA530 wrote:

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

ADD COMMENTlink written 3.5 years ago by DVA530
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