Finding dbSNP 129 rsIDs for lifting over hg18 sumstats to hg38

Question

[marcelofrancia]

Hi all,

I'm currently working on lifting a summary statistics file from the genome build hg18 to hg38. The file format for the sumstats is as follows:

marker Allele1 Allele2 beta1 SE pValue chr Bp

chr10:100004799 a c 0.3528 0.2808 0.2089 10 100004799

chr10:100011120 a t 0.0673 0.2327 0.7726 10 100011120

I have followed other questions on this and other forums into how to perform the lift over, and it seems that it is best to start with adding the correct rsIDs to these variants.

My current issue is that I have tried to find the dbSNP 129 files, but I have been unable to do so in the dbSNP page itself, Ensembls' biomart or the UCSC browser.

If anyone could point me towards a download page for this dbSNP version I would greatly appreciate it. Thank you.

Answer 1

[marcelofrancia]

For anyone that is interested in getting this file, I finally found the way.

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The first step is to go to the UCSC Genome browser page, and then within that page use the ftp, or http link to join the server. Once in the server, go to the "database" folder, and then within that folder look for the "snp129.txt.gz" file. There are other snp versions as well within that folder.