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Converting rs number SNP IDs from hg18 to hg19

Hi. I have data back from my DNA samples that were run on the Illumina Neuro consortium array. The SNP list for this array is based on UCSC Hg19. There are a few SNPs of interest from a previous GWAS whose data I would like to extract from my current data. However, the SNP ID and chromosomal position of these GWAS hits are based on the UCSC hg18 and therefore cannot be found when searched for on the Neuro consortium array SNP list (the list has both a SNP rs ID column and a corresponding SNP position column).

I've used an online converter (http://genome.ucsc.edu/cgi-bin/hgLiftOver) but the equivalent hg19 SNP position I get, again, cannot be found in the Neuro consortium array SNP list.

Can anyone please help me get over this obstacle??

Best wishes, Ed

snp
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written by e.jabbari • e.jabbari

So you have the rs IDs? Or you have the coordinates? Always helpful to show an example of how exactly your data looks like.

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written by WouterDeCoster WouterDeCoster
  1. Find out genome build of Neuro consortium array SNP list.
  2. Then you can use liftover to corresponding genome build to update the SNPs in your list
  3. Otherway is to take the rsIDs (assuming that your list is fully annotated with rsIDs) and extract corresponding coordinates from latest dbSNP vcf).
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written by cpad0112 cpad0112

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