How to figure out which genotyping chips a SNP is on?
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8.2 years ago
dweeks.pitt ▴ 40

Is there a database that would answer this type of query:

Given an rs ID of a SNP, which commercial SNP chips is this SNP on?

I found this one, the SNAP database at the Broad:

https://www.broadinstitute.org/mpg/snap/ldsearch.php

which answers the question if the query SNP is in HapMap3 or 1000 Genomes Pilot 1, but our query SNP was not in either, so I’m not 100% certain this web site is doing the search I want it to do.

I suppose I could do it by downloading and searching all of these files

http://www.well.ox.ac.uk/~wrayner/strand/

but that is slow and cumbersome.

Seems like this is a particular type of annotation that should be available in at least one annotation database somewhere.

Thank you.

SNP SNP chip genotyping chip Illumina Affymetrix • 1.7k views
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