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Does anyone know of a way to convert single nucleotide polymorphism (SNP) IDs from rs# to SNP_A-#? I have two SNPs, rs429358 and rs4420638, and need to determine whether these SNPs are included in a different dataset. The dataset uses SNP_A-xxxxx symbols for SNP IDs. Any help would be greatly appreciated!
The SNP_A### identifiers are very likely Affymetrix SNP ids. You will need to know which array they come from but it is probably the human Genomewide SNP 6.0.
You can download annotation data from Affymetrix website which will give a rs# to affyid# mapping. Try starting at: http://www.affymetrix.com/support/mas/index.affx#1_1
Select “Annotation Files” under “Software and Data” for the Genomewide SNP 6.0 array product.
One gotcha is that some probesets on the array are redundant – for a small subset you will have multiple affyid# mapping to one rsid#