How To Interpret Snp Annotations In The Pharmapgkb Database
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8.5 years ago
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I'looking at the PharmaPGKB database for SNPs.

I'm trying to understand what the following annotation means:

rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP)


Ok, the SNP identified by rs1801131 occur in the first chromosome, at the position 11854475.

Then, the two genes' identifiers come: the position rs1801131 is inside the gene MTHFR, why do they also annotate the SNP to the gene CLCN6 (which is a "neighbour" of MTHFR) ?

snp • 1.5k views
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8.5 years ago

I agree that this is a bit confusing. I suspect that this is generated by some kind of automated or semi-automated process by which SNPs are associated with genes by proximity. This SNP is within MTHFR but the closest gene that this SNP is upstream of is CLCN6. Many researchers are interested in SNPs in a regulatory context perhaps they associate SNPs with a gene where they are within N bases of a transcription start site of that gene...

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Of course we can speculate about this, but I would suggest to contact PharmaPGKB to ask for an explanation. Maybe they associate SNPs with genes by proximity as Malachi suggests, maybe they get the associations from literature, maybe they have done association studies themselves, I have no idea and I also couldn't find any documentation on their website .... so you better go to the source of the data.