Why some SNP databases don't contain the strand information

Question

[camelbbs]

Hi all,

While I checked the database such as ClinVar and COSMIC, I didn't find the strand information (+ or -) for their SNP sites. But the dbSNP database such as SNP142 contains the strand information. So if there is no strand info, how I can know the SNP is located in plus or minus strand? Does the ClinVar and COSMIC SNP sites represent both strand?

I want to check if there are SNPs located in promoter sequence that changing a special sequence structure in promoter, and because the promoter have sequence direction, so I think I need to know the SNP strand, is that right?

Thanks very much for any help,

Cam

Answer 1

[Pablo]

It depends in which format you retrieve the database. For instance, ClinVar is available in VCF and by definition VCF represents variants ok the plus strand, so there is no need to specify the strand (it is implied by the file format).

For what you are trying to achieve you don't need any of that. You can just annotate the variants and filter those annotated as "upstream". Furthermore, most variant annotation software lets you specify the up/downstream size, so you can customize it according to your definitions of "promoter", e.g. in SnpEff you can use -ud parameter option (See here).