dbSNP: getting the population/country information from rs dbSNP id's

Question

[hrbrt.sch]

Hi,

I just want to get all informations (countries) for multiple dbSNP ID's.

For example:

"rs9934438", where was the data collected?

So is it from nord africa, from caucasian or something like that.

The results should like like this:

rs9934438 from "nord africa" (this is still just an arbitrary example)

I tried biomart but I didn't found this information in this R package.

In general, I want to calculated the frequencies from multiple rs ID's and where there are occurred (countries, population).

I am very grateful for your help.

[Jautis]

I'm not sure what resources exist, but are all the data you want in a downloadable file? If so, you can then use the match function in R to help fill in a new column.

[Ram]

This might be achievable, but not with match. It's way too complicated - you might need to create your own snp id - set of populations list and that might not be worth the effort. Better off picking populations where AF>0.00, no?

[hrbrt.sch]

I have a list with #rs ID's, and for this I can use the match function from bioMart?

Answer 1

[Ram]

This depends on the source of the information. dbSNP is a portal through which variants (not just SNVs) from a multitude of sources. If the variants are sourced from 1000 genomes or NHLBI ESP, you can get the underlying population (or even the individual in the case of 1000genomes).

Your example is from 1000 genomes, so the details can be seen here

Answer 2

[kautilya]

You could also have a look at ALFRED. It is a database of allele frequency data. Obviously it will also give you the countries/populations where the variation has occurred. Sadly I doesn't seem to have the variation(rs9934438) you have quoted here. But you could still fetch the information for those that are available. The frequency data is also can be downloaded here for scripting/automation purposes.

[hrbrt.sch]

Thank you for your help, I really appreciate it!!!

I will try it with the recommended sites.