Is There A Snp Database With Geography Specific Annotations?

Question

[munch]

I am looking for known homo sapiens SNP informations for probes taken in different countries or geographic regions. I have tried to filter dbSNP but without much success.

Thank you in advance for your efforts.

Answer 1

[Ryan D]

You should talk to my friend, Alfred. He doesn't know it for every SNP, but he sure knows it for a lot.

http://alfred.med.yale.edu/

Alfred is the ALlele FREquency Database and for many SNPs has a link to Google Maps. Also, 1000 Genomes has the following populations. The left column is an indicator of the specific population it is drawn from, while the right column is a more continental indicator. Information about where these samples are drawn from is here:

http://www.1000genomes.org/about#ProjectSamples

ASW     AFR
CEU     EUR
CHB     ASN
CHS     ASN
CLM     AMR
FIN     EUR
GBR     EUR
IBS     EUR
JPT     ASN
LWK     AFR
MXL     AMR
PUR     AMR
TSI     EUR
YRI     AFR

[munch]

Alfred seems really suitable for my work. Thank you!

Answer 2

[Jorge Amigo]

dbSNP first intention has always been to catalogue polymorphic genomic sites. but since the availability of the data has drastically changed in the last few years, the database has also evolved. although dbSNP contains population frequency information from several sources we can't forget that dbSNP is not a population focused tool. it's true that if you're looking for a particular site you may have population information for it, but it's not intended to have this information for all its sites (in fact, population information in dbSNP is patchy, yet useful if it has what you're looking for).

the major source for human variation information until a couple of years ago was the HapMap project. right now, there are giant public efforts like 1000genomes or other NGS massive projects that represent new and much more dense sources of variation. we currently host a human variation collating effort called SPSmart, population genetics oriented as we report indexes such as MAF or Fst for any particular population combination, which contains data from 1000genomes (~10 populations, ~30M sites), hapmap (~10 populations, ~4M sites), and the CEPH panel (~50 populations, ~600K sites).