Browser of 1000 genome phase 3 showing allele frequency in each population

Question

[qwzhang0601]

I am interested in several genes and what to look at their SNP information in different populations from 1000 genome data phase3. I wonder whether there are such browser or tracks showing allele frequency of SNPs in each population (five super populations or 26 subpopulations). Then I can check which SNP show difference among populations, and whether this SNP is in coding region or regulatory regions.

Thanks

[Pierre Lindenbaum]

how about using Exac instead of 1000g ? the information about each population is available in the VCF file.

Answer 1

[Giovanni M Dall'Olio]

• the 1000Genomes browser itself. Select any variant, click on Population Genetics, and get a summary of the frequency like the following: http://browser.1000genomes.org/Homo_sapiens/Variation/Population?db=core;r=9:22125003-22126003;v=rs1333049;vdb=variation;vf=896935

• EBI EVA: Select any variant from 1000G or ExAc, then on Variant Data click Population Statistics

[qwzhang0601]

Thanks, this can be useful. But is there a way to show the allele frequencies (of different populations) of all SNPs in a gene (or a region), instead of one specific SNP? Then I can see (by eyes) in a gene where show differences among populations, and then I can take a loser look to such SNPs.

[Denise CS]

If you had a VCF file, you could use the Allele Frequency Calculator.