Question: Browser of 1000 genome phase 3 showing allele frequency in each population
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gravatar for qwzhang0601
4.2 years ago by
qwzhang060170
United States
qwzhang060170 wrote:

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

snp sequence gene genome • 1.7k views
ADD COMMENTlink modified 4.2 years ago by Giovanni M Dall'Olio27k • written 4.2 years ago by qwzhang060170
2

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

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum130k
2
gravatar for Giovanni M Dall'Olio
4.2 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

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ADD COMMENTlink written 4.2 years ago by Giovanni M Dall'Olio27k

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.

ADD REPLYlink written 4.2 years ago by qwzhang060170

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

ADD REPLYlink written 4.2 years ago by Denise CS5.1k
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