Question: Browser of 1000 genome phase 3 showing allele frequency in each population
0
gravatar for qwzhang0601
3.2 years ago by
qwzhang060160
United States
qwzhang060160 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 • 1.4k views
ADD COMMENTlink modified 3.2 years ago by Giovanni M Dall'Olio26k • written 3.2 years ago by qwzhang060160
2

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

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum122k
2
gravatar for Giovanni M Dall'Olio
3.2 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

enter image description here

enter image description here

ADD COMMENTlink written 3.2 years ago by Giovanni M Dall'Olio26k

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 3.2 years ago by qwzhang060160

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

ADD REPLYlink written 3.2 years ago by Denise - Open Targets5.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2185 users visited in the last hour