Question: Investigating a SNP with incomplete information on 1000 Genomes
0
gravatar for Nasir
3.4 years ago by
Nasir140
United Kingdom
Nasir140 wrote:

Hi All

I have encountered an issue which, I expect, will be relevant to others as well. My own example is as below:

rs12987787 is the most significant SNP in one phenotype of the GWAS published in this paper (PMID: 25087078). I wanted to investigate if it is in LD with any known eQTLs. However, it is not included in the 1000 genomes VCF files for the European population (downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/). It can be found by searching on the 1000 Genomes web browser, but on clicking the population genetics link, the browser says 'No population or frequency data'. In contrast, a nearby SNP from the same GWAS (rs496571) is in the VCF files and has population genetics data on the 1000 Genomes web browser.

What are the possible reasons for a SNP being present on the 1000 Genomes browser but having incomplete information and being absent from the VCF files? How can the reasons be investigated for any particular SNP?

Thank you!

1000 genomes snp gwas • 873 views
ADD COMMENTlink modified 3.4 years ago by Emily_Ensembl17k • written 3.4 years ago by Nasir140
2
gravatar for Emily_Ensembl
3.4 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

The 1000 Genomes browser contains known SNPs from dbSNP, not just data from 1000 Genomes.

ADD COMMENTlink written 3.4 years ago by Emily_Ensembl17k
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