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!
