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?