Please follow this and you will then have obtained all of the final release of the 1000 Genomes Phase III data in both VCF and PLINK format: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

You can use the PED file that's also downloaded for the purposes of seeing in which populations your variant of interest is present.

Other [easier] ways of looking up variant allele frequency information exist outside of PLINK:

• http://phase3browser.1000genomes.org/index.html
• dbSNP

Then there are also annotation tools, like ANNOVAR and VEP, which can automatically annotate lists of variants with information from 1000 Genomes.

Kevin