PLINK was used to compute the minor allele frequencies (MAF) using all the 273,464 SNPs that passed the quality control (QC) procedures. Since the Estonian biobank sample (www.geenivaramu.ee) has been part of several previous GWAS, it was interesting to compare the MAF spectrum seen particularly in Estonia with that of other populations. The correlation coefficient r2 obtained varied markedly, from 0.9247 for Latvia and 0.8913 for Finland (Helsinki) to 0.7312 for Southern Italy. In order to examine the extent and likely impact of MAF differences between the studied populations in general, we next examined LD structure, undertook PCA, and calculated fixation indexes Fst and inflations factor λ (see below).
