Marker-wise significance test for allelic differences in pair-wise comparisons between the studied samples resulted in 2,263 loci. As our sample included some genetically and geographically distant cohorts (Finns and Italians) where the strong founder effect and isolation driven genetic drift has changed respective allele frequencies, therefore only loci that were present in non-Italian and non-Finnish comparisons were considered. This step decreased the number of significantly different loci to 18 (Table S4). Four genes were within LCT loci (haplotype block covering more than 1 Mb [30]) and it has been shown, that LCT region differentiates European populations [11], but also within a given population [16]. Three genetically most variable SNPs revealed by PC analysis represented the same loci also present in the previously mentioned list of 18 loci.
