Initial evaluation of this north-ESAIM set showed a distortion of the PCA in which the individuals were divided in three groups diagonally across the first two axes. Deletion of markers within the Chromosome 8 inversion (see above) resulted in a set of 1211 SNPs that no longer showed this pattern. This north-ESAIM set distinguished “northern” European individuals in a pattern similar to that observed using the 500K SNP set along the first PC (Figure 4C and see Table S2 for SNP list). The PC scores using these north-ESAIMs in the “northern” European only set correlated with the 500K first PC result; r2 = 0.46 (p < 10−15). Smaller north-ESAIM sets showed dramatically smaller correlations if the individual individual values compared to the 500K PCA (data not shown). Larger panels of SNPs (up to 5000 SNPs) chosen using the same criteria showed similar results to the 1211 ESAIMs.
