PC analysis has been used in most previous studies of the European genetic structure. Here, PC analyses were performed using EIGENSOFT with default parameters. In total, 1,564 individuals plus 203 HapMap members and 266,356 autosomal SNPs were used as the input dataset. After the removal of outliers, 1,539 individuals (or 1,742 including the HapMap members) remained (Table S1). The first PC explains 8.7% of the genetic variance, the second PC explains 4.9%; all other PC explained much smaller fractions demonstrating that the Europe is genetically quite uniform. If we add African and Asian HapMap populations to European samples, the two first PCs describe 36.6% and 23.8% of the genetic variance (Figure 2). At a more detailed level, however, several distinct regions can be distinguished within Europe: 1) Finland, 2) the Baltic region (Estonia, Latvia and Lithuania), Eastern Russia and Poland, 3) Central and Western Europe, and 4) Italy, with the southern Italians being more “distant” (Figure 2). PC analysis of the 1,026 Estonians revealed the fine-structure of this population, with the first two PCs describing 1.9% and 1.5% of the
