The integrated data set provides a detailed view of variation across multiple populations (illustrated in Fig. 2a). Most common variants (94% of variants with frequency ≥5% in the figure) were known prior to the current phase of the project and had their haplotype structure mapped through earlier projects2,9. In contrast, only 62% of variants in the range 0.5-5% and 13% of variants with frequency ≤ 0.5% had been described previously. For analysis, populations are grouped by the predominant component of ancestry: Europe (CEU, TSI, GBR, FIN, IBS), Africa (YRI, LWK, ASW), East Asia (CHB, JPT, CHS) and the Americas (MXL, CLM, PUR). Variants present at 10% and above across the entire sample are almost all found in all populations studied. In contrast, 17% of low-frequency variants in the range 0.5-5% were observed in a single ancestry group and 53% of rare variants at 0.5% were observed in a single population (Fig. 2b). Within ancestry groups, common variants are weakly differentiated (most within-group estimates of FST are < 1%; Table S11), although below 0.5% frequency variants are up to twice as
