PMC

Northern European F_ST values by genomic location. (A) Proportion of SNPs that are inside (genic) or outside (nongenic) genes by F_ST bin category. X-axis F_ST values refer to the lower boundary of the bin. (B) Genome-wide distribution of the top 10,000 F_ST (>0.00888) values by chromosome and genomic position.

PCA of Northern European population structure. (A) PC1 versus PC2 from 2051 individuals genotyped for 296,553 autosomal SNPs. PCA was conducted including the Australian sample (n = 451), but these are not shown here (see Supplemental Fig. S4). (B) PC1 versus PC2 focused on the United Kingdom, Irish, and Australian populations. For ease of illustration, PC1 has been constrained to between 0.02 and −0.06 and PC2 to between 0 and 0.025. Only those U.K. samples with birthplace information are displayed (n = 143), and these are distinguished as England, Scotland, and Wales. Australian samples whose four grandparental ancestries are from one country are also shown.

PC3 and PC4 in Northern European populations. (A) PC3 versus PC4 derived from 2051 individuals genotyped for 296,553 autosomal SNPs. (B) An 8-Mb section of chromosome 8 (6 Mb to 14 Mb) showing the distribution of SNP δ values derived from extreme PC4 cohorts. (C) A 10-Mb section of chromosome 6 (24 Mb to 34 Mb) showing the distribution of SNP δ values derived from extreme PC3 cohorts. Whereas δ values remain high over the entire chromosome 8 inversion region (8 Mb to 12 Mb), those on chromosome 6 show a gradual decay upstream and downstream from the peak δ value observed at rs2508049 (position 29.99 Mb).

EHH patterns around rs2508049 on chromosome 6. (A) EHH for the rs2508049 G and A alleles over a 5-cM (or ≈9 Mb, from 25.06 Mb to 33.93 Mb) region around the SNP in all Northern European populations. The EHH pattern for rs2508049-A in the HapMap Yoruban and Asian (Chinese and Japanese) is also shown, although the absence or very low frequency of the G allele precludes similar analysis of it in these populations. (B) EHH for the rs2508049-A and G alleles using the pre-phased CEU HapMap data, over a 4-cM region (or ≈8 Mb, from 25.06 Mb to 33.07 Mb). A 95 percentile boundary curve from an empirical EHH distribution of 15,325 chromosome 6 SNPs (30650 observations), calculated at 0.1-cM intervals over a 2-cM distance from the cores, is also indicated. Population codes are as follows: (ASN) East Asian HapMap; (AUS) Australia; (CEU) European-American HapMap; (DEN) Denmark; (FIN) Finland; (IRL) Ireland; (NET) Netherlands; (SWE) Sweden; (UK) United Kingdom; (YRI) Yoruba HapMap.