Extended Data Fig. 4: Haplotypes that carry the rs200342067 allele are longer than what is expected under neutral selection.

a, Haplotype decay around rs200342067 in our cohort (n = 3,134 individuals and 6,268 haplotypes). The position of rs200342067 is marked below the haplotypes. Haplotypes above the dashed line carry rs200342067*C allele (derived/minor, n = 297 haplotypes) and haplotypes below the dashed line carry the rs200342067*T allele (ancestral/major, n = 5,971 haplotypes). b, Integrated EHH of haplotypes carrying the rs200342067*C allele (n = 297 haplotypes) compared with the integrated EHH of haplotypes carrying 2,380 variants with similar DAF (4.7 ± 1%) that overlap the neutral regions of the genome in our cohort (n = 3,134 individuals). Haplotypes that carry the rs200342067*C allele are taller than 99.2% of the haplotypes carrying similar variants in neutral regions of the genome. Vertical red line, integrated EHH of haplotypes carrying the rs200342067*C allele (integrated EHH = 0.115). c, The same as a, but excluding the nine haplotypes that carry both rs200342067*C and rs12441775*G alleles. d, EHH decay curves for haplotypes carrying the rs200342067*C allele excluding the nine haplotypes that carry both rs200342067*C and rs12441775*G alleles (n = 288 haplotypes) compared with haplotypes carrying 2,309 variants that have a similar DAF to the updated frequency of rs200342067*C (4.6 ± 1%) and that overlap the neutral regions of the genome in our cohort (n = 3,134 individuals). Haplotypes with the rs200342067*C allele are longer than 99.7% of the haplotypes carrying similar variants in the neutral genomic regions. e, Integrated EHH for data shown in d. Vertical red line, integrated EHH for haplotypes carrying the rs200342067*C but not the rs12441775*G allele (integrated EHH = 0.124).