Extended Data Figure 2: Height ExomeChip association results.

a, Quantile–quantile plot of ExomeChip variants and their association to adult height under an additive genetic model in individuals of European ancestry. We stratified results on the basis of allele frequency. b, Manhattan plot of all ExomeChip variants and their association to adult height under an additive genetic model in individuals of European ancestry with a focus on the 553 independent SNPs, of which 469 have a MAF > 5% (grey), 55 have MAF between 1–5% (green), and 29 have a MAF < 1% (blue). c, Linkage disequilibrium (LD) score regression analysis for the height association results in European-ancestry studies. In the plot, each point represents a linkage disequilibrium score quantile, where the x axis of the point is the mean linkage disequilibrium score of variants in that quantile and the y axis is the mean χ² statistic of variants in that quantile. The linkage disequilibrium score regression slope of the black line is calculated using equation 1 in ref. 34, which is estimated upwards owing to the small number of common variants (n = 15,848) and the design of the ExomeChip. The linkage disequilibrium score regression intercept is 1.4, the λ_GC is 2.7, the mean χ² is 7.0, and the ratio statistic of (intercept − 1)/(mean χ² − 1) is 0.067 (s.e.m. = 0.012). d, Scatter plot comparison of the effect sizes for all variants that reached significance in the European-ancestry-discovery results (n = 381,625) and results including only studies with sample sizes of more than 5,000 individuals (n = 241,453).