Fig. 5. Per-allele squared effect size of height as a function of MAF.

We applied RHE-mc to N = 291,273 unrelated white British individuals and M = 7,774,235 imputed SNPs. SNPs were partitioned into 144 bins based on LD score (4 bins based on quartiles of the LD score with i denoting the ith quartile) and MAF (36 MAF bins) (see “Methods” section). Per-allele effect size squared for bin k is defined as $\frac{h_k^2}{M_k*2f_k*\left(1-f_k\right)}$, where $h_k^2$ is the heritability attributed to bin k, M_k is the number of SNPs in bin k, and f_k is the average MAF in bin k. Each point represents the estimated allelic effect size. Bars mark  ±2 standard errors centered on the estimated allelic effect size. See Supplementary Fig. 9 for results on all 22 traits.