Figure 6. Varying quality control for the UCLEB traits.

We consider three SNP filterings: 353 K high-quality common SNPs (information score > 0.99, MAF > 0.01), 8.8 M common SNPs (MAF > 0.01) and all 17.3 M SNPs (MAF > 0.0005). (a) Blocks indicate SNP filtering; bars report (inverse variance weighted) average estimates of $h_{\text{SNP}}^2$ using LDAK (vertical lines provide 95% confidence intervals). Bar color indicates the value of α used. For Blocks 1, 2 & 3, $h_{\text{SNP}}^2$ is estimated using the non-partitioned model. For Block 4, SNPs are partitioned by MAF; we find this is necessary when rare SNPs are included, and also allows estimation of the contribution of MAF < 0.01 SNPs (hatched areas). (b) bars report our final estimates of $h_{\text{SNP}}^2$ for height, body mass index and QT interval, the three traits for which common SNP heritability has been previously estimated with reasonable precision⁶ (orange lines mark the 95% confidence intervals from these previous studies). Bar colors now indicate SNP filtering; all estimates are based on α = –0.25, using either a non-partitioned model (red and blue bars) or with SNPs partitioned by MAF (purple bars).