Extended Data Fig. 2: Estimated proportions of SNP heritability.

This is an expanded version of Fig. 1d, and shows that estimates of functional enrichments tend to converge as the heritability model becomes more complex. Plots report the estimated proportion of SNP heritability contributed by each category of SNPs, averaged across either the 14 UKBb or 17 Public GWAS (vertical segments indicate 95% confidence intervals). Bars indicate the heritability model used and are ordered by number of parameters (see Supplementary Table 13 for definitions): GCTA + 1Fun Model (two parameters, used by Gusev et al.¹²), LDAK + 1Fun Model (two parameters, Speed et al.¹), LDAK + 24Fun Model (25 parameters, Speed et al.⁴), Baseline Model (53 parameters, Finucane et al.⁹), BLD-LDAK and BLD-LDAK + Alpha Models (66 and 67 parameters, this paper) and Baseline LD Model (75 parameters, Gazal et al.¹⁰). The estimated enrichment of a category is obtained by dividing its estimated proportion of SNP heritability by the proportion of SNPs it contains (horizontal dashed lines). Numerical values are provided in Supplementary Tables 5 & 6.