To estimate var[βi|ai], PolyFun incorporates a regularized extension of S-LDSC with the baseline-LF model17,24–26, which we extend to a new version 2.2.UKB (Supplementary Table 1, see below). S-LDSC uses the linear model var[βi|ai]=∑cτcaic and jointly estimates all τc parameters by minimizing the term ∑i(χi2−n∑cτcl(i,c)−nb−1)2, where c are functional annotations, τc is the coefficient of annotation c, χi2 is the χ2 statistic of SNP i, n is the sample size, b measures the contribution of confounding biases, and l(i,c)=∑jrij2ajc.
