Under this model, the expected marginal chi-square association statistic for SNP i reflects the causal contributions not only of SNP i but of SNPs in LD with SNP i. Specifically, E[χi2]= 1+Na+N∑kτkl(i,k), where N is the GWAS sample size, a is a constant that reflects population structure and other sources of confounding,68 and l(i,k) is the LD score of SNP i to category Ck, defined as l(i,k)= ∑jr2(i,j)1{j∈Ck}, where r2(i,j) is the squared correlation between SNPs i and j in the population. To estimate the τk, we first estimate l(i,k) from a reference panel, and we then perform weighted regression χi2 on N⋅l(i,k), using a jackknife over blocks of SNPs to estimate standard errors.
