estimated factor variances in Step 2 are scaled proportionally relative to the genome-wide factor variance (i.e., the numerator of the enrichment ratio). This estimate and its SE are subsequently divided by the proportion of SNPs in the corresponding annotation (i.e., the denominator of the enrichment ratio). For clarification, we note that genome-wide enrichment across all SNPs is exactly equal to 1. That is, for Step 2, if the genome-wide S-LDSC matrix is used as input, this produces a parameter estimate of 1, which is then divided by a proportion of 1.0, which reflects the ratio of M/M (i.e., all SNPs over all SNPs).
