Consider a situation in which L contains two classes, rare and common SNPs, with FST 0.054 and 0.182 respectively. If rare variants explained 10% of the heritability and common variants explain 90% of the heritability, then FSTC=0.1692. We estimated FSTC over the HapMap337 data set by using CEU and YRI as proxies for the ancestral populations of African-Americans, using an admixture proportion of 18.3% European ancestry, and assuming distribution of causal variant frequencies. We estimated a value of 0.182 assuming causal variant MAF > 5% (which we used in this work), 0.165 assuming MAF < 5%, and 0.054 assuming MAF < 1%.
