The simulated genotypes were used to construct six different factor structures for six causal annotations. All orthogonal genotypes were scaled M = 0, SD = 1. For three of the causal annotations (DHS Peaks, H3K27ac, and PromoterUSC), seven genotypes for each annotation were used to construct six new correlated genotypes, each as the weighted linear combination of a domain-specific genetic factor and a general genetic factor, which was constructed from the seventh genotype. For the remaining three causal annotations (FetalDHS, H3K9ac, and TFBS), eight genotypes for each annotation were used to construct two sets of three correlated genotypes for two correlated general genetic factors, constructed from the seventh and eighth genotypes. A set of six “total” genotypes was created by summing a factor indicator genotype from each of the six causal annotations. As each genotype within each annotation was specified to have 10,000 causal SNPs, the “total” genotypes created as the sum of six annotations had 60,000 causal SNPs in the population generating model.
