Percentage of loci by minor allele frequency (MAF), scenario and data set.

FHS = Framingham Heart Study, GEN = GENEVA, RAND: in this scenario causal and marker loci were drawn from the same distribution, Low-MAF: in this scenario marker loci were drawn at random and causal loci were drawn over-sampling loci with extreme minor-allele frequency (MAF). In the Low-MAF scenario, the sampling of causal loci was done using average MAF of the FHS and GEN data sets. Although MAF were very similar across data sets, these were not exactly equal, and this explains why in the Low-MAF roughly 1% of the causal loci had MAF (within-data set) greater than 15%.