The MAF distribution for SNPs showing reproducible associations with complex human traits is markedly different from the MAF distribution for all SNPs on the high density SNP genotyping platforms, or the minor allele frequency distribution of SNPs included on high throughput platforms used for GWAS (Figure S1). Thus, any study focused on enrichments among SNPs reproducibly associated with complex human phenotypes must be conditioned on MAF. To enable us to conduct simulations conditional on MAF, we constructed MAF bins as follows: allele frequencies were calculated from HapMap genotype data on the CEU. Only the parents' genotypes were included in the frequency calculations since the children's alleles are not independent. We used the toolkit PLINK [31] to calculate frequencies. We classified SNPs on Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina's High Density Human 1M-Duo into non-overlapping minor allele frequency (MAF) bins, each of width .05, using the MAFs of the SNPs in the CEU samples, as most of the published reports summarized in the NHGRI catalog are from GWAS on individuals of recent European descent.
