Our next step was to select variants in the 50 kb region to have similar properties to the Affymetrix Human SNP Array 6.0 in terms of mean density and MAF profile in the population of 40,000 haplotypes. All SNPs on the GWA chip were analysed independently, using conventional trend tests of association, with Bonferroni correction for multiple testing, and jointly, using standard haplotype-based techniques. Over all simulations, the mean number of GWA chip SNPs in the region was 14.8, while the mean number of SNP haplotypes with population frequency greater than 1% was 18.0. We attempted to apply RVT1 and RVT2 to the GWA chip data, but the mean number of rare variants in the region was just 0.2, and provided minimal power to detect accumulations of minor alleles at these loci. As a result, we extended our analysis to include “low-frequency” SNPs (1%<MAF<5%), which are less scarce on the GWA chip (mean 1.6 variants in the region).
