Correspondence between estimated pooled allele frequency differences and actual differences determined by individual genotyping. For this analysis, we included data for single nucleotide polymorphisms (SNPs) having call rates of at least 90 per cent. (A) The correlation between estimated and actual allele frequency differences for 267 SNPs is 0.82. (B) For 164 SNPs in haplotype blocks with fitted p < 0.05, the correlation between allele frequency difference and the estimate based on the haplotype-fitting procedure is 0.90. In the upper right corner of each plot are five SNPs in the genomic interval encoding CETP.