Figure 4. Histograms of the proportion of SNPs in the 22 1Mb regions (see Methods) in HapMap Phase II for which the maximum r² with a SNP on the genotyping chip in in one of eleven bins (increasing in correlation (LD) from left to right).

The same histograms are coloured in two ways. The top row shows in red the percentage of the SNPs in each bin detected (See Methods and text) when selected to be the causal SNP in our simulations (the proportion of the total volume of the bars coloured red is therefore an estimate of power). In the bottom row all r² bins above 0.8 are coloured red (the proportion of the total volume of all the bars is therefore an estimate of coverage). Note that the use of HapMap data in choosing SNPs for the Illumina chip leads to a higher proportion of SNPs in high r² bins.