All of our experiments were based on phased haplotypes from HapMap 3, release 2, in NCBI Build 36 coordinates. HapMap 3 includes samples from 11 analysis panels, which are listed in Table 1. After some minor processing (which is described in the Table 1 legend), there was a total of 1011 unrelated individuals from 10 panels in this dataset. Recent work on the HapMap data has revealed a small number of close relatives among these putative unrelateds (Pemberton et al. 2010). We conducted the analyses for this study before those relationships were revealed, but we do not anticipate that removing the related individuals would have a major effect on our results or conclusions.
