Linkage disequilibrium (LD) between SNPs was calculated using Haploview [17] (for HapMap data) and also the verbose option of ldmax [18] (for EA and AA cases and controls). Both CEU and YRI (Yoruba in Ibadan, Nigeria) HapMap data were used, separately. Plots for LD in the case-control data were generated using a custom program (A. Hinrichs, personal communication).
