Figure 3

Genetic associations with GFR, in the region around the ABCB1 gene. Associations are shown for both directly genotyped and imputed SNPs. The bottom panel shows the pattern of linkage disequilibrium in the HapMap CEU panel. We imputed genotypes for all HapMap SNPs in the region around ABCB1. In this region, linkage disequilibrium patterns in CoLaus were similar to the ones observed in HapMap, although they were resolved at a coarser scale due to lower SNP density. Since it was not computationally feasible to combine imputation and permutation approaches, we plot P values calculated assuming the normal linear model. For directly genotyped SNPs, the differences between calculated and permutation P values were small. The top three hits (and P values) are rs17327624 (0.0006), rs4148733 (0.0008) and rs17327442 (0.0008). The former two were directly genotyped and are in strong LD (D' = 0.96 in CoLaus and 1.00 in HapMap CEU, r² = 0.63 and 0.72 respectively), and the imputed SNP rs17327442 is in perfect LD with rs17327624 in HapMap CEU.