Finally, in the pruned SNP-set we used the Mann–Whitney U test to probe for systematic differences in Pv and Pm ranks. P-values were ordered from least significant to most significant, and the lowest 100th centile (i.e. the most significantly associated SNPs) was compared to the remaining 99th percentile for each of the five traits. For BMI, SNPs in the lowest 100th centile of the Pm distribution had markedly higher Pv ranks (i.e. more significant Pv) than the remaining SNPs (PMann–Whitney = 1.46×10−5; Table 5). Even when excluding previously established lead SNPs (Pm<5×10−8) for BMI (or SNPs +/-500kb proximal), SNPs from the lowest 100th centile of the Pm rank-ordered distribution had higher Pv ranks than the remaining SNPs (PMann–Whitney = 4.30×10−4; Table 5). Conversely, no difference in Pv ranks was observed for SNPs from the lowest 100th centile of the Pm rank-ordered distribution for the four blood lipid traits; this may reflect trait-specific G×E effects or differences in statistical power by trait. No differences in Pv ranks between SNPs from the lowest 99th centile of the Pm rank-ordered distribution compared to SNPs from the 98th to 1st centiles of the distribution were observed for any trait (PMann–Whitney>0.05; Table 5). Similarly, no difference in Pm ranks was observed for SNPs from the lowest 100th centile of the Pv rank-ordered distribution for any traits (PMann–Whitney>0.05; Table 6).