SNPs that reached P < 5 × 10−8 (a threshold that corresponds to P < 0.05 after adjusting for ~1 million independent tests) in this stage 1 analysis all mapped within the FTO gene (association peak at rs1421085, P = 2.6 × 10−19), were in linkage disequilibrium (LD) with each other (r2 > 0.51), and strongly confirm previous reports of association at this locus6-8. A locus located near MC4R (rs17782313, P = 3.9 × 10−7) and recently associated with BMI9,10 was the fourth most significant region in the stage 1 data (Fig. 1). Even after excluding SNPs in these two established BMI loci, we observed an excess of SNPs with small P values compared to chance expectations, suggesting that some of the remaining loci with strong but not definitive evidence of association in stage 1 are truly associated with BMI (Fig. 1b).
