Newly identified loci generally have lower minor allele frequency and/or smaller effect size estimates than previously known loci (Extended Data Fig. 2a, b). On the basis of effect estimates in the discovery data set, which may be inflated owing to winner’s curse, the 97 loci account for 2.7% of BMI phenotypic variance (Supplementary Table 4 and Extended Data Fig. 2a, b). We conservatively used only GWS single nucleotide polymorphisms (SNPs) after strict double genomic control correction, which probably over-corrects association statistics given the lack of evidence for population stratification in family-based analyses13 (Extended Data Fig. 3 and Extended Data Table 1). Polygene analyses suggest that SNPs with P values well below GWS add significantly to the phenotypic variance explained. For example, 2,346 SNPs selected from conditional and joint multiple-SNP analysis with P < 5 × 10−3 explained 6.6 ± 1.1% (mean ± s.e.m.) of variance, compared to 21.6 ± 2.2% explained by all HapMap3 SNPs (31–54% of heritability; Fig. 1a). Furthermore, of 1,909 independent SNPs (pairwise distance >500 kb and r2 < 0.1) included on Metabochip for replication of suggestive
