of variance explained by all the HapMap3 (ref. 11) SNPs without SNP selection was ~50% (Table 1), consistent with previous estimates4,5. Thus, a group of ~9,500 SNPs (representing <1% of common SNPs) selected at P<5×10−3, explained ~29% of phenotypic variance. Since ~50% of phenotypic variance is explained by all common SNPs, the selected set of SNPs, despite being limited to <1% of common SNPs, accounts for the majority of variance attributable to all common SNPs (29/50 ~ 60%). This set of ~9,500 SNPs strongly clustered with the newly established height loci: 1,704 (19%) variants were located within 250kb of one of the 697 genome-wide associated SNPs, suggesting that a substantial fraction of “missing heritability” is within already identified loci. This clustering of additional variants within identified loci was confirmed in a parallel analysis based on two left-out studies where we observed that SNPs in closer physical proximity with the top associated SNPs explained disproportionally more variance (Online Methods and Supplementary Fig. 6).
