Highly significant and well-replicated SNPs identified to date explain only ~5% of the phenotypic variance for height19. Our results show that common SNPs in total explain another ~40% of phenotypic variance. Hence, 88% (40/45) of the variation due to SNPs has been undetected in published GWASs because the effects of the SNPs are too small to be statistically significant. Our results also suggest that the discrepancy between 80% heritability and 45% accounted for by all SNPs is due to incomplete LD between causal variants and the SNPs, possibly because the causal variants have a lower MAF on average than the SNPs typed on the array. We cannot tell from these results whether or not some of this discrepancy is due to causal variants with very low frequency – for example, MAF < 0.001 (ref. 4). However, the results show that the total genetic variance could be explained by causal variants similar to the SNPs, with MAF < 0.1. If causal variants affecting height had no effect on fitness, they would show a complete range of MAF but with a higher
