SNPs on the chip used. Such a frequency difference causes imperfect LD between the genotyped SNPs and unobserved causal variants. Traditional pedigree analysis is not affected by such imperfect LD because it is based on the correct expected identity-by-descent coefficients at loci (including loci with causal variants) of relatives. It is also possible that causal variants are present in regions of the genome not well covered by the commercial SNP arrays. Nevertheless, our results suggest that common SNPs that are in LD with unknown causal variants account for more than half of all additive genetic variation for human intelligence. The method we have used here does not attempt to test the effects of single SNPs; rather, it tests their accumulated effects. It estimates the joint effect of genotyped SNPs and that effect reflects their linkage disequilibrium (LD) with unknown causal variants. These variants are not necessarily common SNPs or, indeed, even SNPs; however, causal variants are in sufficient LD with the genotyped SNPs to be captured30.
