If genetic variation is a function of the length of a chromosome segment occupied by genes then this implies that causal variants are more likely to occur in the vicinity of the genes than in intergenic regions. These causal variants could either change the protein structure or regulate the expression of the gene in cis. However, regulatory elements sometimes occur a long distance away from the gene they regulate and our results show that SNPs situated > 50 Kb from any gene still explain some of the variance although less than SNPs nearer to a gene. These results are consistent with analyses of published genome-wide significant SNPs for complex traits, in that a substantial proportion is found in intergenic regions1.
