To quantify these effects genome-wide, we partitioned the variance explained by all the SNPs onto genic ( hGg2) and intergenic ( hGi2) regions of the whole genome (Online Methods). We defined the gene boundaries as ± 0 Kb, 20 Kb and 50 Kb of the 3′ and 5′ UTRs. A total of 213,509, 282,058, and 336,127 SNPs were located within the boundaries of 13,406, 17,277 and 17,652 protein-coding genes for the three definitions (± 0 Kb, 20 Kb and 50 Kb) respectively, which covered 35.8%, 49.4% and 58.7% of the genome. Some genes did not have any SNPs within them, especially if the most stringent definition of gene boundary (± 0 Kb) was used. We tested the estimates of hGg2 and hGi2 against the expected values from the genic and intergenic coverages by a goodness-of-fit test. We found strong evidence for height and vWF, and less so for BMI and QTi, that genic regions proportionally explain more variation than intergenic regions (legends of Fig. 2 and Supplementary Fig. 6). As an example we consider the case of genes ± 20
