To quantify the proportion of height variance that is explained by GWS SNPs identified in our METAFE, we stratified all HM3 SNPs into two groups: SNPs in the close vicinity of GWS SNPs, hereafter denoted GWS loci; and all remaining SNPs. We defined GWS loci as non-overlapping genomic segments that contain at least one GWS SNP, such that GWS SNPs in adjacent loci are more than 2 × 35 kb away from each other (that is, a 35-kb window on each side). We chose this size window because it was predicted that causal variants are located within 35 kb of GWS SNPs with a probability greater than 80% (ref. 25). Accordingly, we grouped the 12,111 GWS SNPs identified in our METAFE into 7,209 non-overlapping loci (Supplementary Table 12) with lengths ranging from 70 kb (for loci containing only one signal) to 711 kb (for loci containing up to 25 signals). The average length of GWS loci is around 90 kb (s.d. 46 kb). The cumulative length of GWS loci represents around 647 Mb, or about 21% of the genome (assuming a genome length of around 3,039 Mb)26.
