We then sought to investigate whether or not there is an enrichment of additional association signals at the top associated loci. We varied the window size from 20Kb to 50Kb, 100Kb, 150Kb, 200Kb, 300Kb, 400Kb, 500Kb, 750Kb and 1Mb, and fitted a two-component model in GCTA-GREML analysis, with the first component being the top associated SNPs and the second component being the rest of SNPs within the window. We found that the per-SNP variance explained excluding the top SNPs (variance explained by the second component divided by the number of SNPs included in this component) decreased with the size of window (Supplementary Fig. 6b), implying that SNPs in closer physical proximity to the top associated SNPs tend to explain disproportionally more variance.
