(B) We quantify the observed overlap: the proportion of loci where at least one linked SNP overlaps annotation X (shaded boxes). We estimate the significance of the observed overlap by comparing to a null distribution generated by random shifting of X sites (black arrows) within each locus. After each shift, we calculate the proportion of loci overlapping the annotation. To ensure that the same number of shifted annotations remains within locus boundaries, we circularize each region.