Quantifying Observed Enrichment by Using Delta-Overlap
To quantify the effect size of the observed enrichment, we calculated the “delta-overlap” parameter: the difference between the observed proportion of loci overlapping an annotation and the mean of the proportion of loci overlapping the annotation under the null derived by local shifting. If there is no enrichment, the observed overlap will be close to the mean overlap under the null, and delta-overlap will be close to 0. Conversely, larger delta-overlap values correspond to stronger enrichment. In practice, delta-overlap is independent of the number of SNPs in LD and the TSS or TES proximities of associated SNP sets (Figure S1).