Table 1.

The impact of modeling consideration of AH on FDR and power in colocalization analysis

AH modeling	Dataset
	scenarios (1,2,3)		scenarios (1,2,4)
	FDR	power	FDR	power
Yes	0.047	0.997	0.041	0.971
No	0.039	0.937	0.044	0.411

fastENLOC and coloc are selected to represent the approaches with and without explicit AH modeling, respectively. Both approaches maintain the proper false discovery rate levels in all settings. However, the power difference is quite large when AH is indeed present in the molecular QTL data (i.e., scenarios (1,2,4)).