Table 3.

LD mismatch impact on enrichment estimation, FDR, and power

Datasets	${\hat{\alpha }}_1$	${\hat{p}}_{\gamma }$	Realized FDR	Power
FIN versus FIN	4.076	1.25 × 10−3	0.029 (0.036)	0.129 (0.129)
FIN versus GBR	3.964	1.23 × 10−3	0.023 (0.027)	0.102 (0.103)
FIN versus TSI	3.935	1.27 × 10−3	0.023 (0.028)	0.101 (0.099)
FIN versus CEU	3.842	1.10 × 10−3	0.030 (0.047)	0.075 (0.077)
FIN versus YRI	3.438	1.19 × 10−3	0.001 (0.006)	0.065 (0.067)

The enrichment estimates $\left({\hat{\alpha }}_1\right)$ and from all combinations of eQTL and GWAS datasets we used for this analysis. The estimated frequency of GWAS hits $\left({\hat{p}}_{\gamma }\right)$ reflects the GWAS power of each GWAS dataset. (Note that true $p_{\gamma }=1.92\times {10}^{-3}$.) The quantities in parentheses show the realized FDR and power when using the true enrichment parameter in the colocalization analysis.