Table 1.

Empirical type I error rates of SS2, SMR, and SMR-multi and false positive rates of COLOC2 and COLOC for a single hypothesis test

Locus	Null scenarios	Type I error of SS2	Type I error of SMR	Type I error of SMR-multi	False positive rate of COLOC	False positive rate of COLOC2
MUC20/MUC4	H01	0.0021	<10−4	<10−4	<10−4	0.0011
	H02	0.0450	0.0377	0.0332	1.00 × 10−4	0.0245
	H03	0.0229	<10−4	<10−4	4.00 × 10−4	0.0858
	H04	0.0262	0.0389	0.0367	<10−4	1.00 × 10−4
SLC6A14	H01	0.0025	<10−4	<10−4	<10−4	0.0022
	H02	0.0507	0.0372	0.0342	5 × 10−4	0.0468
	H03	0.0099	<10−4	<10−4	9 × 10−4	0.088
	H04	0.0133	0.0368	0.0336	<10−4	0.0012

The LD pattern at the simulated region follows that at the MUC20/MUC4 and SLC6A14 loci, respectively. Each row corresponds to a specific null scenario when there is no co-localization. H₀₁ represents the scenario when there are no SNP-phenotype associations and no eQTL; H₀₂ represents the scenario when there are no SNP-phenotype associations but eQTLs are present; H₀₃ represents the scenario where SNP-phenotype associations are present but no eQTL; H₀₄ represents the scenario where both SNP-phenotype association and eQTLs are present, but occurring at two independent SNPs. For SS2, SMR,¹¹ and SMR-multi,¹² the nominal type I error was set at $\alpha =0.05$. SMR and Multi-SNP-based SMR test (SMR-multi) are conducted under the default setting such that a SNP is picked only if the eQTL p value is less than 5 × 10⁻⁸. For COLOC2¹⁴ and COLOC,⁴ the false positive rates are calculated by applying the 0.8 threshold (as recommended by Dobbyn et al.¹⁴) for the colocalization posterior probability. In total, 10⁴ replications are simulated for each null scenario.