Table 3.

Power of SS2, SMR, and SMR-multi and true positive rate of COLOC2 for multiple genes

Locus	EQTL height for the 5% genes have colocalization	Power of SS2	Power of SMR	Power of SMR-multi	True positive rate of COLOC2
MUC20/MUC4	5.48–5.73	0.8181	0.6826	0.6059	0.6218
	5.73–5.98	0.8178	0.6935	0.6119	0.6355
	5.98–6.25	0.8171	0.7033	0.6169	0.6447
	6.25–6.57	0.8161	0.7144	0.6216	0.6507
	6.57–7.01	0.8143	0.7270	0.6254	0.6536
SLC6A14	5.48–5.73	0.6855	0.6323	0.5531	0.6605
	5.73–5.98	0.6992	0.6462	0.5614	0.6684
	5.98–6.25	0.7076	0.6588	0.5679	0.6741
	6.25–6.57	0.7138	0.6706	0.5745	0.6786
	6.57–7.01	0.7184	0.6831	0.5817	0.6821

The LD pattern at the simulated region follows that at the MUC20/MUC4 and SLC6A14 loci, respectively. The height of the GWAS peak is set at 5.06 on the −log10p scale such that 10% power is achieved to detect the GWAS association at significance level of 10⁻⁸. Each row corresponds to a different range of the eQTL height for the 5% genes that have colocalization ([5.48, 5.73], [5.73, 5.98], [5.98, 6.25], [6.25, 6.57], and [6.57, 7.01]). The eQTL peaks are set with 5 different intervals such that 40%–50%, 50%–60%, 60%–70%, 70%–80%, 80%–90% power is achieved to detect the eQTL association at the significance level of 10⁻⁸. For the remaining 95% of genes, there is eQTL evidence with a mixture of null cases under H₀₃ and H₀₄ and details are demonstrated in the supplemental material and methods. 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. In total, 10⁵ replications are simulated to evaluate power at 0.05 significance level and the true positive rates by applying the 0.8 threshold (as recommended by Dobbyn et al.¹⁴) for the colocalization posterior probability. The power (or true positive rate for COLOC and COLOC2) is calculated by counting the proportions of 10⁵ replications where at least one gene is correctly identified with colocalization.