Table 4. Rejection rates.

1000 iterations. α = 0.05. Same subjects for two traits. For CMC, B = 10³. τ = 0.2. Regions A1-A2: without colocalization (type I errors for JLIM and conditional, power for coloc). Regions B1-B6: with colocalization (power for JLIM and conditional, type I errors for coloc). For MA, B = 10³, u = 10. s = 3 for loci with more than 50 SNPs, s = 2 otherwise.

Region	# SNPs (*)	JLIM	Conditional				coloc
			1st SNP	CB	CMC	MA
A1	43 (2/0/0)	0.039	0.011	0	0.014	0.026	0.027
A2	58 (17/2/0)	0.054	0.010	0.010	0.030	0.046	0.047
B1	28 (9/4/1)	0	0.018	0.189	0.276	0.288	1
B2	53 (7/18/2)	0	0.005	0.429	0.542	0.581	1
B3	62 (12/6/2)	0.724	0.011	0.546	0.721	0.739	1
B4	43 (18/10/5)	0	0.009	0.154	0.238	0.281	1
B5	43 (9/7/6)	0.179	0.016	0.683	0.859	0.877	1

(*) Numbers of SNPs that are causal for trait 1 / trait 2 / both traits.