Table 3. Replication of MR effect estimates in OpenGWAS database.

Exposure	Outcome & data source	MR method	Beta	SE	OR (95%CI)	P-value1	Intercept2	P-value2	Cases	Participants
Vitamin B6	Calculus of kidney and ureter
	UKBB	PheWAS	-0.058	0.014	0.94 (0.92, 0.97)	4.03E-05	-	-	4748	381150
	OpenGWAS: finn-N14_CALCUKIDUR	Wald ratio3	-0.453	0.213	0.64 (0.42, 0.97)	0.033	-	-	3856	176613
Homocysteine	HDL cholesterol levels
	OpenGWAS: ieu-4844	IVW	-0.055	0.027	0.95 (0.90, 1.00)	0.041	-	-	-	77409
		Weighted median4	-0.061	0.027	0.94 (0.89, 0.99)	0.022	-	-
		MR-Egger4	-0.065	0.061	0.94 (0.83, 1.06)	0.311	0.001	0.853
		MR-PRESSO4	-0.059	0.026	0.94 (0.90, 0.99)	0.044	-	-
	Hypercholesterolemia
	UKBB	PheWAS	0.122	0.028	1.13 (1.07, 1.19)	1.34E-05	-	-	50143	381727
	OpenGWAS: finn-E4_HYPERCHOL	IVW	0.245	0.103	1.28 (1.04, 1.56)	0.018	-	-	6840	167301
		Weighted median	0.210	0.106	1.23 (1.00, 1.52)	0.047	-	-
		MR-Egger	0.093	0.230	1.10 (0.70, 1.72)	0.695	0.013	0.471
		MR-PRESSO	0.245	0.103	1.28 (1.04, 1.56)	0.035	-	-
	Creatinine levels
	OpenGWAS: met-Creatinine	IVW	0.103	0.046	1.11 (1.01, 1.21)	0.027	-	-	-	110058
		Weighted median	0.013	0.022	1.01 (0.97, 1.06)	0.553	-	-
		MR-Egger	0.087	0.108	1.09 (0.88, 1.35)	0.437	0.001	0.875
		MR-PRESSO	0.071	0.031	1.07 (1.01, 1.14)	0.490	-	-
	Chronic kidney disease
	UKBB	PheWAS	0.252	0.065	1.29 (1.13, 1.46)	1.04E-04	-	-	7753	362882
	OpenGWAS: ebi-GCST008026	IVW	0.276	0.110	1.32 (1.06, 1.63)	0.012	-	-	1533	20920
		Weighted median	0.134	0.149	1.14 (0.85, 1.53)	0.368	-	-
		MR-Egger	0.070	0.250	1.07 (0.66, 1.75)	0.784	0.017	0.376
		MR-PRESSO	0.276	0.110	1.32 (1.06, 1.63)	0.026	-	-

¹The p value of the MR effect estimates from different methods.

²The Egger regression interceopt and horizontal pleiotropy p value of MR-Egger analysis.

³Wald ratio method was applied to examine MR estimates for vitamin B6 as only one SNP was used as instrumental variable for vitamin B6.

⁴These three sensitivity methods were applied to detect any pleiotropic effect when performing multivariable MR analysis.