Table 3.

Sensitivity analysis for the genome-wide significant hits in the meta-analysis across both stages

Probe	Model	Puerto Ricans				Mexicans				Meta-analysis
		Coef	SE	P	CQP	Coef	SE	P	CQP	Coef	SE	P	CQP
cg16405908	M0	− 2.53E−02	5.05E−03	5.13E−07	2.48E−01	− 1.79E−02	5.70E−03	1.64E−03	7.87E−01	− 2.21E−02	3.78E−03	5.02E−09	5.02E−01
	M1	− 1.75E−02	5.99E−03	3.40E−03	8.09E−01	− 2.45E−02	5.18E−03	2.33E−06	2.98E−01	− 2.15E−02	3.92E−03	4.06E−08	5.93E−01
	M2	− 1.70E-02	5.75E−03	3.17E−03	9.94E−01	− 2.63E−02	5.35E−03	8.54E−07	2.99E−01	− 2.20E−02	3.92E−03	1.97E−08	4.76E−01
	M3	− 1.79E-02	5.77E−03	1.93E−03	8.63E−01	− 2.54E−02	5.08E−03	5.69E−07	2.54E−01	− 2.21E−02	3.81E−03	6.50E−09	5.16E−01
	M4	− 1.83E-02	6.02E−03	2.33E−03	9.32E−01	− 2.49E−02	5.06E−03	8.73E−07	2.36E−01	− 2.22E−02	3.87E−03	1.04E−08	5.50E−01
	M5	− 1.77E-02	5.78E−03	2.15E−03	7.22E−01	− 2.57E−02	5.04E−03	3.55E−07	2.41E−01	− 2.22E−02	3.80E−03	4.77E−09	4.64E−01
	M6	− 1.86E-02	5.74E−03	1.22E−03	6.95E−01	− 2.50E−02	5.10E−03	9.14E−07	2.21E−01	− 2.22E−02	3.81E−03	5.95E−09	5.01E−01
	M7	− 1.87E-02	6.46E−03	3.86E−03	8.96E−01	− 2.36E−02	5.66E−03	3.03E−05	2.11E−01	− 2.15E−02	4.26E−03	4.62E−07	5.90E−01
cg07428101	M0	7.21E-03	1.47E−03	8.72E−07	6.55E−01	5.64E−03	2.04E−03	5.70E−03	4.64E−01	6.68E−03	1.19E−03	2.05E−08	7.71E−01
	M1	5.65E-03	2.15E−03	8.61E−03	6.04E−01	6.91E−03	1.50E−03	3.93E−06	5.84E−01	6.50E−03	1.23E−03	1.23E−07	8.50E−01
	M2	4.62E-03	1.91E−03	1.57E−02	6.79E−01	7.13E−03	1.57E−03	5.93E−06	6.70E−01	6.11E−03	1.22E−03	4.87E−07	7.10E−01
	M3	5.88E-03	2.07E−03	4.58E−03	4.20E−01	7.24E−03	1.47E−03	9.03E−07	6.66E−01	6.78E−03	1.20E−03	1.64E−08	7.72E−01
	M4	5.51E-03	2.22E−03	1.32E−02	3.45E−01	7.29E−03	1.48E−03	8.49E−07	6.69E−01	6.75E−03	1.23E−03	4.44E−08	6.78E−01
	M5	5.18E-03	2.05E−03	1.14E−02	2.86E−01	7.24E−03	1.47E−03	8.04E−07	7.14E−01	6.54E−03	1.19E−03	4.14E−08	5.84E−01
	M6	5.81E-03	2.12E−03	6.10E−03	6.48E−01	7.02E−03	1.49E−03	2.60E−06	6.11E−01	6.62E−03	1.22E−03	5.89E−08	8.77E−01
	M7	4.68E-03	2.22E−03	3.49E−02	5.99E−01	6.36E−03	1.69E−03	1.71E−04	5.85E−01	5.74E−03	1.35E−03	1.98E−05	8.16E−01
cg06035600	M0	3.35E-01	6.89E−02	1.15E−06	6.11E−01	1.81E−01	6.22E−02	3.69E−03	8.84E−01	2.50E−01	4.62E−02	6.13E−08	3.83E−01
	M1	3.38E-01	7.29E−02	3.51E−06	5.64E−01	1.78E−01	6.23E−02	4.31E−03	8.72E−01	2.46E−01	4.74E−02	2.17E−07	3.70E−01
	M2	3.51E-01	7.23E−02	1.24E−06	7.26E−01	1.57E−01	6.52E−02	1.59E−02	7.88E−01	2.44E−01	4.84E−02	4.72E−07	2.46E−01
	M3	3.34E-01	6.91E−02	1.30E−06	5.08E−01	1.64E−01	6.25E−02	8.63E−03	8.73E−01	2.41E−01	4.63E−02	2.05E−07	2.83E−01
	M4	3.06E-01	7.24E−02	2.45E−05	9.92E−01	1.76E−01	6.18E−02	4.30E−03	9.31E−01	2.31E−01	4.70E−02	9.08E−07	6.05E−01
	M5	3.38E-01	6.99E−02	1.35E−06	5.80E−01	1.93E−01	6.26E−02	2.05E−03	9.23E−01	2.58E−01	4.67E−02	3.39E−08	4.41E−01
	M6	3.02E-01	7.02E−02	1.68E−05	8.44E−01	1.79E−01	6.27E−02	4.30E−03	8.77E−01	2.34E−01	4.68E−02	5.86E−07	6.20E−01
	M7	3.09E-01	8.78E−02	4.41E−04	8.14E−01	1.51E−01	6.62E−02	2.21E−02	7.30E−01	2.08E−01	5.29E−02	8.05E−05	5.29E−01
cg00914963	M0	− 2.53E-02	4.96E−03	3.33E−07	6.70E−01	− 1.08E−02	4.55E−03	1.77E−02	7.24E−02	− 1.89E−02	5.76E−03	1.04E−07	4.50E−02
	M1	− 2.70E-02	5.13E−03	1.47E−07	9.72E−01	− 9.98E−03	4.72E−03	3.44E−02	6.19E−02	− 1.99E−02	6.44E−03	1.10E−07	2.41E−02
	M2	− 2.49E-02	4.97E−03	5.51E−07	2.69E−01	− 1.17E−02	1.19E−02	5.66E−02	2.09E−02	− 1.73E−02	7.33E−03	3.77E−07	5.02E−03
	M3	− 2.46E-02	4.98E−03	7.73E−07	6.30E−01	− 1.04E−02	4.55E−03	2.18E−02	6.74E−02	− 1.84E−02	5.74E−03	2.66E−07	4.62E−02
	M4	− 2.92E-02	4.77E−03	9.43E−10	8.75E−01	− 1.16E−02	4.51E−03	9.92E−03	9.80E−02	− 2.15E−02	6.18E−03	4.06E−10	1.91E−02
	M5	− 2.57E-02	5.03E−03	3.30E−07	7.70E−01	− 1.06E−02	4.55E−03	2.03E−02	9.03E−02	− 1.88E−02	5.76E−03	1.44E−07	4.77E−02
	M6	− 2.31E-02	5.09E−03	5.63E−06	2.79E−01	− 1.08E−02	4.64E−03	2.05E−02	6.91E−02	− 1.64E−02	3.43E−03	1.83E−06	5.28E−02
	M7	− 2.94E-02	5.40E−03	5.16E−08	4.47E−01	− 1.05E−02	1.30E−02	9.29E−02	1.64E−02	− 1.89E−02	8.90E−03	1.01E−07	1.01E−03
cg20515679	M0	− 1.86E-01	1.35E−01	2.58E−06	3.54E−04	− 8.53E−02	2.59E−02	9.90E−04	4.04E−01	− 1.24E−01	4.84E−02	1.13E−07	1.94E−03
	M1	− 1.83E-01	1.35E−01	2.78E−06	4.47E−04	− 8.96E−02	2.65E−02	7.13E−04	5.04E−01	− 1.26E−01	4.91E−02	8.80E−08	2.55E−03
	M2	− 1.85E-01	1.36E−01	5.02E−06	3.84E−04	− 8.76E−02	2.63E−02	8.67E−04	4.05E−01	− 1.24E−01	4.83E−02	1.79E−07	2.42E−03
	M3	− 1.95E-01	1.31E−01	5.58E−07	4.10E−04	− 8.32E−02	2.60E−02	1.37E−03	4.81E−01	− 1.28E−01	4.89E−02	3.89E−08	1.60E−03
	M4	− 2.14E-01	1.59E−01	8.13E−06	2.90E−04	− 8.15E−02	2.60E−02	1.68E−03	4.47E−01	− 1.28E−01	5.10E−02	8.87E−07	1.75E−03
	M5	− 1.94E-01	1.42E−01	1.24E−06	2.05E−04	− 8.51E−02	2.61E−02	1.12E−03	4.23E−01	− 1.27E−01	5.06E−02	7.13E−08	1.12E−03
	M6	− 1.97E-01	1.40E−01	7.92E−06	5.76E−04	− 8.42E−02	2.58E−02	1.12E−03	4.27E−01	− 1.25E−01	4.78E−02	4.34E−07	3.13E−03
	M7	− 2.21E-01	1.44E−01	7.86E−05	4.00E−03	− 8.46E−02	2.70E−02	1.73E−03	6.83E−01	− 1.27E−01	4.52E−02	6.22E−06	1.82E−02

BMI: BMI category; CM2: Use of controller medication in the 2 weeks preceding spirometry; CQP: P value of Cochran’s Q; Coef: Regression coefficient estimate; FEV₁: forced expiratory volume in 1 s; FVC: Forced vital capacity; SHS: Second-hand smoking exposure; P: P value; SE: Standard error of the regression coefficient estimate. Genome-wide significant p values are shown in bold

M0: CpG ~ PFT + Age + Sex + Height + In utero maternal smoking exposure + Genetic ancestry + Cellular heterogeneity + Batch; M1: CpG ~ M0 + BMI; M2: CpG ~ M0 + SHS; M3: CpG ~ M0 + Controller medication use in the past two weeks; M4: CpG ~ M0 + insurance status; M5: CpG ~ M0 + maternal education level; M6: CpG ~ M0 + Preterm birth; M7: CpG ~ M0 + BMI + SHS + Controller medication use in the past two weeks + insurance status + maternal education level + preterm birth