Table 2.

Tests for non-additive allelic effects in the discovery and replication samples

SNP	Gene	BAF	AOSW-inferred myopia status								Refractive error
			Additive effect			Dominance deviation			Full dom. or rec		Additive effect			Dominance deviation
			Beta	SE	P value	Beta	SE	p value	AB_AA p value	AB_BB p value	Beta	SE	p value	Beta	SE	p value
rs7829127	ZMAT4	(G) 0.20	− 0.06	0.01	4.61E−06	0.13	0.03	8.42E−05	3.99E−28	9.20E−01	0.06	0.02	9.59E−03	− 0.24	0.06	4.76E −05
rs55885222	SNTB1	(A) 0.39	0.06	0.01	2.45E−11	0.07	0.02	2.60E−03	6.09E−02	4.05E−08	− 0.06	0.02	2.09E−04	− 0.04	0.04	3.06E−01
rs35337422	RD3L	(C) 0.14	0.06	0.02	6.54E−04	0.12	0.04	5.34E−03	7.73E−01	1.26E−03	− 0.13	0.03	9.28E−05	− 0.21	0.08	7.21E−03
rs12193446	LAMA2	(G) 0.09	− 0.16	0.03	3.57E−08	0.16	0.06	1.03E−02	2.65E−62	1.88E−01	0.33	0.05	6.35E−11	− 0.25	0.11	2.57E−02
rs7624084	ZBTB38	(C) 0.45	− 0.03	0.01	2.96E−04	0.05	0.02	2.75E−02	2.34E−05	7.79E−01	0.10	0.01	4.03E−13	0.02	0.04	6.15E−01
rs17382981	CYP26A1	(T) 0.42	0.02	0.01	2.46E−02	− 0.05	0.02	2.86E−02	6.04E−04	6.64 E−01	− 0.06	0.01	6.01 E−05	− 0.01	0.04	7.05E−01
rs1969091	TMC3	(A) 0.29	− 0.02	0.01	2.36 E−02	0.05	0.03	3.52 E−02	9.93 E−06	8.09 E−01	0.10	0.02	1.11 E−07	0.08	0.05	8.78E−02
rs11101263	FRMPD2	(T) 0.27	0.06	0.01	3.61 E−08	− 0.05	0.03	4.69 E−02	5.94 E−14	1.48 E−01	− 0.11	0.02	1.76 E−09	− 0.10	0.05	5.23E−02

Results are presented for variants selected for testing in the replication sample (i.e. p < 0.05 for the dominance deviation term and p > 0.05 for either the AB vs. AA or AB vs. BB comparison in the AOSW-inferred myopia phenotype in the discovery sample)

BAF B allele frequency, SE standard error, AOSW age-of-onset of spectacle wear