Table 4.

Replication analysis using the J-MICC samples for previously-reported SNPs.

SNP	Chrb	Positionc	Gene(s)	EAd	NEAe	Rsqf	AFg	Betah	SE (Beta)i	Variance explained (%)	P	Effect direction in European GWASj
rs1260326 a	2	27,730,940	GCKR (missense) SIFT: tolerated PolyPhen: benign	C	T	0.996	0.442	0.0476	0.0207	0.05	0.02	+
rs1481012	4	89,039,082	ABCG2 (intron)	A	G	0.975	0.704	0.0339	0.0226	0.02	0.13	+
rs4410790 a	7	17,284,577	AGR3–AHR (intergenic)	C	T	0.996	0.375	0.0959	0.0207	0.19	3.7 × 10 −6	+
rs6968554 a	7	17,287,106	AGR3–AHR (intergenic)	G	A	0.999	0.341	0.0908	0.0212	0.16	1.9 × 10 −5	+
rs6968865 a	7	17,287,269	AGR3–AHR (intergenic)	T	A	1.000	0.340	0.0908	0.0212	0.16	1.9 × 10 −5	+
rs7800944	7	73,035,857	MLXIPL (intron)	C	T	0.930	0.114	0.0430	0.0331	0.02	0.19	+
rs17685 a	7	75,616,105	POR (3′ UTR)	A	G	0.999	0.363	0.0554	0.0209	0.06	0.008	+
rs382140a	7	107,782,200	LAMB4–NRCAM (intergenic)	A	G	0.997	0.254	0.0302	0.0230	0.02	0.19	+
rs6265 a	11	27,679,916	BDNF (missense)SIFT: tolerated PolyPhen: probably damaging	C	T	1.000	0.592	0.0460	0.0206	0.05	0.03	+
rs6495122a	15	75,125,645	CPLX3–ULK3 (intergenic)	A	C	1.000	0.808	0.0068	0.0257	0.00	0.79	—
rs9902453	17	28,349,095	EFCAB5 (intron)	A	G	0.983	0.338	0.0072	0.0218	0.00	0.74	—

^aDirectly genotyped; ^bChromosome; ^cChromosomal position (GRCh37/hg19); ^dEffect allele; ^eNon-effect allele; ^fImputation quality in terms of R-square calculated by the Minimac3 software version 1.0.11; ^gAllele frequency of effect allele; ^hEffect size; ⁱStandard error of effect size; ^jConsistent direction is denoted as ‘+’ and inconsistent direction is denoted as ‘−’

Results listed in bold are associations whose P-value is less than genome-wide significance (P < 5 × 10⁻⁸).