Table 1.

12 novel PCa-susceptibility loci identified by GWAS and replication study in Japanese population

	SNP ID	Chr	Position	Effect Allele	NonEffect Allele		Case Frequency	Control Frequency	RSQRa	ORb	95% CI	P-value	Nearby genes
1	rs7542260	1	5743196	C	T	GWAS	0.892	0.910	0.980	0.832	(0.750–0.914)	6.64 × 10−06	–
						Replication	0.887	0.902	–	0.850	(0.784–0.916)	1.14 × 10−06
						Meta	–	–	–	0.843	–	3.99 × 10−11
2	rs11125927	2	62752975	A	G	GWAS	0.738	0.774	0.980	0.837	(0.779–0.895)	4.74 × 10−10	TMEM17
						Replication	0.748	0.772	–	0.876	(0.828–0.924)	4.22 × 10−08
						Meta	–	–	–	0.860	–	3.95 × 10−16
3	rs73862213	3	128217499	A	G	GWAS	0.908	0.929	0.996	0.754	(0.666–0.842)	1.71 × 10−10	GATA2
						Replication	0.902	0.923	–	0.766	(0.694–0.838)	6.49 × 10−14
						Meta	–	–	–	0.761	–	5.87 × 10−23
4	rs75777376	8	127796183	T	C	GWAS	0.896	0.908	0.528	0.779	(0.669-0.889)	6.08 × 10−06	–
						Replication	0.900	0.923	–	0.744	(0.672–0.816)	3.20 × 10−16
						Meta	–	–	–	0.754	–	1.20 × 10−20
5	rs16901814	8	127881952	G	A	GWAS	0.854	0.833	0.993	1.176	(1.108–1.244)	2.00 × 10−06	–
						Replication	0.857	0.838	–	1.161	(1.101–1.221)	6.35 × 10−07
						Meta	–	–	–	1.167	-	5.64 × 10−12
6	rs4554825	10	80244623	C	T	GWAS	0.790	0.764	1.000	1.170	(1.110-1.230)	1.06 × 10−07	ZMIZ1-AS
						Replication	0.786	0.766	–	1.122	(1.070–1.174)	6.29 × 10−06
						Meta	–	–	–	1.142	–	8.43 × 10−12
7	rs77911174	10	80826833	A	G	GWAS	0.604	0.643	0.957	0.853	(0.801–0.905)	6.14 × 10−10	ZMIZ1
						Replication	0.599	0.634		0.864	(0.820–0.908)	8.68 × 10−12
						Meta	–	–	–	0.859	–	5.28 × 10−20
8	rs11055034	12	12890626	C	A	GWAS	0.601	0.577	0.999	1.123	(1.073-1.173)	3.11 × 10−06	CDKN1B, APOLD1
						Replication	0.606	0.580	–	1.115	(1.073–1.157)	3.74 × 10−07
						Meta	–	–	–	1.119	–	6.05 × 10−12
9	rs8023793	15	66942093	A	C	GWAS	0.595	0.559	0.997	1.137	(1.087-1.187)	2.56 × 10−07	–
						Replication	0.592	0.569	–	1.098	(1.056–1.140)	1.27 × 10−05
						Meta	–	–	–	1.114	–	2.81 × 10−11
10	rs6117562	20	753310	G	A	GWAS	0.485	0.516	0.989	0.874	(0.824–0.924)	3.64 × 10−08	SLC52A3, FAM110A
						Replication	0.498	0.512	–	0.945	(0.903-0.987)	7.12 × 10−03
						Meta	–	–	–	0.915	–	3.34 × 10−08
11	rs138708	22	39138332	G	A	GWAS	0.855	0.831	0.983	1.172	(1.104-1.240)	3.74 × 10−06	SUN2
						Replication	0.859	0.834	–	1.218	(1.158-1.278)	5.12 × 10−11
						Meta	–	–	–	1.198	–	1.13 × 10−15
12	rs4826594	X	54454406	G	A	GWAS	0.482	0.525	0.967	0.924	(0.888-0.960)	8.21 × 10−06	FGD1, GNL3L, TSR2
						Replication	0.479	0.508	–	0.943	(0.913-0.973)	1.08 × 10−04
						Meta	–	–	–	0.935	–	7.13 × 10−09

^aRSQR, imputation accuracy. SNPs were imputed in the GWAS

^bNon-effect alleles were considered as reference