Table 2. Results from discovery stage, replication stage and meta-analysis.

				MAF
SNP	Chr	Gene(s)	Stage*	Cases	Controls	OR (95% CI)	P
rs393152†	17q21	MAPT	Discovery	0.079	0.24	3.45 (2.29–5.34)	6.71 × 10−9
		(H1/H2)	Replication	0.068	0.24	4.37 (2.16–8.83)	4.12 × 10−5
			Meta-analysis			3.70	1.42 × 10−12
rs643472	8p12	lnc-KIF13B-1	Discovery	0.35	0.23	1.88 (1.46–2.40)	7.12 × 10−7
			Replication	0.32	0.22	1.67 (1.11–2.52)	0.014
			Meta-analysis			1.82	3.41 × 10−8
rs963731	2p22	SOS1	Discovery	0.12	0.054	2.46 (1.70–3.57)	2.04 × 10−6
			Replication	0.09	0.049	2.21 (1.09–4.50)	0.029
			Meta-analysis			2.41	1.76 × 10−7
rs1768208	3p22	MOBP	Discovery	0.39	0.29	1.65 (1.30–2.09)	3.86 × 10−5
			Replication	0.39	0.25	1.89 (1.28–2.77)	1.30 × 10−3
			Meta-analysis			1.71	2.07 × 10−7
rs242557	17q21	MAPT	Discovery	0.45	0.35	1.48 (1.17–1.88)	1.50 × 10−3
		(H1c)	Replication	0.48	0.36	1.77 (1.25–2.52)	1.50 × 10−3
			Meta-analysis			1.57	7.91 × 10−6
rs1860743	7q36	PRKAG2	Discovery	0.20	0.11	2.05 (1.52–2.78)	3.46 × 10−6
			Replication	0.09	0.13	0.71 (0.39–1.31)	0.27
			Meta-analysis			1.25	0.67
rs875125	21q22	TSPEAR	Discovery	0.17	0.10	2.02 (1.48–2.75)	7.92 × 10−6
			Replication	0.05	0.08	0.65 (0.29–1.46)	0.29
			Meta-analysis			1.22	0.73

^*Discovery stage (152 CBD, 3,311 controls); Replication stage (67 CBD, 457 controls). The discovery and replication stages were analysed by logistic regression under an additive model. The discovery stage analysis was adjusted for the first multidimensional scaling principle component, and the replication stage was adjusted for age and sex.

^†The OR for rs393152 is referencing the risk associated with the major allele (MAPT H1 haplotype). The protective allele (MAPT H2 haplotype) has an OR (95% CI) of 0.29 (0.19–0.44) in the discovery stage and 0.23 (0.11–0.46) in the replication stage. Genome-wide significantceis defined as variants associated with P<5 × 10⁻⁸. Chr, chromosome; CI, confidence interval; lnc, long non-coding (RNA); MAF, minor allele frequency; OR, odds ratio.