Table 5. Haplotype association test of SNP1 (rs3129882) and SNP4 (rs9268515) with PD in NGRC and Replication.

Haplotype SNP1 (rs3129882) SNP4 (rs9268515)	NGRC				Replication				Pooled NGRC + Replication
	Freq incasesN = 4000	Freq incontrolsN = 3972	OR(95%CI)	P	Freq incasesN = 1686	Freq incontrolsN = 1712	OR(95%CI)	P	Freq incasesN = 5686	Freq incontrolsN = 5684	OR(95% CI)	P
AC	0.14	0.18	reference		0.17	0.22	Reference		0.15	0.19	reference
GC	0.02	0.02	1.59(1.01–2.51)	0.05	0.02	0.02	1.71(0.85–3.44)	0.07	0.02	0.02	1.63(1.11–2.39)	0.01
AG	0.40	0.43	1.23(1.07–1.42)	3×10−3	0.38	0.38	1.28(1.04–1.57)	0.01	0.40	0.41	1.25(1.11–1.40)	2×10−4
GG	0.44	0.38	1.51(1.32–1.72)	10−9	0.43	0.39	1.41(1.16–1.71)	2×10−4	0.44	0.38	1.48(1.33–1.65)	2×10−12

OR and P values were calculated for each haplotype relative to the low-risk haplotype (AC) for association with PD. N = number of chromosomes. The bolded alleles are associated with higher risk. Freq = haplotype frequency. P values are two sided for NGRC, one-sided for replication.