Table 3. Haplotype analysis.

Haplotypes SNP1 (rs3129882) SNP3 (rs2844505) SNP4 (rs9268515)	Freq.Cases	Freq.Controls	OR (95% CI)	P
AAC	0.11	0.15	Reference
AAG	0.33	0.36	1.27 (1.07–1.50)	5×10−3
AGC	0.03	0.03	1.34 (0.93–1.91)	0.11
GAC	0.02	0.01	1.75 (1.07–2.87)	0.03
AGG	0.07	0.06	1.56 (1.22–1.99)	4×10−4
GGC	0.006	0.007	-	-
GAG	0.26	0.23	1.57 (1.32–1.86)	2×10−7
GGG	0.18	0.15	1.65 (1.38–1.97)	4×10−8

Haplotypes were composed of SNP1, SNP3 and SNP4, shown in that order. These SNPs and SNP2 survived conditional analysis at P<0.05. SNP2 had low frequency and any haplotype with minor allele of SNP2 was too infrequent (<0.01) to be included in haplotype association tests. For each SNP, the allele that was associated with higher risk for PD (see Table 2 ) is shown in bold. OR and P values were calculated for each haplotype relative to AAC haplotype which has the lowest risk for PD. Analyses were adjusted for age at enrollment, sex, PC1, and PC2 (principal components that define Jewish/non-Jewish origin and the European country of ancestry). AAG consists of major alleles for each SNP; GGC consists of minor alleles for each SNP. Haplotype GGC was not tested because its frequency was <0.01.