TABLE 2.

Association Analyses of SNCA Risk Variants

SNP	rs356182	rs763443	rs2870004
Alleles, effect/reference	A/G	C/T	A/T
b37 chr4 base position	90626111	90819961	90471245
Discovery, n cases/controls = 5,542/5,886
Effect allele frequency	0.37	0.52	0.21
Stepwise conditional analysis
Conditioned on	Not conditioned	rs356182	rs356182 and rs763443
OR (95% CI)	0.78 (0.74–0.82)	1.20 (1.12–1.28)	0.88 (0.82–0.93)
P	2.7e-20	4.1e-10	0.00010
Combined model
OR (95% CI)	0.70 (0.65–0.74)	1.21 (1.14–1.28)	0.88 (0.82–0.94)
P	9.7e-31	2.9e-10	0.00010
Independent replication, n cases/controls = 6,961/6,636
OR (95% CI)	0.67 (0.63–0.71)	1.15 (1.09–1.22)	0.88 (0.83–0.94)
P	2.8e-42	4.5e-07	4.2e-05
Combined analysis discovery + replication
OR (95% CI)	0.68 (0.66–0.71)	1.17 (1.13–1.22)	0.88 (0.84–0.92)
P	1.1e-69	4.9e-15	3.0e-08

The table lists variants passing our SNPSpD-adjusted significance threshold of p < 0.00023 using stepwise forward conditional analysis in the discovery phase. Stepwise conditional results are followed by statistics for the joint model in discovery data, independent replication, and finally combined analysis in a logistic regression model including all 3 SNPs, with sex, study, and top 5 principal components as covariates. Genomic coordinates correspond to GRCh37, and directions of effect are shown for the nonreference allele.

CI = confidence interval; OR = odds ratio; SNP = single nucleotide polymorphism.