. 2011 Nov 1;1(6):505–514. doi: 10.1534/g3.111.001164

Table 4 . Association results of NINJ2 in the GEOS Study.

		Previously Reported Variant				Best SNP within the Gene
	No. of SNPs^a	Variant	Effect/Noneffect Allele	OR (95% CI)	P^b	Variant	Effect/Noneffect Allele	OR (95% CI)	P^b	Empirical P^c
EA^d	70	rs12425791	A/G	0.96 (0.76, 1.21)	0.74	rs12229103	A/C	1.34 (0.90, 2.00)	0.15	0.95
EA^d	70	rs11833579	A/G	1.00 (0.81, 1.24)	0.99	rs12229103	A/C	1.34 (0.90, 2.00)	0.15	0.95
AA^d	70	rs12425791	A/G	1.02 (0.73, 1.42)	0.91	rs11063749	T/C	0.74 (0.60, 0.93)	0.008	0.27
AA^d	70	rs11833579	A/G	1.04 (0.80, 1.35)	0.76	rs11063749	T/C	0.74 (0.60, 0.93)	0.008	0.27

Abbreviations: CI, confidence interval; OR, odds ratio; P, association P value.

Number of SNPs within the gene that were either directly genotyped (SNP call rate > 95% and HWE P > 1.0 × 10⁻⁷ in either European or African ancestry) or imputed (imputation dosage r2 > 0.3).

Nominal P was obtained by t-statistics in the logistic regression.

Empirical P was obtained by permutations as described in Materials and Methods.

European ancestry (EA) and African ancestry (AA) are defined based on multidimensional scaling (MDS) analysis.