Table 3.

Variation in nicotine dependence risk explained by selected variants in primary sample

Variant Class	Variant	European Americans (n=1432)			African Americans (n=1388)
		MAF	R2	p-value	MAF	R2	p-value
Common	rs16969968	0.355	1.0%	0.001	0.058	0.4%	0.04
Low Frequency	rs2229961	0.016	0.4%	0.03	0.002	0.1%	0.24
	rs80087508	0	.	.	0.014	0.3%	0.07
	rs79109919	0.0003	0.2%	0.15	0.057	0.1%	0.34
Rare	aggregate term	0.005	1.0%	0.0009	0.009	0.1%	0.37
All CHRNA5 genetic terms			2.4%	5.5 ×10−5		1.0%	0.07

This table shows the variance explained by each individual variant and aggregate term by itself, as well as the variance explained by all CHRNA5 genetic variants examined jointly in the final model. This final model includes rs16969968, rs2229961, rs800087508, rs79109919, and the aggregate rare variant term;

R² is the Nagelkerke’s adjusted R² difference from logistic regression, comparing the base model with intercept, sex, age, and ancestry specific PCs to models with genetic variants;

p-values calculated by taking the difference between the -2logliklihoods in the base model and those with variants as a chi-square statistic.