Background Ischemic stroke is likely caused by interactions of multiple genes and environmental determinants. However, large-scale sequencing studies to discern functional genetic variants and their interactions with clinical and lifestyle risk factors on ischemic stroke are limited. Methods and Results We sequenced functional regions of 740 previously identified genes associated with atherosclerotic disease among 999 ischemic stroke cases and 1001 controls of Chinese ancestry. Multiple logistic regression models were used to examine the associations between variants and ischemic stroke and test interactions between variants and clinical and lifestyle risk factors. Functional variants achieving suggestive significance were replicated in an independent sample of 4724 ischemic stroke cases and 5029 controls. Driven by variant main effects, each minor allele of the correlated rs174535, rs174545, and rs3834458 variants at conferred an average 0.83-fold (95% CI, 0.78-0.88) decreased odds of stroke. Significant main effects of rs1801133 missense variant were also observed, with each copy of the A allele associated with a 1.20-fold (95% CI, 1.13-1.27) higher odds of ischemic stroke. The functional rs671 variant was identified in interaction analyses with alcohol drinking (=3.39×10). Each minor allele conferred a 0.54-fold (95% CI, 0.45-0.64) decreased odds of stroke among drinkers and a 0.89-fold (95% CI, 0.83-0.97) decreased odds among nondrinkers. Conclusions Significant associations at indicate that genetically elevated polyunsaturated fatty acids may decrease ischemic stroke risk in East Asians. Significant associations at and robustly confirm deleterious effects of genetically elevated homocysteine and alcohol intake, respectively, on ischemic stroke.