The findings revealed that plasma HIF‐1α was identified to be genetically associated with cardioembolic stroke (CES) (OR = 0.885; 95% confidence interval [CI] = 0.796–0.985, p = 0.026), migraine (OR = 0.941, 95% CI = 0.888–0.998, p = 0.041), and drug‐induced migraine without aura (MOA) (OR = 0.586, 95% CI = 0.375–0.916, p = 0.019). Here, HIF1A is linked to cardioembolic stroke.