For migraine with aura, SERPINC1, ALMS1, ZKSCAN8P1, PAM, and NCF2 were significant (p < 0.05); SERPINC1 was significant in nine regions, with the most pronounced association in the Nucleus accumbens (basal ganglia) (p = 0.014). Here, ZKSCAN8P1 is linked to migraine with aura.