In migraine, SERPINC1, ZKSCAN8P1, C12orf76, and PAM showed significant associations across brain regions (p < 0.05); notably, SERPINC1 was significant in 12 of the 13 regions (all except Frontal cortex BA9), and the strongest signal was observed for PAM in the Putamen (basal ganglia) (p = 1.05 × 10−4). Here, C12orf76 is linked to migraine disorder.