Under our dominant model hypothesis, the FLT4 rs383985 (OR = 1.088–1.871, P = 0.00956), HYDIN rs7198975 (OR = 1.012–1.759, P = 0.04065), and rs1774266 genes (OR = 1.012–1.759, P = 0.04065) were still significantly associated with the risk of ASD. Here, FLT4 is linked to atrial septal defect.