Children with gains in NEGR1 had a 24% lower risk of abdominal obesity (OR = 0.76; 95% CI: 0.59–0.97), whereas children with gains in ARHGEF4 and CPXCR1 and losses in INS presented 1.35 (p = 0.025), 1.57 (p < 0.001), and 1.63 (p < 0.001) times higher risk of abdominal obesity, respectively, compared with that in children with low copy numbers (0–2). Here, ARHGEF4 is linked to Abdominal obesity.