The risk allele [C] of IRX6 rs6499755 was associated with increased susceptibility to overall hypospadias (OR = 1.547, 95% CI = 1.108–2.160, p=0.01), anterior (OR = 3.579, 95% CI = 1.468–8.724, p=0.003) and posterior hypospadias (OR = 1.737, 95% CI = 1.179–2.560, p=0.005). The gene discussed is IRX6; the disease is hypospadias.