We identified the rs11170516 with risk allele G (the major allele) as the most significantly moderate-severe hypospadias associated SNP at this locus [Pcombine = 3.5 × 10− 9, OR = 1.96 (1.59–2.44)], and we believe that this variant might affect the expression of the proximal SP1 gene and subsequently regulate a variety of hypospadias-related pathways. Here, SP1 is linked to hypospadias.