We identified several regions associated with subtype differentiation: cleft type differences in 8q24 (p = 1.00 × 10<sup>-4</sup> ), laterality differences in IRF6, a gene previously implicated with wound healing (p = 2.166 × 10<sup>-4</sup> ), sex differences and side of unilateral CL differences in FGFR2 (p = 3.00 × 10<sup>-4</sup> ; p = 6.00 × 10<sup>-4</sup> ), and sex differences in VAX1 (p < 1.00 × 10<sup>-4</sup> ) among others.