The invention discloses a SNP marker rs12107 associated with diagnosis of non-syndromic cleft lip with or without cleft palate, and develops an application of the marker in a diagnosis kit for non-syndromic cleft lip with or without cleft palate susceptibility according to the marker. The marker and applications of the invention can make the diagnosis of non-syndromic cleft lip with or without cleft palate more convenient and convenient, and enable the clinician to quickly and accurately grasp the patient's condition, lays the foundation for clinical treatment evaluation, and helps to discovernew small molecule drug targets with potential therapeutic value.