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To investigate the association between PTCH1 single nucleotide polymorphism(SNP) and non-syndromic cleft lip with or without palate (NSCL/P) in the Ningxia Hui Autonomous region and predict the function of single nucleotide polymorphism through bioinformatics analysis. A case-control analysis of 31 single nucleotide polymorphism locus alleles on PTCH1 gene (504 cases and 455 controls) was performed to explore the association between PTCH1 gene polymorphisms and non-syndromic cleft lip with or without palate in Ningxia region. Transcription factors, 3D single nucleotide polymorphism and other related information of single nucleotide polymorphism loci with statistical significance were screened by the case-control experiments, and then analyzed the corresponding transcription factors through the NCBI database. The case-control study showed that 5 of the 31 single nucleotide polymorphism loci rs357564 (P = 0.0233), rs1805155 (P = 0.0371), rs28446116 (P = 0.0408), rs2282041 (P = 0.0439), rs56119276 (P = 0.0256) had statistically significant differences in allele frequencies between the case and control groups. Bioinformatics analysis revealed that EP300 and RUNX3 , among the transcription factors associated with rs28446116, may be associated with the development of non-syndromic cleft lip with or without palate. PTCH1 gene may be associated with the occurrence of non-syndromic cleft lip with or without palate in the Ningxia region, which may be related to the role of EP300 and RUNX3 in the development of cleft lip and palate. • PTCH1 gene is associated with non-syndromic cleft lip with or without palate. • Transcription factors EP300 and RUNX3 interact with PTCH1 gene in 3D spatial structure. • 3D single nucleotide polymorphism analysis can predict gene interactions. [ABSTRACT FROM AUTHOR]