Abstract: Objective: To analyze the four intron SNPs of ARHGAP29 from previously reported GWAS results by bioinformatics, and performing information annotation and function prediction of target SNPs. Methods: Four statistically significant SNP loci were selected from the case-control experiment. The biological information of SNPs and the functions of related LncRNAs were predicted by using SNP database in NCBI website, 3DSNP database, RegulomeDB database, and LncSNP2.0 database. Results: Minor allele frequency (MAF) of rs72964308 was lower than 0.05, be excluded in subsequent analysis. The analysis of chromatin state showed that SNPs mainly locate in the enhancer region in various cell types, and also in the transcription initiation sites of rare tissues. The high DNA accessibility of the transcription factors that interacted with rs17396055 indicates a strong transcriptional activity. The prediction of LncRNA related with rs17396055 and rs7540684 showed that the disease with the highest correlation was cleft lip and palate. Conclusions: Rs3814019, rs17396055 and rs7540684 play regulatory roles in various cell types, and the LncRNA related to rs17396055 and rs7540684 may be associated with craniofacial development.

Key words: cleft lip and palate, ARHGAP29, SNP, LncRNA, bioinformatics