By integrating multiple databases and carrying out a series of functional annotations for dental-caries- and periodontitis-related SNPs, we found that 47 SNPs were located in 66 gene regions, and could affect the expression of 68 genes through cis-eQTL and/or trans-eQTL (Figure 3); among them, only 13 genes (AAK1, ADCY3, FAM118A, LINC00511, MAMSTR, MTMR3, NEO1, PBX3, RP11-1055B8.4, RP11-115J16.2, RP11-291B21.2, SYT14, and TMEM219) were both SNP-located and regulated by these SNPs, which may play a central role in the pathological process of disease (Figure 3). This evidence concerns the gene PBX3 and dental caries.