In conclusion, our study reported susceptible loci of SLE patients in Thai ancestry, which were variants on the HLA class II allele, STAT4, GTF2I, and BLK. Additionally, we confirmed those variants which had been reported previously in the Thai populations, which were ARID5B, TNFSF4, BANK1, TNFAIP3, CXCR5 SLC15A, ITGAM, WDFY4, and ETS1. Interestingly, we identified novel variants associated with the Thai SLE patients, which were on the FNB2 allele. This evidence concerns the gene GTF2I and systemic lupus erythematosus.