Genetic variants in the 6p21.3 region influence hepatitis B virus clearance and chronic hepatitis B risk in the Han Chinese population

Abstract

Background and aim: A genome-wide association study has indicated the association of numerous genes in the 6p21.3 region with chronic hepatitis B virus (HBV) infection. In this study, we screened 12 representative single-nucleotide polymorphisms (SNPs) from the 6p21.3 region and investigated their association with the risk of chronic hepatitis B (CHB) to better understand the molecular etiology underlying CHB risk in the Han Chinese population.

Methods: Between March 2021 and November 2022, we included 183 patients with CHB (case group) and 196 with natural HBV clearance (control group). Allele typing of the selected SNPs was performed using snapshot technology. The correlation between the 12 chosen SNPs and the risk of chronic HBV infection was examined using binary logistic regression analysis. Interacting genes of the variants were identified, and expression quantitative trait loci (eQTL) were analyzed using the 3DSNP database.

Results: We validated 12 previously reported CHB susceptibility sites, including rs1419881 of transcription factor 19 (TCF19), rs3130542 and rs2853953 of human leukocyte antigen (HLA)-C, rs652888 of euchromatic histone-lysine-methyltransferase 2 (EHMT2), rs2856718, rs9276370, rs7756516, and rs7453920 of HLA-DQ, rs378352 of HLA-DOA, and rs3077, rs9277535, and rs9366816 of HLA-DP. Logistic regression analyses revealed that polymorphisms such as rs9276370, rs7756516, rs7453920, rs3077, rs9277535, and rs9366816 were positively correlated with natural HBV clearance in the dominant model. Conversely, rs3130542 and rs378352 were identified as risk factors for CHB. Haplotype analysis revealed that rs9276370, rs7756516, and rs7453920 in HLA-DQ were TTG and GCA haplotypes. Although the TTG haplotype was positively correlated with a higher risk of CHB, the GCA haplotype significantly influenced the natural clearance of HBV. Bioinformatics analysis demonstrated that rs378352, rs3077, and rs9366816 were located within enhancer states; rs3077 and rs9366816 overlapped with nine transcription factor-binding sites, whereas rs378352 altered five sequence motifs. Furthermore, eQTL analysis demonstrated the functional tendencies of eight statistically significant SNPs (rs3130542, rs9276370, rs7756516, rs7453920, rs378352, rs3077, rs9277535, and rs9366816).

Conclusions: Genetic variations within the 6p21.3 region were associated with chronic HBV infection in the Han Chinese population in southern China. Furthermore, the GCA haplotype including rs9276370, rs7756516, and rs7453920 of HLA-DQ contributed significantly to natural HBV clearance, implying that multiple SNPs exert a cumulative allelic effect on HBV infection.

Keywords: Chronic hepatitis B (CHB); Expression quantitative trait loci (eQTL); Haplotype; Hepatitis B virus (HBV); Human leukocyte antigen (HLA); Single-nucleotide polymorphism (SNP).

Fig. 1

Linkage disequilibrium (LD) analysis of the 12 single-nucleotide polymorphisms (SNPs) in the 6p21.3region. The top horizontal bar depicts the position of the SNPs on a physical scale. Shades of gray indicate the strength of the pairwise LD based on r². The haplotype block was defined by the confidence interval approach.

Fig. 2

Radar chart depicting the functional tendencies of eight single-nucleotide polymorphisms (SNPs) across six functional categories. The functionality scores of rs3130542 (A), rs9276370 (B), rs7756516 (C), rs7453920 (D), rs378352 (E), rs3077 (F), rs9277535 (G), and rs9366816 (H) include six functional categories: 3D interacting genes, measures of evolutionary conservation (conservation), sequence motifs, transcription factor-binding sites (TFBSs), and enhancer/promoter states. Taking rs3077 (F) as an example, the total functionality score of this SNP was 7.49 with the majority of points attributed to the following four functional categories: 3D interacting gene (3.00), TFBS (3.71), motif alterations (0.53), and enhancer state (0.09).