The minor allele PD-1.9 T increased CHB patients’ risk towards disease progression either as LC, HCC or LC + HCC [LC vs. CHB: OR = 1.7(1.2–2.4), padj = 0.00014; HCC vs. CHB: OR = 1.3 (1.1–1.8), padj = 0.029; LC + HCC vs. CHB: OR = 1.5 (1.1–2.0); padj = 0.0043]. Here, PDCD1 is linked to hepatocellular carcinoma.