Transmembrane protein 106B (TMEM106B) has been identified as a functional receptor facilitating ACE2-independent SARS-CoV-2 entry. However, its role in supporting a broad range of SARS-CoV-2 variants, including the emerging Omicron BA.2.86 and JN.1 subvariants, remains to be determined. To address this question, we generated 293- and A549-derived TMEM106B knockout cell lines and assessed their ability to support viral entry for various SARS-CoV-2 variants (D614G, E484D, Omicron BA.1, BA.2, XBB.1.5, BA.2.86, and JN.1) using pseudoviral infection systems. We also examined the role of transmembrane protease serine 2 (TMPRSS2) and other type II transmembrane serine proteases (TTSP) in viral entry and syncytium formation. Our results showed that TMEM106B knockout significantly reduced viral entry across all tested variants. Additionally, overexpression of TMPRSS2, TMPRSS11F and TMPRSS13 in TMEM106B-expressing cells enhanced viral entry and syncytium formation, including BA.2.86 and JN.1 variants. Importantly, we identified two single-nucleotide polymorphisms (SNPs) that result in G2A and N151S variant, respectively, affects TMEM106B receptor function, indicating that selected genetic polymorphisms of TMEM106B gene may impact cell susceptibility to SARS-CoV-2 infection. These findings highlight TMEM106B as a functional receptor for SARS-CoV-2 across different variants, including the latest Omicron subvariants, and provide new insights for the therapeutic interventions targeting viral entry.