Influenza A virus (FLUAV) causes serious diseases in both poultry and humans. Various host proteins, including Mx1, are considered candidates for avian influenza (AI) resistance. After infecting Jeju Native chicken embryo fibroblasts (CEFs) with three types of AI viruses, we performed gene expression profiling, identified single nucleotide polymorphisms (SNPs) through RNA-sequencing, and confirmed phenotypes showing antiviral activity . Highly pathogenic AI viruses upregulated , and and downregulated , , and , while a low pathogenicity AI upregulated , , and and downregulated , , and . However, no virus affected expression. Although SNPs in could not discriminate antiviral activity alone, the only CEF resistant to H5N6, strain AN4, contained the Mx1 631 R/R genotype and strongly expressed an oligoadenylate synthetase-like (OASL) variant with a unique SNP: c.G880A (p.E294K). Using transfected cell lines, H5N6-infected cells expressing with the c.G880A SNP showed minimal cytopathic effects and the lowest gene expression. This study confirms that Jeju Native chickens with specific SNP combinations in both and showed H5N6 resistance and demonstrates the interplay of genetic factors in host-pathogen dynamics, suggesting a need for integrated analyses of multiple resistance genes to inform AI prevention strategies.