Autoimmune thyroid diseases (AITD) arise from complex interactions between genetic, epigenetic, and environmental factors. Whole genome linkage scans and association studies have established thyroglobulin (TG) as a major AITD susceptibility gene. However, the causative TG variants and the pathogenic mechanisms are unknown. Here, we describe a genetic/ epigenetic mechanism by which a newly identified TG promoter single-nucleotide polymorphism (SNP) variant predisposes to AITD. Sequencing analyses followed by case control and familybased association studies identified an SNP (؊1623A3 G) that was associated with AITD in the Caucasian population (p ؍ 0.006). We show that the nucleotide substitution introduced by SNP (؊1623A/G) modified a binding site for interferon regulatory factor-1 (IRF-1), a major interferon-induced transcription factor. Using chromatin immunoprecipitation, we demonstrated that IRF-1 binds to the 5 TG promoter motif, and the transcription factor binding correlates with active chromatin structure and is marked by enrichment of mono-methylated Lys-4 residue of histone H3, a signature of active transcriptional enhancers. Using reporter mutations and siRNA approaches, we demonstrate that the disease-associated allele (G) conferred increased TG promoter activity through IRF-1 binding. Finally, treatment of thyroid cells with interferon ␣, a known trigger of AITD, increased TG promoter activity only when it interacted with the disease-associated variant through IRF-1 binding. These results reveal a new mechanism of interaction between environmental (IFN␣) and genetic (TG) factors to trigger AITD.Autoimmune thyroid diseases (AITD), 4 including Graves disease (GD) and Hashimoto thyroiditis (HT), are characterized by infiltration of the thyroid by T and B cells that react with local antigens leading to immune destruction of the thyroid in HT and production of thyroid-stimulating hormone receptor (TSHR) antibodies in GD. These result in the clinical manifestations of hypothyroidism in HT and hyperthyroidism in GD (1, 2). There is solid evidence that interactions between susceptibility genes and environmental triggers activate the sequence of cellular and humoral immune responses to thyroid antigens that cause AITD (1, 3, 4). Several environmental factors, including exposure to excess iodine, selenium deficiency, various infectious diseases, certain drugs, and pollutants have been associated with AITD (5, 6). Among these factors, interferon ␣ (INF␣), a therapeutic agent widely used for the treatment of chronic hepatitis C infection, has recently emerged as a major factor that triggers AITD (7,8).To date, several gene loci have been associated with AITD, including immune genes (HLA-DR, CTLA-4, CD40, FOXP3, and CD25) and thyroid-specific genes (TSHR and TG). Whole genome linkage screens, performed by our group (9) and others (10), have shown that the thyroglobulin (TG) locus on chromosome 8q24 is strongly linked with AITD. Moreover, TG has emerged as the only thyroid-specific gene that confers susceptibili...