We next dissect disease-specific evidence: longitudinal epigenomic studies in T1D showing preclinical DNA methylation changes and altered Alu/LINE-1 patterns, together with HERV-H/W upregulation at onset, SLE studies demonstrating LINE-1 hypomethylation in neutrophils and cell-type-specific TE overexpression that tracks with IFN signatures and nucleic acid sensor pathways, and RA studies linking global and LINE-1 methylation to methotrexate response when integrated with serostatus. The gene discussed is IFNA1; the disease is rheumatoid arthritis.