BACKGROUND: Genome-wide association studies (GWAS) have uncovered the genetic basis behind many diseases and conditions. However, most of these genetic loci affect regulatory regions, making the interpretation challenging. Chromatin conformation has a fundamental role in gene regulation and is frequently used to associate potential target genes to regulatory regions. However, previous studies mostly used small sample sizes and immortalized cell lines instead of primary cells. RESULTS: Here we present the most extensive dataset of chromatin conformation with matching gene expression and chromatin accessibility from primary CD4 CONCLUSIONS: Given these genes' significant role in T cell development and maturation, our work deepens our comprehension of autoimmune disease pathogenesis, suggesting potential treatment targets. In addition, our dataset provides a valuable resource for the investigation of immune-mediated diseases and gene regulatory mechanisms.