Introduction: Juvenile idiopathic arthritis (JIA) is the most common rheumatic disease of childhood, affecting approximately 1 in 1000 children in Europe. A large JIA fine-mapping study found that many JIA associated SNPs were in non-coding or intergenic regions. This suggested a potential regulatory role in disease. Furthermore, many of the JIA associated SNPs were located near to genes involved in the IL2 pro-inflammatory cytokine and T-cell signalling pathways. These novel regions posed good candidates for bioinformatic and functional follow-up. Methods: SNPs in IL2 pathway gene regions were analysed using logistic regression in an expanded cohort of JIA cases and controls. A bioinformatic pipeline was established using publically available data to investigate these genomic regions and determine the most likely causal SNP. A candidate region was selected and genotype and stimulation specific chromosome conformation capture and chromatin immunoprecipitation were performed to identify regulatory mechanisms between the candidate SNP and local genes. Results: Based on initial analysis and bioinformatic investigation of the IL2 gene regions the RUNX1 region was selected for experimental follow-up. rs9979383 was found to be the most likely functional SNP within the RUNX1 region. In unstimulated B-cell lines, long range interactions were captured between the rs9979383 anchor fragment and the RUNX1 proximal promoter. Stimulated cells carrying the protective genotype showed a stronger interaction. Enhancer marks were enriched near the promoter in unstimulated cells carrying the protective genotype but not when stimulated, or in cells carrying the risk genotype. RUNX1 expression was relatively high in unstimulated cells carrying the protective genotype. Conclusions: The gene region harbouring JIA susceptibility SNPs was involved in the distal regulation of RUNX1. The regulation of RUNX1 is dependent on both genotype and stimulation status of B-cells. In cells with the protective genotype, expression of RUNX1 is relatively high but downregulates upon stimulation indicating the proximal promoter is under stimulation dependant repression. High RUNX1 expression at baseline in B-cells may help to regulate the IL2 pathway under non-inflammatory conditions. These findings suggest RUNX1 regulation in B-cells may be an important driver of JIA susceptibility.