In conclusion, our work has strengthened the case for the AHI1 gene candidate but also identified other potential MS gene targets, such as SGK1, BCLAF1 IL20RA, IL22RA2, IFNGR1 and TNFAIP3. Additionally, we have shown a possible co-regulation of MS GWAS associations in the 6q23 region, which could help elucidate the pathogenesis of MS as well as other autoimmune diseases. Here, TNFAIP3 is linked to autoimmune disease.