Whole group associations of BATF, with better SDMT-z scores [+0.715, 95% CI: (0.02, 1.42), P = 0.046] and overall BICAMS scores [+15.23, bootstrapped 95% CI: (4.94, 26.31), P = 0.016], and HDAC9, with better SDMT-z scores [+0.736, 95% CI: (0.05, 1.42), P = 0.035], were not seen in MS patients and appeared driven by differences in those with CIS. Here, BATF is linked to in situ carcinoma.