InsulatorLeak, a mechanism-first pipeline for variant prioritization by predicted CTCF insulator disruption across seven autoimmune diseases

Abstract Genome-wide association studies have mapped hundreds of autoimmune risk loci, yet fewer than 5% of associated variants have established causal mechanisms. CTCF-bound insulators partition the genome into regulatory domains. When disrupted, enhancers can activate genes they normally do not regulate, a phenomenon termed insulator leakage that has been implicated in malignancy and may contribute to autoimmunity. We reasoned that prioritizing variants by predicted insulator disruption, then validating that prioritization empirically across independent cohorts and diseases, would yield candidates suitable for functional follow-up and target selection. InsulatorLeak combines SuSiE fine-mapping, Enformer-predicted CTCF disruption (Scaled Average Difference, SAD), locus-matched null calibration for empirical p-values, chromatin enrichment (ChromHMM, Hi-C), eQTL and pQTL colocalization, and benchmarking against FUMA, Sei, and Boltz-2. We applied the pipeline to 14 non-MHC autoimmune loci across seven diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis, type 1 diabetes, systemic lupus erythematosus, psoriasis, and atopic dermatitis) using 19 GWAS datasets spanning more than 2.5 million total participants. In MS, TNFRSF1A replicated in 4/6 cohorts (p = 0.022), and IL2RA reached p = 0.006 in IMSGC MS Chip (N = 115,803). Pan-autoimmune replication across seven diseases showed IL7R in 6/7 expansion cohorts (p = 0.011–0.052) and TNFRSF1A in 5/7 (p = 0.011–0.033), indicating insulator disruption as a shared autoimmune mechanism. Thirteen of 14 loci replicated in at least two ancestry groups. IL12AB was significant in all four ancestries, and TYK2 reached FDR q = 0.040 in South Asian. Chromatin enrichment was strongest at drug-target loci (CD58 21×, IL2RA 23×, IL7R 12×, TNFRSF1A 5.3× in MS, CD40 8.6× and IL7R 34× in IBD). pQTL colocalization yielded cognate validation at CD58 (0.996), CD40 (0.958), CD6 (0.79 in IBD), and IL2RA (0.79). Both MS and IBD showed the full validation stack from fine-mapping through pQTL. Overlap with FUMA lead SNPs was 2/120, indicating complementary rather than redundant prioritization. In RA, four loci reached p