Additional file 1: of Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Table S1. Case/control datasets included in the study. Table S2. Loci reaching genome-wide level of significance in the subset-based meta-analysis and showing independent effect after linkage disequilibrium (LD)-clumping (r2 < 0.05 within 500 kB up- or downstream of the lead SNP). Table S4. Comparison of the results obtained with ASSET and CCMA for the 38 pleiotropic variants identified in our study. Table S5. Novel genome-wide associations for celiac disease, systemic sclerosis and type 1 diabetes (p value < 5 × 10–6 in the subset based meta-analysis and p value < 5 × 10–8 in each disease-specific meta-analysis). Table S7. Potential role of the lead polymorphisms (pleiotropic and single-disease associated variants), and their proxies (r2 ≥ 0.8) as expression quantitative trait loci (eQTLs) in whole blood, immune cell lines or tissues relevant for the diseases under study. Table S8. Specific cell types showing enrichment among regulatory DNA elements, Dnase 1 hypersensitivity sites and histone marks, and pleiotropic variants. (XLSX 77 kb)