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Sarcoidosis is a multiorgan inflammatory disorder with heritability estimates up to 66%. Previous studies have shown the major histocompatibility complex (MHC) region to be associated with sarcoidosis, suggesting a functional role for antigen-presenting molecules and immune mediators in the disease pathogenesis. To detect variants predisposing to sarcoidosis and to identify genetic differences between patient subgroups, we studied four genes in the MHC Class III region () and with tag-SNPs and their relation to alleles. We present results from a joint analysis of four study populations (Finnish, Swedish, Dutch, and Czech). Patients with sarcoidosis ( = 805) were further subdivided based on the disease activity and the presence of Löfgren's syndrome. In a joint analysis, seven SNPs were associated with non-Löfgren sarcoidosis (NL; the strongest association with rs3177928,  = 1.79E-07, OR = 1.9) and eight with Löfgren's syndrome [Löfgren syndrome (LS); the strongest association with rs3129843,  = 3.44E-12, OR = 3.4] when compared with healthy controls ( = 870). Five SNPs were associated with sarcoidosis disease course (the strongest association with rs3177928,  = 0.003, OR = 1.9). The high linkage disequilibrium (LD) between SNPs and an challenged the result interpretation. When the SNPs and alleles were analyzed together, independent association was observed for four SNPs in the region: rs3135365 (NL;  = 0.015), rs3177928 (NL;   0.001), rs6937545 (LS;  = 0.012), and rs5007259 (disease activity;  = 0.002). These SNPs act as expression quantitative trait loci (eQTL) for and/or . In conclusion, we found novel SNPs in and regions associating with sarcoidosis. Our finding further establishes that polymorphisms in the and have a role in sarcoidosis susceptibility. This multi-population study demonstrates that at least a part of these associations are independent (e.g., not due to LD) and shared across ancestral origins. The variants that were independent of associations acted as eQTL for and/or , suggesting a role in regulating gene expression.