To determine whether these disease-associated genetic variants (Passoc<0.05) were related to the altered expression levels of their nearby differentially expressed IFN signature genes, we performed cis- and trans-eQTL analyses for all SNPs with Passoc<0.05 (173 SNPs in 44 regions; S1 Table) using a linear model by integrating the transcriptome and genotype datasets in 178 European individuals (108 anti-Ro/SSA positive SS cases, 55 anti-Ro/SSA negative SS cases, and 15 healthy controls). This evidence concerns the gene IFNA1 and synovial sarcoma.