Expression quantitative trait loci (eQTL) data have emerged as a reliable source for functional follow-up of disease associations identified from genome-wide association studies (GWAS). Cell type specific data have recently allowed a refined mapping of several GWAS loci that was unattainable with tissue level eQTL studies. However, a significant part of GWAS loci with a putative regulatory potential have not been functionally characterized yet. Activation of cells and data derived from patients, instead of healthy controls, could allow a further refinement of GWAS functional mapping. To address these questions, we generated eQTL data for three peripheral immune cells – naïve CD4+ T cells, memory CD4+ T cells, and classical monocytes – from multiple sclerosis (MS) subjects, untreated (UNT; n=55) or treated with glatiramer acetate (GA; n=84), and healthy controls (HC; n=38). Transcriptomic data were generated both for baseline - unstimulated - and stimulated, i.e. activated, state of the three immune cells. Joint analysis of all subjects, MS and HC, identified an extended number of transcripts (eGenes) that were genetically controlled: 4,016 in naïve CD4+ T cells, 3,843 in memory CD4+ T cells, and 3,652 in monocytes. Stimulation resulted in a reduced number of eGenes across all three cells. A strict formal statistical comparison of the response to stimulation identified 196 response eGenes (reGenes) in naïve CD4+ T cells, 165 reGenes in memory CD4+ T cells, and 338 reGenes in monocytes. We further observed differences in eGene and reGenes that were driven by the MS patient samples and were seemingly disease-specific.