H3K27ac ChIP in stimulated primary CD4 T cells - effect of disease-associated haplotype on 6q23

Numerous genomic loci have been implicated in autoimmune disorders, but attempts to identify causal variants, and thereby disease mechanisms, have been hampered by strong linkage disequilibrium – leaving most loci unresolved and the potential of GWAS unfulfilled. To overcome this, we developed a massively-parallel reporter assay for use in primary CD4 T-cells, a key effector of many autoimmune diseases, and sought to resolve potential causal variants via their functional effects. We identified a specific functional variant at a pleiotropic locus that has been associated with multiple immune mediated diseases, and confirmed that this modulated expression by disrupting an NFKB binding site. To determine the resulting effect on enhancer activity we performed H3K27ac ChIP in stimulated CD4 T cells from 3 major allele homozygotes and 3 minor allele homozygotes at rs6927172. We performed H3K27ac ChIP in stimulated CD4 T cells that were freshly purified from 3 minor allele homozygotes and 3 major allele homozygotes at rs6927172. Stimulations were performed for 4 days using anti-biotin beads coated with anti-CD3, anti-CD2 and anti-CD28 (1:2 bead-to-cell ratio) and IL-2 (10ng/ml). Raw data are provided as 50bp single-end Illumina reads from both the immunoprecipitated DNA and the input chromatin. We also provide bigWig files for individual samples and the output from ROSE (rank ordering of super-enhancers) for merged samples - according to genotype at rs6927172.