%0 Journal Article %A Oliver S Burren %A Arcadio Rubio GarcĂ­a %A Biola-Maria Javierre %A Daniel B Rainbow %A Jonathan Cairns %A Nicholas J Cooper %A John J Lambourne %A Ellen Schofield %A Xaquin Castro Dopico %A Ricardo C Ferreira %A Richard Coulson %A Frances Burden %A Sophia P Rowlston %A Kate Downes %A Steven W Wingett %A Mattia Frontini %A Willem H Ouwehand %A Peter Fraser %A Mikhail Spivakov %A John A Todd %A Linda S Wicker %A Antony J Cutler %A Chris Wallace %T Chromosome contacts in activated T cells identify autoimmune disease-candidate genes %D 2017 %R 10.1101/100958 %J bioRxiv %P 100958 %X Autoimmune disease-associated variants are preferentially found in regulatory regions in immune cells, particularly CD4+ T cells. Linking such regulatory regions to gene promoters in disease-relevant cell contexts facilitates identification of candidate disease genes. Here we show that, within four hours, activation of CD4+ T cells invokes changes in histone modifications and enhancer RNA transcription that correspond to altered expression of the interacting genes identified by promoter capture Hi-C (PCHi-C). By integrating PCHi-C data with genetic associations for five autoimmune diseases we prioritised 252 candidate genes, of which 116 were related to activation-sensitive interactions. This included IL2RA, where allele-specific expression analyses were consistent with its interaction-mediated regulation, illustrating the utility of the approach. %U https://www.biorxiv.org/content/biorxiv/early/2017/01/17/100958.full.pdf