GSE112337
Novel risk variants affecting enhancers of TH1 and TREG cells in type 1 diabetes [ChIP-seq]
Most type 1 diabets (T1D) associated SNPs are located in non-coding regions, making it hard to understand their functional impact. We performed epigenomic profiling of two enhancer marks, H3K4me1 and H3K27ac, using primary TH1 and TREG cells from healthy  and T1D subjects. By integrating enhancers predicted using these ChIP-Seq data, T1D associated SNPs and additional supporting data, we found and validated several novel risk SNPs for T1D. Overall design: Effector momory TH1 and effector memory TREG cells were purified using FACS from 5 health and 6 T1D subjects. With these cells, we generated the profiling of H3K4me1 and H3K27ac using a low-cell number ChIP-Seq protocol. Enhancers were predicted using these ChIP-Seq data and analyzed by integrating RNA-Seq, eQTL, T1D associated SNPs and additional data, we predicted and validated several novel T1D risk SNPs.