Additional file 5: Table S4. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

PCHi-C interactions called with the CHiCAGO pipeline. Annotation for baited fragments is given in Additional file 4: Table S3. PIRs are called other ends (‘oe’). CHICAGO scores for activated (‘Total_CD4_Activated’) and non-activated (‘Total_CD4_NonActivated’) CD4+ T cells were considered called with confidence if above 5. We also conducted differential analysis, and the read counts input into that are given by the columns P1.non - P3.act, with the results summarised by their log fold change (logFC) and FDR. Bait-PIR pairs are shown only if the CHiCAGO score is ≥ 5 for at least one CD4+ T cell. (GZ 14529 kb)