Additional file 2: Figures S1–S14. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Figure S1. Comparison of longer and shorter CD4+ T cell activation timecourses. Figure S2. Summary distributions of interacting fragments. Figure S3. Validation of PCHi-C by ChIA-PET. Figure S4. Chromatin state profiles of interacting fragments. Figure S5. Relationship of gene expression to PIR number and mRNA half-life. Figure S6. Definition and quantification of regulatory RNAs. Figure S7. blockshifter calibration. Figure S8. MDN1 is prioritised for RA through ImmunoChip but not GWAS data. Figure S9. Gene prioritisation using COGS. Figure S10. Multiple genes on chromosome 1q32.1 (IL10, IL19, IL20, IL24, FCAMR/PIGR) are prioritised for T1D, CRO and UC. Figure S11. Histograms show the distribution of summed PIR length by gene in non-activated CD4+ T cells (top panel) and TAD length in naive CD4+ T cells. Figure S12. IRF8 and EMC8/COX4I1 on chromosome 16 are prioritised for RA and SLE. Figure S13. AHR on chromosome 7 is prioritised for RA in activated CD4+ T cells. Figure S14. Allelic imbalance in mRNA expression in individuals heterozygous for group A SNPs is confirmed with reporter SNP rs12244380 (IL2RA 3’ UTR). (PDF 4243 kb)