Fig. 5

TROVE2 and UCLH5 on chromosome 1 are prioritised for CEL. The ruler shows chromosome location, with HindIII sites marked by ticks. The top tracks show PIRs for prioritised genes in non-activated (n) and activated (a) CD4⁺ T cells. Green and purple lines are used to highlight those PIRs containing credible SNPs from our fine-mapping. The total number of interacting fragments per PCHi-C bait is indicated in parentheses for each gene in each activation state. Dark grey boxes indicate promoter fragments; light grey boxes, PIRs containing no disease associated variants; and red boxes, PIRs overlapping fine-mapped disease-associated variants. The position of the fine-mapped variant area is indicated by red boxes and vertical red lines. Gene positions and orientation (Ensembl v75) are shown above log2 read counts for RNA-seq forward (red) and reverse (blue) strands. H3K27ac background-adjusted read count is shown in non-activated (green line) and activated (purple line) and boxes on the regRNA track show regions considered through ChromHMM to have regulatory marks