This repository contains Capture Hi-C (CHi-C) data from a study on genetic susceptibility to psoriasis (Ray-Jones et al., BMC Biology 2020). HindIII CHi-C was performed on two cell lines: HaCaT (keratinocyte) and MyLa (CD8+ T cell). The baits targeted restriction fragments harbouring SNPs associated with various immune-mediated conditions (Psoriasis, Rheumatoid Arthritis, Juvenile Idiopathic Arthritis, Asthma, Systemic Sclerosis). For each cell line there are two biological replicates. Please note that the baitmap differs slightly between the two cell lines; whilst the vast majority of baits are shared, the HaCaT baitmap has some additional loci. For the purposes of the CHiCAGO user workflow, the fastq files were downsampled to 20-40 million reads, in order to obtain ~10 million on target ditags after filtering. The following command was used for each read (note that the same seed was used for read 1 and read 2): `seqtk sample -s${seed} -2 ${fq} ${DS_number}` The downsampled fastq files were processed using HiCUP and then CHiCAGO input (Chinput) files were generated using restricted design files: the baitmap and rmap, named "HindIII_GWAS_all_common_chrs", contain only those chromosomes that were identical between the two baitmaps (chromosomes 7, 9, 13, 17, 20, 21 and 22). CHiCAGO was run on either individual replicates or using two biological replicates in the same command. The full fastq files were also analysed as individuals or as biological replicates using CHiCAGO using the full HindIII rmap and respective baitmap per cell line.