Comprehensive epigenomic profiling reveals disease-specific chromatin states and enhances therapeutic target discovery in ankylosing spondylitis

We performed comprehensive epigenetic profiling in immune cell samples from patients with ankylosing spondylitis and healthy controls. 

We used ChromHMM to integrate epigenomic data. ChromHMM filenames are in the format ChromHMM_sampleID_celltype_n.bed.gz where n is the number of states in the ChromHMM emission model.

We performed Capture-C to detect chromosome looping interactions between gene promoters and SNPs associated with ankylosing spondylitis. 

Capture-C count data are shown in the format: CaptureC_celltype_gene_Pro/SNP_normalised.unionbdg

We used PeakY to calculate a score for each interaction. PeakY scores are given in the following format: PeakY_AS/HV_celltype_tier_chrloc_gene_Pro/SNP.txt

gene_Pro and gene_SNP relate to the baitsets given in Table S8.