REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti- CD14-PE	BioLegend	Cat#325602; RRID AB_830675
Anti-CD4-BUV295	BD Biosciences	Cat# 563550, RRID:AB_2738273
Anti-CD8-BUV737	BD Biosciences	Cat#612754; RRID:AB_2870085
Anti-CD3-BV786	BD Biosciences	Cat #563918; RRID:AB_2738487
Anti-CD14-FITC	BD Biosciences	Cat #555397; RRID:AB_395798
Anti-CD16-APC	BioLegend	Cat #360706; RRID:AB_2562751
Ani-HLA-DR-BV605	BD Biosciences	Cat #562845
anti-H3K27ac	Diagenode	Cat#C15410196; RRID:AB_2637079
anti-H3K4me3	Diagenode	Cat# pAb-003-050, RRID:AB_2616052
anti-H3K4me1	Diagenode	Cat# C15410194, RRID:AB_2637078
Biological samples
AS patients and HC blood samples	This study	N/A
Chemicals, peptides, and recombinant proteins
Ficoll-Paque Plus	Sigma-Aldrich	GE17-1440-02
CD4 MicroBeads	Miltenyi Biotec	Cat# 130-045-101, RRID:AB_2889919
CD8 MicroBeads	Miltenyi Biotec	Cat#130-045-201; RRID:AB_2889920
CD14 MicroBeads	Miltenyi Biotec	Cat#130-050-201; RRID:AB_2665482
Trypan Blue	Gibco	15250061
FACS Lysing Solution 10x concentrate	BD Biosciences	Cat# 349202, RRID:AB_2868862
eBioScience™ Flow Cytometry Staining Buffer	ThermoFisher Scientific	Cat# 00-4222-26
7-AAD Viability Staining Solution	BioLegend	Cat# 420403
eBioScience™ 1-Step Fix/Lyse Solution	ThermoFisher Scientific	Cat# 00-5333-54
PBS, pH 7.4	Gibco	Cat#10010031
BSA	New England Biolabs	Cat#B9000S
Trizma® hydrochloride solution (Tris-HCl) pH 7.4	Sigma-Aldrich	Cat#T2194
Sodium chloride solution, 5M	Sigma-Aldrich	Cat#S5150
MgCl2 (1M)	Invitrogen	Cat#AM9530G
Digitonin	Promega	Cat#G9441
Tween 20	Sigma-Aldrich	Cat#P1379
TD Tagment DNA Buffer	Illumina	Cat#15027866
TDE1 Tagment DNA Enzyme	Illumina	Cat#15027865
AMPure XP Beads	Beckman Coulter	Cat#A63881
Formaldehyde solution	Sigma-Aldrich	Cat#F8775
Glycine	Sigma-Aldrich	Cat#G7403
Sodium dodecyl sulphate solution	Sigma-Aldrich	Cat#71736
EDTA (0.5M) pH8	Sigma-Aldrich	Cat#102161034
Tris (1 M), pH 8.0, RNase-free	Invitrogen	Cat#AM9855G
Complete Protease Inhibitor Cocktail	Sigma-Aldrich	Cat#COEDTAF-RO
Triton X-100	Sigma-Aldrich	Cat#T8787
Dynabeads Protein G for Immunoprecipitation	Invitrogen	Cat#10003D
10% Igepal CA-630	Sigma-Aldrich	Cat#I8896
DpnII 50,000 U/ml	New England Biolabs	Cat#R0543M
T4 DNA HC ligase (30 Weiss U/μL)	Thermo Fisher Scientific	Cat#EL0013
RNase, DNase free	Roche	Cat#1119915
Proteinase K	Thermo Fisher Scientific	Cat#EO0491
Dynabeads M-270 Streptavidin	Invitrogen	Cat#65305
Ribonucleic acid, transfer from baker's yeast	Sigma-Aldrich	Cat#R5636
Lithium chloride solution, 8M	Sigma-Aldrich	Cat#L7026
Sodium deoxycholate monohydrate	Alfa Aesar	Cat#B20759
Tris-EDTA buffer solution	Sigma-Aldrich	Cat#T9285
Critical commercial assays
Live/Dead Fixable Violet Dead cell stain kit	Invitrogen	Cat#L34955
AllPrep DNA/mRNA/miRNA Universal kit	Qiagen	Cat#80224
Ribo-Zero rRNA Removal kit	Illumina	Cat#20040526
TruSeq Stranded Total RNA	Illumina	Cat#20020596
MinElute PCR purification kit	Qiagen	Cat#28004
NEBNext High-Fidelity 2x PCR master mix	New England Biolabs	Cat#M0541S/L
NEBNext DNA Library Prep Master Mix Set	New England Biolabs	Cat#E6040S/L
Herculase II Fusion Enzyme with dNTPs Combo	Agilent	Cat#600677
Nimblegen SeqCap EZ Hybridisation and wash kit	Roche	Cat#05634261001
Nimblegen SeqCap EZ Accessory kit v2	Roche	Cat#07145594001
KAPA Library Quantification Complete Kit (Universal)	KAPA	Cat#KK4824
NextSeq 500/550 High Output kit v2.5 (150 Cycles)	Illumina	Cat#20024907
TapeStation D1000 Screen Tape	Agilent	Cat#5067-5582
TapeStation High Sensitivity D1000 Screen Tape	Agilent	Cat#5067-5584
TapeStation D1000 Reagents	Agilent	Cat#5067-5583
Infinium Global Array V2.0	Illumina	Cat#20024444
Deposited data
PCHi-C	Javierre et al.38	https://osf.io/u8tzp/
Ankylosing spondylitis Immunochip summary statistics	Cortes et al.9	N/A
Cross-disease GWAS summary statistics	Ellinghaus et al.10	N/A
eQTL catalogue	Kerimov et al.43	https://www.ebi.ac.uk/eqtl/
Human PBMC scRNA-seq data	COvid-19 Multi-omics Blood Atlas (COMBAT) consortium77	https://www.combat.ox.ac.uk/
RNA-seq, ATAC-seq, ChIPm fastq data	This study	European Genome-Phenome Archive: EGAS00001006233
Genotype data	This study	European Genome-Phenome Archive: EGAS00001006945
RNA-seq, ATAC-seq, ChIPm raw and normalised count data; Capture-C count data and PeakY scores; ChromHMM data	This study	https://doi.org/10.5281/zenodo.6373353
Oligonucleotides
Capture-C baits	This study	Table S8
NEBNext Multiplex Oligos for Illumina (Index Primers set 1)	New England Biolabs	Cat#E7335S/L
NEBNext Multiplex Oligos for Illumina (Index Primers set 2)	New England Biolabs	Cat#E7500S/L
Nimblegen HyperCap Universal Blocking Oligos	Roche	Cat#08286396001
Modified Nextera Index primers	Buenrostro78	N/A
Software and algorithms
CapSequm2	Telenius et al.79	https://capsequm.molbiol.ox.ac.uk/cgi-bin/CapSequm.cgi
CaptureCompare	Telenius et al.79	https://github.com/djdownes/CaptureCompare
QTLtools	Delaneau et al.80	https://qtltools.github.io/qtltools/
CIBERSORTx	Newman et al.37	https://cibersortx.stanford.edu/
Eagle2	Loh et al.81	https://alkesgroup.broadinstitute.org/Eagle/
PBWT	Durbin et al.82	https://github.com/richarddurbin/pbwt
STAR	Dobin et al.83	https://github.com/alexdobin/STAR/releases; RRID:SCR_004463
Picard tools	Picard Toolkit. 2019. Broad Institute, GitHub Repository.	https://broadinstitute.github.io/picard/; RRID:SCR_006525
HTSeq	Anders et al.84	https://htseq.readthedocs.io/en/release_0.11.1/count.html; RRID:SCR_011867
BEDTools	Quinlan et al.85	https://bedtools.readthedocs.io/en/latest/; RRID:SCR_006646
DESeq2	Love et al.86	https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID:SCR_015687
XGR	Fang et al.33	http://galahad.well.ox.ac.uk:3030/
Bowtie2 v2.3.5.1	Langmead et al.87	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml; RRID:SCR_016368
Samtools v.1.12	Danecek et al.88	http://www.htslib.org/; RRID:SCR_002105
bedGraphToBigWig	Kent et al.89	https://www.encodeproject.org/software/bedgraphtobigwig/
MACS2	Zhang et al.90	https://macs3-project.github.io/MACS/; RRID:SCR_013291
featureCounts	Liao et al.91	http://subread.sourceforge.net; RRID:SCR_012919
ChIPseeker	Yu et al.92	http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html; RRID:SCR_021322
ChromHMM	Ernst et al.39	http://compbio.mit.edu/ChromHMM/; RRID:SCR_018141
FactoMineR	Lê et al.93	http://factominer.free.fr/; RRID:SCR_014602
GARFIELD	Iotchkova et al.42	https://www.ebi.ac.uk/birney-srv/GARFIELD/
FastQC v0.11.4	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/fastqc; RRID:SCR_014583
cutadapt v 1.10	Martin et al.94	https://cutadapt.readthedocs.io/en/stable/; RRID:SCR_011841
TrimGalore v 0.4.4	Babraham Bioinformatics	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
FLASH	Magoč et al.95	https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz/; RRID:SCR_005531
PeakY	Eijsbouts et al.96	https://github.com/cqgd/pky
Pi	Fang et al.33	http://pi.well.ox.ac.uk:3010/; 97
Dnet	Fang et al.98	https://cran.r-project.org/package=dnet
ggplot2	Wickham et al.99	https://ggplot2.tidyverse.org; RRID:SCR_014601
EnhancedVolcano v1.12.0	EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labelling	https://github.com/kevinblighe/EnhancedVolcano; RRID:SCR_018931
Venny 2.1	VENNY. An interactive tool for comparing lists with Venn Diagrams.	https://bioinfogp.cnb.csic.es/tools/venny/; RRID:SCR_016561
KEGG mapper – Colour	Kanehisa et al.100	https://www.genome.jp/kegg/mapper/color.html
GenomicInteractions	Harmston et al.101	https://www.bioconductor.org/packages/release/bioc/html/GenomicInteractions.html
Gviz	Hahne et al 2016102	https://bioconductor.org/packages/release/bioc/html/Gviz.html
Limma	Ritchie et al.103	https://bioconductor.org/packages/release/bioc/html/limma.html; RRID:SCR_010943
R	R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria	https://www.R-project.org/; RRID:SCR_001905
ICeCAP pipeline	This paper	https://doi.org/10.5281/zenodo.7760066
Other
DynaMag-2 Magnet	Invitrogen	12321D
AutoMACS Pro Separator	Miltenyi Biotech	https://www.miltenyibiotec.com/GB-en/products/automacs-pro-separator-starter-kit.html#gref; RRID:SCR_018596
LSRFortessa X-20-flow cytometer	BD Biosciences	https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-cell-analyzers/lsrfortessa; RRID:SCR_018655
HiSeq4000 platform	Illumina	https://emea.illumina.com/systems/sequencing-platforms/hiseq-3000-4000.html
NextSeq 500 platform	Illumina	https://emea.illumina.com/systems/sequencing-platforms/nextseq.html
M220 focussed ultrasonicator	Covaris	https://www.covaris.com/m220-focused-ultrasonicator-500295
TapeStation 4200	Agilent	https://www.agilent.com/en/product/automated-electrophoresis/tapestation-systems/tapestation-instruments/4200-tapestation-system-228263