Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network

Table 1 Autoimmune and autoinflammatory diseases show widespread association with functional variants of the TNFSF network

Disease	λ whole genome^a	λ eQTL SNP set^b	eQTL SNP set association p value^c
Behçet’s disease (BEH)	1.05	2.48	0.0002
Crohn’s disease (CD)	1.04	2.39	0.0003
Multiple sclerosis (MS)	1.06	1.59	<0.0001
Primary biliary cirrhosis (PBC)	1.06	1.49	<0.0001
Rheumatoid arthritis (RA)	1.02	1.48	0.003
Ulcerative colitis (UC)	1.04	1.44	0.0021
ANCA-associated vasculitis (AAV)	1.11	1.25	0.17
Type 1 diabetes (T1D)	1.04	1.00	0.77

^a λ values were calculated for the whole genome filtered for relative SNP independence
^b λ values were calculated for the TNFSF eQTL SNP set defined as follows: for each TNFSF-related gene in each cell subset with a significant cis-eQTL (FDR < 0.1), the strongest eQTL SNP was identified; SNPs with LD r² ≥ 0.8 with these eQTL SNPs were then extracted from the GWAS dataset and filtered for relative independence
^c Permutation-based p values for TNFSF eQTL SNP set association with disease were calculated from the same set of SNPs as in the TNFSF eQTL SNP set^b

ISSN: 1756-994X