Table 2

Pathways showing significant (p≤0.05) enrichment for CHi-C genes for each disease using the Benjamini-Hochberg FDR controlling procedure

DiseasePathwayMolecules in pathway n)Benjamini-Hochberg p valueSNP associations (n)Interacting genes (n)Interacting drug targets (n)Cell type-specific significance
RACD40 signalling817.08×10−4 1192Both
iNOS signalling457.08×10−4 772Both
T helper cell differentiation731.38×10−3 883Both
IL-12 signalling and production in macrophages1484.90×10−3 10103Both
Th17 activation pathway914.90×10−3 883Both
Toll-like receptor signalling767.76×10−3 770Both
Dendritic cell maturation1968.13×10−3 12113Both
April-mediated signalling391.05×10−2 650Both
Molecular mechanisms of cancer7891.05×10−2 15165Both
B cell activating factor signalling411.20×10−2 650Both
IL-1 signalling911.23×10−2 771Both
NF-κB signalling1871.23×10−2 11102Both
Role of JAK family kinases in IL-6-type cytokine signalling251.23×10−2 442Both
Th1 and Th2 activation pathway1871.23×10−2 9106Both
IL-10 signalling691.29×10−2 862Both
ErbB signalling1061.86×10−2 873Both
RANK signalling in osteoclasts1041.86×10−2 872Both
Th1 pathway1371.86×10−2 785Both
TNFR2 signalling301.86×10−2 640Both
4-1BB signalling in T lymphocytes322.14×10−2 540Both
IL-17A signalling in airway cells802.14×10−2 762Both
IL-17A signalling in fibroblasts352.82×10−2 540Both
Small cell lung cancer signalling872.82×10−2 761Both
Th2 pathway1522.82×10−2 784Both
Production of nitric oxide and reactive oxygen species in macrophages1963.63×10−2 1094Both
LPS-stimulated MAPK signalling953.80×10−2 762Both
NF-κB activation by viruses953.80×10−2 762Both
IL-8 signalling2044.07×10−2 893Both
Role of PKR in interferon induction and antiviral response414.07×10−2 540Both
STAT3 pathway1324.17×10−2 773Both
mTOR signalling2084.37×10−2 894Both
IL-6 signalling1364.47×10−2 872GM12878
PI3K signalling in B lymphocytes1354.47×10−2 972Both
PsARole of JAK1, JAK2 and TYK2 in interferon signalling244.07×10−2 331
Epithelial adherens junction signalling1494.47×10−2 451Both
Interferon signalling364.47×10−2 331GM12878
Regulation of actin-based motility by rho894.47×10−2 340Both
JIAiNOS signalling453.63×10−3 331Both
Interferon signalling363.63×10−3 331
Th17 activation pathway911.95×10−2 331GM12878
Role of JAK1, JAK2 and TYK2 in interferon signalling242.09×10−2 221Both
Role of JAK family kinases in IL-6-type cytokine signalling252.09×10−2 221Both
IL-15 production282.14×10−2 221Both
PI3K/AKT signalling1292.14×10−2 231Both
STAT3 pathway1322.14×10−2 331Both
Th1 pathway1372.14×10−2 232Both
Oncostatin M signalling402.57×10−2 221Both
Role of PKR in interferon induction and antiviral response412.57×10−2 220Both
Th1 and Th2 activation pathway3743.89×10−2 232Both
Production of nitric oxide and reactive oxygen species in macrophages1964.07×10−2 331Both
IL-8 signalling2044.27×10−2 331Both
  • The total number of molecules in the pathway is shown together with the number of SNP associations and the corresponding numberof genes and drug targets on the pathway. ‘Cell type specific significance’ specifies whether a pathway is significant using T cell (Jurkat) only or Bcell (GM12878) only genes (online supplementary methods). ‘Both’ states that the pathway was significant in both T cell-only genes and B cell-onlygenes

  • CHi-C, Capture Hi-C; FDR, false discovery rate; IL, interleukin; JIA, juvenile idiopathic arthritis; LPS, Lipopolysaccharide; MAPK, mitogen-activated protein kinase; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; PKR, protein kinase R; PsA, psoriatic arthritis; RA, rheumatoid arthritis; RANK, Receptor activator of nuclear factor κ B; SNP, single nucleotide polymorphism; STAT3, signal transducer and activator of transcription 3; iNOS, inducible nitric oxide synthase; mTOR, mechanistic target of rapamycin.