Table 1 Notable genes within regions associated with Crohn's disease

Innate immunity

   NOD2 (nucleotide binding oligomerization domain 2)

2.2-4.0 [58]

Involved in pattern recognition

   ATG16L1 (ATG16 autophagy related 16-like 1)

1.34 (1.29-1.40) [5]

Involved in autophagy

   IRGM (immunity-related GTPase family, M)

1.37 (1.28-1.47) [5]

Involved in autophagy

   TLR4 (Toll-like receptor 4)

1.29 (1.08-1.54) [59]

Involved in pattern recognition

   CARD9 (caspase recruitment domain family, member 9)

1.18 (1.13-1.22) [5]

Involved in pattern recognition

   VAMP3 (vesicle-associated membrane protein 3)

1.05 (1.01-1.10) [5]

Involved in autophagy and TNF-α metabolism

   REL (reticuloendotheliosis viral oncogene homolog)

1.14 (1.09-1.19) [5]

Transcriptional activator of NF-кB

   ERAP2 (endoplasmic reticulum aminopeptidase 2)

1.05 (1.02-1.09) [5]

Involved in peptide trimming upon NF-кB stimulation; required for the generation of HLA binding peptides

   UBE2L3 (ubiquitin-conjugating enzyme E2L 3)

0.70 [15]

Ubiquitinates, among others, the NF-кB precursor

Adaptive immunity

   IL23R (IL-23 receptor)

2.66 (2.36-3.00) [5]

Activates Th17 cells

   IL12B (IL-12β)

1.18 (1.13-1.24) [5]

Stimulates Th0 differentiation to Th1 cells

   CCR6 (chemokine (C-C motif) receptor 6)

1.17 (1.12-1.22) [5]

Chemoattractant receptor of immune cells

   HLA-DQA2 (major histocompatibility complex, class II, DQα2)

1.19 (1.13-1.25) [5]

Antigen presenting to Th0

   TNFSF11 (tumor necrosis factor super family 11)

1.10 (1.05-1.15) [5]

Augments the ability of dendritic cells to stimulate naive T-cell proliferation

   TNFSF15 (tumor necrosis factor super family 15)

1.21 (1.15-1.27) [5]

Mediates activation of NF-кB

   ICOSLG (inducible T-cell co-stimulator ligand)

1.18 (1.13-1.23) [5]

Acts as a co-stimulatory signal for T-cell proliferation and cytokine secretion

   IL2RA (IL receptor α)

1.11 (1.05-1.16) [5]

Th0 activation

   TAGAP (T-cell activation GTPase-activating protein)

1.10 (1.05-1.14) [5]

May function as a GTPase activating protein and may play important roles during T-cell activation

   IL10 (IL-10)

1.12 (1.07-1.17) [5]

Inhibits synthesis of pro-inflammatory cytokines

   IL18RAP (IL-18 receptor accessory protein)

1.19 (1.14-1.26) [5]

Protein required for NF-кB activation

   TYK2 (tyrosine kinase 2)

1.12 (1.06-1.19) [5]

Probably involved in intracellular signal transduction by initiation of IFN signaling

   JAK2 (Janus kinase 2)

1.18 (1.13-1.23) [5]

Involved in JAK/STAT pathway; mediates signal transduction of many cytokines

   STAT3 (signal transducer and activator of transcription 3)

1.15 (1.10-1.21) [5]

Involved in JAK/STAT pathway; mediates signal transduction of many cytokines

   SMAD3 (SMAD family member 3)

1.12 (1.07-1.16) [5]

Involved in Treg activation through TGF-β signal transduction

   ICAM1,3 (intercellular adhesion molecule)

1.12 (1.06-1.19) [5]

Homing of leukocytes to inflammation

Other genes of interest

   MUC1,19 (mucin)

1.74 (1.55-1.95) [5]

Involved in mucus production, to protect the epithelial barrier

   FUT2 (fucosyltransferase 2)

1.07 (1.04-1.11) [5]

Involved in the A and B antigen synthesis pathway

   PUS10 (pseudouridylate synthase 10)

1.16 [19]

Post-transcriptional nucleotide modification of structural RNAs, including tRNA, rRNA and sRNAs