Table 1.
Twenty–one regions which are most likely disease specific under our analysis and for which we know of no other immune–mediated diseases (from the 15 diseases curated in ImmunoBase) that have reported association to these regions (as curated in ImmunoBase, accessed July 9th 2014, and NIHR GWAS catalog, accessed 07/10/2014). Regions required posterior probability of single disease association > 0.5 in at least one pairwise analysis (SNP coverage varies between analyses) and posterior probability of association to any other disorder < 0.2. Candidate causal genes are given. In the case where no candidate causal genes are known, we have given, in brackets, the genes in and around the region.
| Chromosome | Position | Disease Association | Posterior Probability of Single Association | Candidate Causal Gene(s)/ Genes in Region |
|---|---|---|---|---|
| 1p22.1 | 92023171–93311800 | MS | 1.00 | EVI5 |
| 1p21.2 | 100982239–101455699 | MS | 0.57 | EXTL2 VCAM1 SLC30A7 |
| 1p13.1 | 116831830–116911865 | MS | 1.00 | CD58 |
| 3p24.1 | 28015774–28105476 | MS | 0.99 | (CMC1) |
| 3q13.33 | 122818149–123329522 | MS | 1.00 | IQCB1 SLC15A2 CD86 |
| 5q21.1 | 102062861–102777130 | RA | 0.58 | C5orf30 |
| 6q23.3 | 137348296–137587799 | MS | 1.00 | IL22RA2 |
| 7p12.2 | 50337180–50662811 | T1D | 0.97 | 3′ IKZF1* region |
| 7p12.2 | 50866661–51640000 | T1D | 1.00 | COBL |
| 8q21.12 | 79575897–79914680 | MS | 1.00 | ZC2HC1A |
| 8q24.21 | 129187117–129368419 | MS | 0.51 | PVT1 MIR1208 |
| 9p24.2 | 4218549–4311558 | T1D | 1.00 | GLIS3 |
| 10q23.31 | 89998026–90268360 | T1D | 0.87 | RNLS |
| 11p15.5 | 2024999–2264880 | T1D | 1.00 | INS |
| 12q24.31 | 121926103–122574026 | MS | 0.59 | PITPNM2 |
| 14q32.2 | 100357783–100398492 | T1D | 0.98 | DLK1 |
| 16q23.1 | 73760230–74086012 | T1D | 1.00 | BCAR1 |
| 19p13.3 | 6564831–6636304 | MS | 1.00 | TNFSF14 |
| 19p13.11 | 16300497–16612240 | MS | 1.00 | (EPS15L1, CALR3, MED26, C19orf44, CHERP, SLC35E1) |
| 19p13.11 | 17905598–18272802 | MS | 0.87 | MPV17L2 IFI30 |
| 20p13 | 1444472–1707590 | T1D | 0.99 | (SIRPD, SIRPB1, SIRPG) |
There are two ImmunoChip regions which overlap IKZF1 and are separated by a recombination hotspot. The region towards the 5′ end has colocalizing associations with MS and T1D while the region towards the 3′ end appears specific to T1D, as shown in Supplementary Figure 7. Note we provide coordinates of the region, and not an index SNP as is conventional in gwas studies because the method synthesises information across the whole region and does not, in most cases, highlight a single SNP responsible for the association.