Colocalization methods are designed to disentangle shared and distinct casual variants in regions where two diseases show association. We extended existing methods to allow for the shared control design common in GWAS.  126 ImmunoChip regions assigned to at least one of the 4 diseases studies - Multiple Sclerosis (MS), Celiac Disease (CEL), Rheumatoid Arthritis (RA) & Type 1 Diabetes (T1D) - were analysed for all six pariwise comparisons. Ninety of the 126 regions (71%) showed association with at least one disease, with 33 regions (26%) showing association shared between at least 2 diseases.

Two colocolaization methods were applied to each of the 126 regions, a Bayesian Approach and a Proportional Approach. 21 regions were found most likely to be disease-specific under the analyses, 14 regions showed evidence for seperate SNP effects (P(H3) > 0.5) and finally 12 regions showed strong evidence of novel association (P(H3H4) > 0.5)

Study Type
Case-Control Study
Exclusion Criteria

All samples included in this study were gathered in the UK and are reported, or self-declared, as European ancestry.

Sample exclusions were applied as described in each of the ImmunoChip papers for CEL (GDXHsS00009 - Trynka et al.), RA (GDXHsS00019 - Eyre et al.), MS (GDXHsS00030 - IMSGC et al.) and T1D (GDXHsS00025 - Onengut et al.)

Markers were excluded due to...

  • Call rate <99%
  • MAF <1%
  • HardyWeinberg Z-score > 5
  • Lying in the MHC region (defiend as hg18 chr6:29,797,978-33,606,563)

Regions were excluded due to...

  • Containing fewer than 10 SNPs
  • SNP density < 1 SNP/kb

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1q24.3chr1:172681545-172896352FASLG  rs12068671T > C0.1871.27e-05D1.14D
2p14chr2:65170461-65489960SPRED2  rs1858037T > A0.3447.26e-04D1.06 (1.02-1.1)D
2q11.2chr2:99928492-100425222AFF3  rs9653442T > C1.37e-05D1.08D
2q37.1chr2:230185270-230371171SP140  rs10201872C > T2.02e-04D1.09D
5q11.2chr5:56122309-56161300ANKRD55  rs71624119G > A0.2465.53e-05D1.11D
6q15chr6:90097116-90319078BACH2  rs72928038G > A0.1768.23e-07D1.13D
6q23.3chr6:137568592-137806067TNFAIP3  rs6920220G > A0.2207.26e-06D1.12D
7p12.2chr7:50212219-50325817IKZF1  rs201847125C > T0.3018.59e-02D1.04D
7p14.1chr7:37323977-37400850ELMO1  rs79758729A > G0.1059.15e-07D1.15D
13q32.3chr13:99240634-99534324GPR183  rs9585056T > C6.17e-01D1.01D
15q25.1chr15:78728401-78968794CTSH  rs34593439G > A6.50e-07D1.16D
19p13.2chr19:10280033-10517872TYK2  ICAM3  ICAM1  rs34536443G > C1.69e-05D1.23D


GDXHsS00040 meets the following criteria:

Criteria Name
Disease Tags
Study for a Disease 


PMIDTitleFirst AuthorJournalDisease(s)Date