Table 2

Genetic association results of the 11 putative MS loci in other autoimmune diseases

LocusIndex SNPIndex SNP associations in other autoimmune diseases with p≤0.05Best genome-wide significant SNP per locus across other autoimmune diseases
LOC100506457rs1534422 (G)ATD: OR=1.17 (G), p=1.76E-07
T1D: OR=1.09 (G), p=9.82E-06
CEL: OR=1.05 (G), p=0.0122
JIA: OR=1.13 (G), p=0.0215
CD28rs6435203 (A)CEL: OR=1.14 (G), p=2.63E-10
RA :OR=1.06 (G), p=2.55E-03
T1D: OR=1.06 (G), p=4.27E-03
NAR: OR=1.10 (G), p=0.0134
ATD: rs11571297, OR=1.37 (A), p=2.09E-23
T1D: rs3087243, OR=1.19 (G), p=7.36E-21
CEL: rs1980422, OR=1.19 (C), p=1.43E-15
ZBTB38rs9846396 (C)PBC: OR=1.11 (C), p=1.07E-03
LPPrs4686953* (G)CEL: OR=1.30 (A), p=2.979E-43
ATD: p=5.77E-06
CEL: rs2030519, OR=1.32 (A), p=3.00E-49
ATD: rs13093110, p=3.69E-08
DQ571824rs727098 (C)T1D: OR=1.04 (C), p=0.0361
NCOA2rs13260060 (A)PSO: OR=1.08 (A), p=0.0275
RA: OR=1.07 (A), p=0.0253
CSGALNACT2rs3004212† (C)
ETS1rs3809006 (G)CEL: OR=1.10 (G), p=5.36E-07
PSO: OR=1.14 (G), p=5.32E-04
ATD: p=0.0118
NAR: OR=1.09 (A), p=0.0187
CEL: rs61907765, OR=1.18 (T), p=3.43E-13
DLEU1rs806349 (T)CEL: OR=1.05 (C), p=0.0119
ATD: p=0.0228
PBC: OR=1.07 (T), p=0.0255
LPIN3rs6072343 (A)PBC: OR=1.14 (A), p=1.90E-03
T1D: OR=1.07 (A), p=0.0124
ATD: p=0.0314
IFNGR2rs9808753 (G)PBC: OR=1.14 (G), p=2.46E-03
RA: OR=1.08 (A), p=3.93E-03
PSO: OR=1.12 (A), p=0.0141
  • This table displays genetic association results of the 11 loci from ImmunoChip studies of eight other autoimmune diseases as available on the ImmunoBase database ( The ‘index SNP’ indicates the most significant SNP in the MS ImmunoChip study.4 The risk allele for each specific disease is listed in brackets if available at ImmunoBase ( Underlined allele names of the index SNP indicate directions of effect inverse to the one observed for MS. Effect size estimates and effect directions were not available for autoimmune thyroid disease (ATD) on Immunobase; instead, for SNPs rs1534422 and rs11571297 they were retrieved from the original study.26 The last column lists the most significant SNP per disease for loci (defined as ±1 Mb around the index SNP) that show genome-wide significant association with the specific disease. Dark grey background indicates loci that did not replicate in this study.

  • *For the diseases ATD and T1D, results for a proxy SNP were available in ImmunoBase (rs2030516, r2>0.9 based on 1000 Genomes CEU data).

  • †For the diseases PSO and T1D only results for a proxy SNP of the index SNP (rs2460554, r2>0.6) were available in ImmunoBase; no data were available for CEL and NAR for the index SNP or proxies down to r2=0.3; for the remaining five diseases, association results for the index SNP were available.

  • CEL, coeliac disease; JIA, juvenile idiopathic arthritis; MS, multiple sclerosis; NAR, narcolepsy; PBC, primary biliary cirrhosis; PSO, psoriasis; RA, rheumatoid arthritis; T1D, type 1 diabetes.