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. Author manuscript; available in PMC: 2014 May 1.
Published in final edited form as: Nat Genet. 2013 Sep 29;45(11):1353–1360. doi: 10.1038/ng.2770

Table 2.

49 Known non-MHC susceptibility loci associated with multiple sclerosis at a genome-wide significance level

Discovery Replication Joint
SNP Chr Positiona RA RAF P-value OR RAF P-value OR P-value OR Geneb Function
rs3748817 1 2525665 A 0.64 1.3 × 10-12 1.14 0.65 1.2 × 10-15 1.15 1.3 × 10-26 1.14 MMEL1 intronic
rs41286801 1 92975464 A 0.14 7.9 × 10-16 1.20 0.16 2.1 × 10-12 1.17 1.4 × 10-26 1.19 EVI5 UTR3
rs7552544* 1 101240893 A 0.56 3.7 × 10-6 1.08 0.43 3.3 × 10-12 1.12 1.9 × 10-16 1.10 VCAM1 intergenic
rs6677309 1 117080166 A 0.88 1.5 × 10-28 1.34 0.88 4.1 × 10-16 1.24 5.4 × 10-42 1.29 CD58 intronic
rs1359062 1 192541472 C 0.82 1.8 × 10-13 1.18 0.83 2.1 × 10-8 1.13 4.8 × 10-20 1.15 RGS1 intergenic
rs55838263 1 200874728 A 0.71 1.4 × 10-9 1.12 0.71 3.9 × 10-11 1.13 4.0 × 10-19 1.13 C1orf106 intronic
rs2163226 2 43361256 A 0.71 7.0 × 10-8 1.10 0.73 3.8 × 10-10 1.14 2.1 × 10-16 1.12 intergenic
rs7595717 2 68587477 A 0.26 3.3 × 10-7 1.10 0.27 6.8 × 10-8 1.10 1.2 × 10-13 1.10 PLEK intergenic
rs9989735 2 231115454 C 0.18 7.8 × 10-14 1.17 0.19 6.8 × 10-11 1.14 4.2 × 10-23 1.16 SP140 intronic
rs2371108 3 27757018 A 0.38 2.1 × 10-6 1.08 0.39 5.8 × 10-11 1.12 1.5 × 10-15 1.10 EOMES downstream
rs1813375 3 28078571 A 0.47 5.7 × 10-18 1.15 0.49 4.4 × 10-16 1.15 1.9 × 10-32 1.15 intergenic
rs1131265 3 119222456 C 0.80 2.0 × 10-15 1.19 0.81 4.8 × 10-10 1.14 1.4 × 10-23 1.17 TIMMDC1 exonic
rs1920296* 3 121543577 C 0.64 6.8 × 10-15 1.14 0.64 5.5 × 10-9 1.10 6.5 × 10-22 1.12 IQCB1 intronic
rs2255214* 3 121770539 C 0.52 5.3 × 10-13 1.13 0.52 3.3 × 10-13 1.13 1.2 × 10-24 1.13 CD86 intergenic
rs1014486 3 159691112 G 0.43 1.2 × 10-9 1.11 0.44 1.4 × 10-10 1.11 1.1 × 10-18 1.11 IL12A intergenic
rs7665090 4 103551603 G 0.52 2.4 × 10-6 1.08 0.53 5.0 × 10-4 1.13 1.0 × 10-8 1.09 MANBA intergenic
rs6881706 5 35879156 C 0.72 4.9 × 10-9 1.12 0.73 1.7 × 10-9 1.12 4.3 × 10-17 1.12 IL7R intergenic
rs6880778 5 40399096 G 0.60 1.7 × 10-8 1.10 0.61 3.9 × 10-13 1.13 8.1 × 10-20 1.12 intergenic
rs71624119 5 55440730 G 0.76 2.7 × 10-9 1.12 0.76 1.9 × 10-5 1.09 3.4 × 10-13 1.11 ANKRD55 intronic
rs72928038 6 90976768 A 0.17 7.6 × 10-7 1.11 0.19 9.0 × 10-11 1.17 1.5 × 10-15 1.14 BACH2 intronic
rs11154801 6 135739355 A 0.37 2.3 × 10-9 1.11 0.37 1.0 × 10-12 1.13 1.8 × 10-20 1.12 AHI1 intronic
rs17066096 6 137452908 G 0.23 5.9 × 10-12 1.14 0.25 4.1 × 10-13 1.15 1.6 × 10-23 1.14 IL22RA2 intergenic
rs67297943 6 138244816 A 0.78 4.8 × 10-8 1.12 0.80 2.5 × 10-6 1.11 5.5 × 10-13 1.11 TNFAIP3 intergenic
rs212405 6 159470559 T 0.62 1.4 × 10-15 1.15 0.64 1.8 × 10-7 1.10 8.0 × 10-21 1.12 TAGAP intergenic
rs1021156 8 79575804 A 0.24 5.6 × 10-10 1.12 0.26 2.1 × 10-8 1.11 8.5 × 10-17 1.11 ZC2HC1A intergenic
rs4410871 8 128815029 G 0.72 2.0 × 10-9 1.12 0.72 3.4 × 10-8 1.11 4.3 × 10-16 1.11 MIR1204 intergenic
rs759648 8 129158945 C 0.31 2.8 × 10-6 1.09 0.31 3.7 × 10-5 1.08 5.0 × 10-10 1.08 MIR1208 intergenic
rs2104286 10 6099045 A 0.72 7.6 × 10-23 1.21 0.73 3.6 × 10-26 1.23 2.3 × 10-47 1.22 IL2RA intronic
rs1782645 10 81048611 A 0.43 4.3 × 10-7 1.09 0.41 6.2 × 10-10 1.11 2.5 × 10-15 1.10 ZMIZ1 intronic
rs7923837 10 94481917 G 0.61 4.6 × 10-9 1.11 0.62 2.0 × 10-9 1.11 4.3 × 10-17 1.11 HHEX intergenic
rs34383631 11 60793330 A 0.40 5.7 × 10-10 1.11 0.39 4.5 × 10-15 1.15 3.7 × 10-23 1.13 CD6 intergenic
rs1800693 12 6440009 G 0.40 6.9 × 10-16 1.14 0.41 1.0 × 10-13 1.14 6.7 × 10-28 1.14 TNFRSF1A intronic
rs11052877 12 9905690 G 0.36 5.4 × 10-9 1.10 0.38 1.2 × 10-5 1.08 5.6 × 10-13 1.09 CD69 UTR3
rs201202118c 12 58182062 A 0.67 7.4 × 10-13 1.14 0.67 1.6 × 10-10 1.12 9.0 × 10-22 1.13 TSFM intronic
rs7132277 12 123593382 A 0.19 1.9 × 10-6 1.10 0.19 1.4 × 10-8 1.13 1.9 × 10-13 1.12 PITPNM2 intronic
rs2236262 14 69261472 A 0.50 1.2 × 10-5 1.08 0.50 3.8 × 10-8 1.09 2.5 × 10-12 1.08 ZFP36L1 intronic
rs74796499 14 88432328 C 0.95 8.5 × 10-11 1.31 0.95 4.5 × 10-11 1.33 2.4 × 10-20 1.32 GALC intronic
rs12927355 16 11194771 G 0.68 8.2 × 10-27 1.21 0.69 4.3 × 10-21 1.18 6.4 × 10-46 1.20 CLEC16A intronic
rs35929052 16 85994484 G 0.89 3.3 × 10-7 1.14 0.88 3.6 × 10-6 1.15 5.9 × 10-12 1.15 IRF8 intergenic
rs4796791 17 40530763 A 0.36 1.8 × 10-8 1.10 0.36 1.2 × 10-13 1.14 3.7 × 10-20 1.12 STAT3 intronic
rs8070345 17 57816757 A 0.45 5.4 × 10-16 1.14 0.46 1.9 × 10-9 1.10 2.2 × 10-23 1.12 VMP1 intronic
rs1077667 19 6668972 G 0.79 3.5 × 10-13 1.16 0.79 8.4 × 10-13 1.16 1.7 × 10-24 1.16 TNFSF14 intronic
rs34536443 19 10463118 C 0.95 1.2 × 10-8 1.28 0.96 2.9 × 10-7 1.30 1.8 × 10-14 1.29 TYK2 exonic
rs11554159 19 18285944 G 0.73 2.6 × 10-13 1.15 0.74 1.4 × 10-12 1.15 1.9 × 10-24 1.15 IFI30 exonic
rs8107548 19 49870643 G 0.25 2.0 × 10-6 1.09 0.26 2.5 × 10-10 1.13 5.7 × 10-15 1.11 DKKL1 intronic
rs4810485 20 44747947 A 0.25 1.8 × 10-5 1.08 0.25 1.4 × 10-12 1.14 7.7 × 10-16 1.11 CD40 intronic
rs2248359 20 52791518 G 0.60 9.8 × 10-5 1.07 0.62 8.2 × 10-11 1.12 2.0 × 10-13 1.09 CYP24A1 intergenic
rs2283792 22 22131125 C 0.51 1.1 × 10-6 1.08 0.53 5.4 × 10-11 1.11 5.5 × 10-16 1.10 MAPK1 intronic
Secondary
rs523604d 11 118755738 A 0.53 2.5 × 10-7 1.09 0.54 4.0 × 10-9 1.11 6.2 × 10-15 1.10 CXCR5 intronic

All listed signals had a discovery P-value ≤ 1.0 × 10-4, a replication P-value ≤ 5.0 × 10-2, and a joint P-value ≤ 5.0 × 10-8

All P-values are two-sided

RA = Risk Allele, RAF = Risk Allele Frequency

a

Position is based on human genome 19 and dbSNP 137.

b

Nearest gene listed if within 50Kb. Bold indicates Gene Ontology Immune System Process.

c

A proxy SNP (rs10431552, r2 = 0.99) was used in replication.

d

The P-value and OR values provided are after conditioning on rs9736016 and rs533646 (both Novel – see Table 1).

*

These three SNPs were not primary in the 2011 GWAS, two were secondary and the third was tertiary in that study.