Skip to main content
. Author manuscript; available in PMC: 2012 Dec 1.
Published in final edited form as: Ann Neurol. 2011 Dec;70(6):897–912. doi: 10.1002/ana.22609

Table 2.

Meta-analysis results for SNPs with p-value <10−6 and known genes/loci.

SNP Position Minor Allele Major Allele CHR MAF$ Locus (±200Kbp) OR p-value p-value for statistical heterogeneity I2 (95%CI)
Never reported as genome-wide significant
rs170934 28054089 T C 3 0.48 EOMES 1.17 1.57E-08 0.407 2% (0–72%)
rs2150702 5883861 G A 9 0.49 MLANA 1.16 3.28E-08 0.682 0% (0–71%)
rs6718520 43179074 A G 2 0.48 THADA 1.17 3.42E-08 0.157 35% (0–73%)
Published genes/loci
rs10492972 10275699 C T 1 0.32 KIF1B 1.04 0.243 0.605 0% (0–71%)
rs2300747 116905738 G A 1 0.09 CD58 0.73 6.46E-09 0.715 0% (0–71%)
rs2760524 190797171 A G 1 0.17 RGS1 0.88 3.00E-04 0.013 63% (16–84%)
rs12122721 199251103 A G 1 0.28 KIF21B 0.91 2.43E-03 0.247 24% (0–66%)
rs9846534a 107064440 C T 3 0.19 CBLB 0.97 0.434 0.327 13% (0–75%)
rs1132200 120633526 T C 3 0.15 TMEM39A 0.90 3.67E-03 0.442 0% (0–58%)
rs4680534 161181639 C T 3 0.37 IL12A 1.12 3.28E-05 0.957 0% (0–71%)
rs1393122 4778148 G A 5 0.16 Intergenic 0.96 0.287 0.949 0% (0–71%)
rs6897932 35910332 T C 5 0.26 IL7RA 0.89 2.26E-04 0.304 16% (0–60%)
rs9260489 30028311 T G 6 0.45 HLA-B 1.21 1.16E-11 0.221 27% (0–68%)
rs3129889 32521523 G A 6 0.20 HLA-DRB1 2.97 1.03E-206 0.506 0% (0–71%)
rs12722489 b 6142018 T C 10 0.15 IL2RA 0.81 3.66E-08 0.818 0% (0–71%)
rs7089861 b 6150332 G C 10 0.27 IL2RA 0.84 3.84E-08 0.113 42% (0–73%)
rs17824933 60517188 G C 11 0.26 CD6 1.14 3.38E-05 4.70E-03 68% (29–86%)
rs1800693 6310270 C T 12 0.42 TNFRSF1A 1.14 1.41E-05 0.349 10% (0–74%)
rs703842 56449006 G A 12 0.31 METTL1 0.88 1.72E-05 0.877 0% (0–71%)
rs1790100 122222678 G T 12 0.23 MPHOSPH9 1.11 6.61E-04 0.486 0% (0–71%)
rs17445836 84575164 A G 16 0.22 IRF8 0.91 5.30E-03 0.211 28% (0–69%)
rs12708716 11087374 G A 16 0.35 CLEC16A 0.90 1.08E-04 0.509 0% (0–71%)
rs744166c 37767727 G A 17 0.43 STAT3 1.13 6.35E-06 0.327 13% (0–75%)
rs2293152c 37735055 G C 17 0.38 STAT3 0.82 4.09E-08 0.486 0% (0–71%)
rs763361 65682622 T C 18 0.48 CD226 1.06 0.045 0.994 0% (0–71%)
rs6074022d 44173603 C T 20 0.27 CD40 1.15 4.91E-06 0.170 34% (0–72%)
Suggestive (5×10−8 <p<1×10−6)
rs2546890 e 158692478 G A 5 0.48 IL12B 0.86 7.95E-08 0.509 0%
rs8070463 43123835 C T 17 0.50 KPNB1/TBKBP1/TBX21 0.87 9.55E-08 0.586 0% (0–71%)
rs10411936 16409375 A G 19 0.30 EPS15L1 1.16 2.04E-07 0.881 0% (0–71%)
rs2681424 123252212 T C 3 0.40 ILDR1/CD86 1.16 2.33E-07 0.996 0% (0–71%)
rs7592330 68500287 G A 2 0.44 PLEK/FBXO48/C2orf13 0.87 2.42E-07 0.983 0% (0–71%)
rs1738074 159385965 T C 6 0.42 TAGAP 0.87 3.724E-07 0.238 25% (0–67%)
rs1250542 80704676 A G 10 0.37 ZMIZ1 1.15 3.97E-07 0.370 8% (0–73%)
rs7191700 11314304 T C 16 0.33 TNP2/PRM3/PRM2/PRM1/C16orf75 0.87 6.40E-07 0.705 0% (0–71%)
rs10866713e 158851472 A G 5 0.22 IL12B 1.17 6.57E-07 0.658 0% (0–71%)
rs9596270 49740441 C T 13 0.07 Intergenic 0.74 7.00E-07 0.347 11% (0–74%)
$

Weighted minor allele frequency across all datasets.

a

The reported SNP in the original publication is rs9657904. These two are in perfect LD (r2=1).

b

rs12722489 and rs7089861 are in week linkage disequilibrium (r2=0.128).

c

rs744166 was reported in the original publication. rs744166 and rs2293152 are in week LD (r2=0. 0.128). These represent one effect.

d

rs6074022 did not reached genome wide significance in the original publication (p=1.30E-07).

e

rs2546890 and rs10866713 are in week LD (r2= 0.01). These represent two independent effects.