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. 2014 Jul 15;23(24):6644–6658. doi: 10.1093/hmg/ddu372

Table 2.

Summary of GWAS, replication and overall meta-analysis for SNPs with P < 5 × 10−6 and the same effect direction in all three GWAS samples

GWAS
 Replication
 Combined analysis
Trait rsa chrb bpc EAd/OAe βf SEg dirh P-adji rsa EAd/OAe MAFj βk SEg Pl EAd/OAe dirm βn SEo Pp
Aβ1–42 2-45978647 2 45 978 642 G/GT −0.382 0.08 −−− 2.1 × 10−6 rs6753292q T/C 0.251 0.01 0.08 0.91 G/GT +− −0.18 0.05 1.1 × 10−3
rs374159788 2 172 759 319 A/AGT 0.608 0.12 +++ 1.6 × 10−6 rs34737109q A/G 0.383 −0.08 0.07 0.23 A/AGT +− 0.07 0.06 0.21
rs62256378 3 67 457 033 A/G 0.89 0.17 +++ 3.0 × 10−7 rs62256378 A/G 0.061 0.61 0.13 1.9 × 10−6 A/G −−− 0.71 0.10 2.5 × 10−12
rs893703 3 139 250 649 G/A 0.639 0.13 +++ 1.2 × 10−6 rs4407373q T/G 0.099 −0.05 0.11 0.68 G/A +− 0.25 0.08 3.2 × 10−3
rs12493397 3 165 284 889 A/G −0.422 0.09 −−− 3.9 × 10−6 rs2222464q C/T 0.274 −0.02 0.07 0.76 A/G −−− −0.18 0.06 1.2 × 10−3
rs388575 4 107 973 286 C/T −0.518 0.09 −−− 1.5 × 10−8 rs388575 C/T 0.252 0.05 0.07 0.50 C/T −+ −0.18 0.06 1.4 × 10−3
6-63065777 6 63 065 777 A/AAAT 1.241 0.20 +++ 2.9 × 10−9 rs12527308q T/C 0.15 0.09 0.09 0.31 A/AAAT ++ 0.28 0.08 7.0 × 10−4
rs2258946 10 93 624 672 A/G 0.521 0.10 +++ 6.6 × 10−7 rs2258946 T/C 0.145 −0.10 0.09 0.29 A/G +− 0.17 0.07 1.1 × 10−2
rs61023801 13 91 828 308 G/A 1.084 0.21 +++ 4.7 × 10−7 rs74922937q A/G 0.026 0.02 0.20 0.92 G/A ++ 0.52 0.14 3.0 × 10−4
APOE-ε4 (rs429358) 19 45 411 941 ε4/ε4(−) −0.48 0.07 −−− 1.8 × 10−10 APOE-ε4 (rs429358) ε4/ε4(−) 0.442 −0.70 0.15 1.1 × 10−5 ε4/ε4(-) −− −0.40 0.05 4.3 × 10−17
pTau181 rs72804029 2 59 273 581 T/C −0.804 0.17 −−− 2.7 × 10−6 rs72804029 T/C 0.089 0.04 0.13 0.73 T/C −+ −0.26 0.10 1.0 × 10−2
rs313541 4 25 263 478 G/A 0.501 0.11 +++ 2.8 × 10−6 rs313561q G/A 0.192 −0.06 0.09 0.50 G/A +− 0.16 0.07 1.3 × 10−2
rs73276571 5 120 616 307 A/G 0.66 0.14 +++ 1.8 × 10−6 rs73276571 A/G 0.082 −0.20 0.13 0.13 A/G +− 0.22 0.10 2.4 × 10−2
rs4896367 6 138 807 281 C/T 0.493 0.10 +++ 1.4 × 10−6 rs4896367 C/T 0.268 −0.04 0.08 0.62 C/T +− 0.16 0.06 1.1 × 10−2
rs9397718 6 154 753 469 C/T 0.397 0.08 +++ 3.4 × 10−6 rs6911312q C/A 0.356 −0.01 0.07 0.90 C/T +− 0.18 0.06 1.4 × 10−3
rs9397794 6 155 575 942 A/G 0.449 0.09 +++ 2.6 × 10−6 rs9397794 A/G 0.245 −0.01 0.08 0.88 A/G +− 0.18 0.06 3.0 × 10−3
rs77131199 10 26 798 222 A/G 1.484 0.32 +++ 3.6 × 10−6 rs77131199 A/G 0.037 0.01 0.18 0.95 A/G ++ 0.37 0.16 1.7 × 10−2
rs12418935 11 11 863 410 A/G 0.615 0.12 +++ 1.1 × 10−6 rs12418935 A/G 0.107 −0.05 0.12 0.65 A/G +− 0.26 0.09 2.1 × 10−3
rs7304039 12 108 736 352 A/G 0.414 0.08 +++ 7.9 × 10−7 rs7304039 A/G 0.295 −0.07 0.08 0.34 A/G +− 0.15 0.06 6.9 × 10−3
rs4942417 13 32 887 389 C/A 0.441 0.09 +++ 2.1 × 10−6 rs4942417 C/A 0.154 −0.08 0.10 0.42 C/A +− −0.19 0.07 3.6 × 10−3
18-13887179 18 13 887 179 GAA/G −0.775 0.14 −−− 5.0 × 10−8 rs7230126q C/T 0.317 0.03 0.07 0.67 GAA/G −+ −0.14 0.06 3.1 × 10−2
rs3794851 18 74 709 351 C/G 1.050 0.22 +++ 3.4 × 10−6 rs3794851 C/G 0.046 −0.01 0.16 0.93 C/G +− 0.36 0.13 6.7 × 10−3
rs149933701 19 6 636 839 C/T 10.678 0.22 +++ 1.6 × 10−6 rs61111347q A/G 0.039 −0.08 0.17 0.63 C/T +− 0.36 0.14 8.0 × 10−3
rs11700591 21 41 507 695 C/T 0.723 0.13 +++ 9.9 × 10−8 rs11700591 C/T 0.069 −0.02 0.13 0.89 C/T +− −0.35 0.09 2.3 × 10−4
X-118495317 X 118 495 317 C/CT 0.619 0.12 +++ 3.0 × 10−7 rs217969q T/A 0.256 0.04 0.07 0.50 C/CT ++ 0.18 0.06 2.0 × 10−3

r2-values for proxy SNPs were computed on the basis of 1000 Genomes reference data, May 2012 release, CEU sample. GWAS, genome-wide association study.

ars number.

bChromosome.

cPhysical position in base pairs, according to dbSNP build 37.

dEffect allele: allele for which the effect estimate is reported.

eOther allele.

fEffect estimate (fixed effects meta-analysis) for Step 1 meta-analysis.

gCorresponding standard error.

hEffect directions in the three initial studies.

iLambda-adjusted P-value (fixed effects meta-analysis), GWAS meta-analysis.

jMinor allele frequency.

kEffect estimate from regression analysis. Represents changes in Aβ1–42 or pTau181 levels in standard deviations per minor allele.

lP-value of regression analysis.

mEffect directions for Step 1 (joint direction) and replication analysis.

nEffect estimate (fixed effects meta-analysis) GWAS meta-analysis plus replication.

oCorresponding standard error.

pP-value (fixed effects meta-analysis) GWAS meta-analysis plus replication.

qProxy SNP supporting the signal of the GWAS.