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Table 2 Summary of PSP GWAS and PSP meta-analysis

From: Replication of progressive supranuclear palsy genome-wide association study identifies SLCO1A2 and DUSP10 as new susceptibility loci

       GWAS Hoglinger et al. (EUR only) New Mayo case-control population Meta-analysis
       GWAS Stage 1 GWAS Stage 2 Joint Analysis
SNP ID chr GRCh38 location Gene or nearby gene Major allele Minor allele MAF cases MAF control MAF cases MAF control OR PJ MAF cases MAF control OR (95% CI) P OR (95% CI) P OR Direction
rs8070723 17 46,003,698 MAPT A G 0.051 0.235 0.060 0.232 5.46 1.5E-116 0.049 0.233 5.74 (4.24–7.78) 1.9E-29 5.51 (4.83–6.28) 5.57E-144 ++
rs242557 17 45,942,346 MAPT G A 0.530 0.348 0.495 0.355 0.51 4.2E-70 0.585 0.403 0.52 (0.45–0.61) 1.2E-18 0.51 (0.48–0.55) 3.78E-85
rs1768208 3 39,481,512 MOBP G A 0.357 0.286 0.353 0.287 0.72 1.0E-16 0.389 0.264 0.56 (0.48–0.66) 6.6E-13 0.69 (0.64–0.74) 3.48E-26
rs12203592 6 396,321 IRF4 C T 0.164 0.200 0.131 0.198 1.49 6.2E-15 0.159 0.173 1.09 (0.89–1.33) 3.9E-01 1.40 (1.28–1.53) 2.31E-13 ++
rs7571971 2 88,595,833 EIF2AK3 C T 0.314 0.257 0.307 0.248 0.75 3.2E-13 0.320 0.291 0.88 (0.75–1.03) 1.0E-01 0.77 (0.72–0.83) 2.76E-13
rs1411478 1 180,993,146 STX6 G A 0.496 0.418 0.464 0.426 0.79 2.3E-10 0.473 0.410 0.77 (0.66–0.89) 4.4E-04 0.79 (0.74–0.84) 7.17E-13
rs11568563 12 21,304,500 SLCO1A2 A C 0.078 0.053 0.077 0.055 0.69 2.0E-07 0.089 0.053 0.60 (0.45–0.80) 4.2E-04 0.67 (0.59–0.76) 5.26E-10
rs6687758 1 221,991,606 DUSP10 A G 0.229 0.189 0.227 0.191 0.8 2.8E-07 0.230 0.192 0.80 (0.67–0.96) 1.7E-02 0.80 (0.74–0.86) 1.14E-08
rs197971 6 23,586,904 LOC105374976 G A 0.403 0.453 0.410 0.448 1.18 6.7E-06 0.395 0.422 1.13 (0.97–1.32) 1.1E-01 1.17 (1.10–1.25) 2.69E-06 ++
rs2107272 7 43,156,788 HECW1 C T 0.342 0.296 0.325 0.301 0.85 3.6E-05 0.332 0.295 0.83 (0.71–0.98) 2.5E-02 0.85 (0.79–0.91) 3.04E-06
rs6846520 4 83,097,119 PLAC8 G A 0.071 0.109 0.089 0.108 1.35 3.9E-06 0.085 0.094 1.14 (0.88–1.47) 3.3E-01 1.30 (1.16–1.46) 4.87E-06 ++
rs12744678 1 204,967,707 NFASC C T 0.331 0.280 0.302 0.287 0.86 2.1E-04 0.319 0.273 0.80 (0.68–0.94) 5.6E-03 0.85 (0.79–0.91) 6.22E-06
rs4733780 8 130,284,009 ASAP1 T C 0.454 0.423 0.446 0.414 0.86 3.2E-05 0.457 0.429 0.89 (0.77–1.03) 1.1E-01 0.86 (0.81–0.92) 9.94E-06
rs6852535 4 122,557,561 IL2/IL21 G A 0.289 0.338 0.277 0.322 1.24 9.2E-08 0.296 0.283 0.93 (0.79–1.09) 3.8E-01 1.17 (1.09–1.26) 1.11E-05 +−
rs10509119 10 60,052,882 ANK3 T C 0.131 0.110 0.133 0.112 0.80 4.1E-05 0.130 0.113 0.83 (0.67–1.04) 1.1E-01 0.81 (0.73–0.89) 1.29E-05
rs11902595 2 48,456,607 PPP1R21 T G 0.146 0.180 0.159 0.180 1.22 8.3E-05 0.161 0.184 1.21 (0.99–1.47) 6.1E-02 1.21 (1.11–1.33) 1.41E-05 ++
rs2142991 10 42,845,657 BMS1/
LOC101929445
T C 0.139 0.173 0.139 0.169 1.30 4.9E-07 0.156 0.150 0.95 (0.77–1.16) 6.0E-01 1.22 (1.11–1.34) 2.13E-05 +−
rs406113 6 28,515,705 GPX6 T G 0.340 0.297 0.343 0.311 0.86 6.9E-05 0.339 0.314 0.90 (0.78–1.06) 2.0E-01 0.87 (0.81–0.93) 3.31E-05
rs4814911 20 19,863,250 RIN2 G A 0.225 0.190 0.212 0.193 0.84 7.7E-05 0.214 0.195 0.89 (0.75–1.07) 2.3E-01 0.85 (0.78–0.92) 4.40E-05
rs17199690 16 25,420,834 LOC105371146 G A 0.172 0.137 0.160 0.136 0.80 1.3E-05 0.144 0.139 0.97 (0.79–1.21) 8.2E-01 0.83 (0.76–0.91) 4.41E-05
rs895606 9 85,388,753 NTRK2/
AGTPBP1
C T 0.496 0.444 0.472 0.449 0.86 3.1E-05 0.475 0.465 0.96 (0.83–1.12) 6.2E-01 0.88 (0.82–0.94) 5.74E-05
rs11532787 7 119,661,732 ANKRD7/KCND2 G A 0.138 0.112 0.121 0.109 0.81 1.9E-04 0.116 0.102 0.86 (0.68–1.08) 1.9E-01 0.82 (0.74–0.91) 9.73E-05
rs3017756 11 95,804,194 CEP57 C T 0.482 0.426 0.438 0.429 0.86 6.6E-05 0.428 0.418 0.95 (0.82–1.10) 5.0E-01 0.88 (0.82–0.94) 9.96E-05
rs11028138 11 24,751,636 LUZP2 T C 0.102 0.081 0.085 0.068 0.75 6.8E-06 0.085 0.089 1.08 (0.83–1.41) 5.7E-01 0.80 (0.71–0.90) 1.42E-04 −+
rs13025979 2 186,000,879 LOC107985783 C T 0.099 0.074 0.098 0.077 0.75 3.9E-06 0.080 0.088 1.15 (0.87–1.51) 3.3E-01 0.80 (0.72–0.90) 1.60E-04 −+
rs10083119 12 125,824,612 TMEM132B/
LOC101927464
G A 0.126 0.096 0.119 0.103 0.80 8.0E-05 0.112 0.106 0.95 (0.75–1.20) 6.6E-01 0.83 (0.75–0.91) 2.07E-04
rs4890490 18 44,857,303 SETBP1 C T 0.436 0.385 0.413 0.402 0.88 9.0E-04 0.434 0.410 0.89 (0.77–1.03) 1.2E-01 0.89 (0.83–0.95) 2.76E-04
rs1433277 10 125,584,032 TEX36 G T 0.431 0.472 0.433 0.466 1.17 2.1E-05 0.460 0.450 0.96 (0.83–1.12) 6.1E-01 1.13 (1.06–1.20) 3.24E-04 +−
rs4256646 9 73,182,919 ANXA1/
LOC101927281
T C 0.458 0.509 0.466 0.490 1.16 9.6E-05 0.484 0.491 1.02 (0.88–1.18) 8.1E-01 1.13 (1.06–1.20) 3.33E-04 ++
rs2075650 19 44,892,362 TOMM40 T C 0.112 0.141 0.117 0.140 1.26 2.8E-05 0.144 0.138 0.96 (0.77–1.19) 6.9E-01 1.19 (1.08–1.32) 3.99E-04 +−
rs9783599 14 77,970,692 ADCK1
NRXN3
C A 0.494 0.443 0.471 0.446 0.87 9.6E-05 0.469 0.475 1.05 (0.90–1.21) 5.4E-01 0.90 (0.84–0.96) 9.93E-04 −+
rs4742987 9 106,119,937 TMEM38B/
LOC100996590
T C 0.393 0.359 0.389 0.364 0.86 6.8E-05 0.368 0.380 1.05 (0.90–1.22) 5.1E-01 0.89 (0.84–0.96) 1.08E-03 −+
rs1001408 12 66,898,508 GRIP1 A G 0.119 0.086 0.103 0.095 0.81 5.1E-04 0.101 0.097 0.96 (0.76–1.23) 7.7E-01 0.84 (0.75–0.93) 1.15E-03
rs10197080 2 223,231,568 KCNE4/RN7SL807P G T 0.113 0.082 0.095 0.087 0.79 1.3E-04 0.100 0.104 1.08 (0.85–1.38) 5.2E-01 0.84 (0.75–0.94) 1.71E-03 −+
rs4768559 12 44,576,131 NELL2 T G 0.262 0.209 0.224 0.214 0.85 2.1E-04 0.199 0.209 1.06 (0.89–1.28) 5.1E-01 0.89 (0.82–0.96) 1.77E-03 −+
rs217727 11 1,995,678 MRPL23/IGF2 G A 0.218 0.178 0.189 0.177 0.85 3.5E-04 0.179 0.184 1.03 (0.85–1.24) 7.9E-01 0.88 (0.81–0.95) 2.02E-03 −+
rs7104402 11 43,019,438 LOC100507205/HNRNPKP3 C T 0.323 0.281 0.302 0.290 0.87 6.2E-04 0.301 0.319 1.08 (0.92–1.27) 3.4E-01 0.91 (0.85–0.98) 8.58E-03 −+