Table 5. PSP GWAS cisSNP/transcript associations in the cerebellar and temporal cortex.
| ALL CER | PSP CER | AD CER | ALL TCX | PSP TCX | AD TCX | PSP GWASb | |||||||||||||
| CHR | SNP | PROBE | Symbol | BETA | P | BETA | P | BETA | P | BETA | P | BETA | P | BETA | P | Gene | OR | CI | P |
| 17 | rs8070723 | ILMN_1710903 | MAPT | −0.473 | 7.02E-69 | −0.428 | 1.38E-08 | −0.429 | 1.49E-31 | −0.498 | 8.61E-44 | −0.276 | 9.05E-02 | −0.495 | 3.12E-37 | MAPT | 5.11 | 4.43–5.91 | 1.5×10−118 |
| 12 | rs11568563 | ILMN_2381020 | SLCO1A2 | −0.397 | 2.33E-08 | −0.371 | 3.62E-03 | −0.438 | 1.98E-05 | −0.730 | 9.14E-18 | −0.644 | 3.89E-05 | −0.715 | 1.23E-08 | SLCO1A2 | 0.68 | 0.59–0.78 | 7.0×10−8 |
| 17 | rs242557 | ILMN_1710903 | MAPT | 0.183 | 8.80E-13 | 0.087 | 1.66E-02 | 0.179 | 2.39E-06 | 0.181 | 1.10E-08 | −0.033 | 6.65E-01 | 0.251 | 4.03E-10 | MAPT | 0.51 | 0.48–0.55 | 2.7×10−71 |
| 3 | rs1768208 | ILMN_2298464 | MOBP | 0.363 | 1.71E-07 | 0.342 | 1.24E-02 | 0.334 | 3.70E-04 | 0.325 | 1.57E-06 | 0.342 | 2.33E-02 | 0.305 | 1.23E-03 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
| 3 | rs1768208 | ILMN_2414962 | MOBP | 0.243 | 1.17E-04 | 0.220 | 8.02E-02 | 0.204 | 1.25E-02 | 0.180 | 1.76E-05 | 0.238 | 1.74E-02 | 0.137 | 8.18E-03 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
| 17 | rs8070723 | ILMN_2298727 | MAPT | −0.173 | 3.36E-07 | −0.063 | 5.91E-01 | −0.161 | 8.40E-04 | −0.137 | 9.03E-04 | −0.073 | 6.15E-01 | −0.211 | 8.67E-05 | MAPT | 5.11 | 4.43–5.91 | 1.5×10−118 |
| 3 | rs1768208 | ILMN_1768947 | MOBP | 0.143 | 7.57E-03 | 0.079 | 4.55E-01 | 0.159 | 1.72E-02 | 0.107 | 3.03E-03 | 0.199 | 1.83E-02 | 0.067 | 1.38E-01 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
| 1 | rs1411478 | ILMN_2157951 | STX6 | −0.005 | 6.41E-01 | −0.031 | 1.32E-01 | −0.002 | 8.97E-01 | 0.027 | 1.17E-02 | −0.003 | 8.90E-01 | 0.041 | 8.50E-03 | STX6 | 0.79 | 0.73–0.84 | 3.5×10-11 |
| 3 | rs1768208 | ILMN_1750271 | MOBP | 0.074 | 2.13E-02 | 0.064 | 2.84E-01 | 0.073 | 8.86E-02 | 0.046 | 1.55E-02 | 0.082 | 1.03E-01 | 0.045 | 4.29E-02 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
| 12 | rs11568563 | ILMN_1656097 | SLCO1A2 | −0.077 | 2.41E-01 | −0.027 | 8.14E-01 | −0.117 | 2.12E-01 | −0.117 | 4.36E-02 | −0.061 | 6.08E-01 | −0.064 | 4.22E-01 | SLCO1A2 | 0.68 | 0.59–0.78 | 7.0×10−8 |
| 17 | rs242557 | ILMN_2310814 | MAPT | 0.002 | 8.27E-01 | −0.032 | 9.13E-02 | 0.008 | 6.19E-01 | −0.026 | 1.09E-01 | −0.054 | 3.49E-01 | −0.022 | 9.33E-02 | MAPT | 0.51 | 0.48–0.55 | 2.7×10−71 |
| 17 | rs8070723 | ILMN_2200636 | KIAA1267 | 0.021 | 1.14E-01 | 0.046 | 2.87E-01 | 0.036 | 4.04E-02 | −0.016 | 1.70E-01 | −0.025 | 5.80E-01 | −0.026 | 1.02E-01 | MAPT | 5.11 | 4.43–5.91 | 1.5×10−118 |
| 17 | rs8070723 | ILMN_1665311 | STH | 0.044 | 1.79E-02 | 0.114 | 7.56E-02 | 0.026 | 3.05E-01 | 0.051 | 1.86E-01 | 0.188 | 2.59E-01 | −0.022 | 6.24E-01 | MAPT | 5.11 | 4.43–5.91 | 1.5×10−118 |
| 17 | rs242557 | ILMN_2298727 | MAPT | 0.071 | 9.78E-03 | 0.086 | 9.40E-02 | 0.075 | 8.56E-02 | 0.041 | 2.17E-01 | −0.054 | 4.26E-01 | 0.110 | 2.26E-02 | MAPT | 0.51 | 0.48–0.55 | 2.7×10−71 |
| 1 | rs1411478 | ILMN_2167416 | MR1 | 0.045 | 4.27E-02 | 0.092 | 4.48E-02 | 0.015 | 6.02E-01 | 0.029 | 2.24E-01 | −0.002 | 9.66E-01 | 0.077 | 1.20E-02 | STX6 | 0.79 | 0.73–0.84 | 3.5×10−11 |
| 17 | rs8070723 | ILMN_2310814 | MAPT | −0.007 | 5.77E-01 | −0.028 | 5.12E-01 | 0.007 | 6.94E-01 | 0.018 | 3.65E-01 | 0.039 | 7.52E-01 | 0.024 | 1.03E-01 | MAPT | 5.11 | 4.43–5.91 | 1.5×10−118 |
| 17 | rs242557 | ILMN_2200636 | KIAA1267 | −0.012 | 2.59E-01 | −0.022 | 2.56E-01 | −0.019 | 2.23E-01 | 0.008 | 3.83E-01 | 0.030 | 1.50E-01 | −0.003 | 8.08E-01 | MAPT | 0.51 | 0.48–0.55 | 2.7×10−71 |
| 17 | rs242557 | ILMN_1665311 | STH | −0.027 | 6.59E-02 | −0.020 | 4.88E-01 | −0.017 | 4.42E-01 | −0.024 | 4.28E-01 | −0.082 | 2.91E-01 | 0.027 | 4.89E-01 | MAPT | 0.51 | 0.48–0.55 | 2.7×10−71 |
| 1 | rs1411478 | ILMN_1721833 | IER5 | −0.041 | 2.12E-01 | −0.074 | 2.56E-01 | NA | NA | 0.016 | 4.76E-01 | 0.025 | 5.73E-01 | 0.000 | 9.95E-01 | STX6 | 0.79 | 0.73–0.84 | 3.5×10−11 |
| 10 | rs2142991 | ILMN_1772713 | BMS1 | 0.001 | 9.36E-01 | −0.007 | 8.18E-01 | 0.006 | 7.26E-01 | 0.003 | 8.02E-01 | 0.028 | 2.30E-01 | −0.014 | 4.56E-01 | BMS1 | 1.3 | 1.18–1.44 | 3.2×10−7 |
| 3 | rs1768208 | ILMN_1781231 | SLC25A38 | 0.004 | 7.76E-01 | −0.020 | 4.33E-01 | 0.025 | 1.47E-01 | 0.002 | 9.02E-01 | 0.001 | 9.78E-01 | 0.019 | 2.84E-01 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
| 2 | rs7571971 | ILMN_1714809 | RPIA | −0.035 | 7.03E-02 | −0.071 | 9.57E-02 | NA | NA | 0.002 | 9.21E-01 | 0.027 | 5.19E-01 | 0.008 | 7.68E-01 | EIF2AK3 | 0.75 | 0.70–0.82 | 4.2×10−13 |
| 3 | rs1768208 | ILMN_2411723 | RPSA | −0.025 | 6.92E-02 | −0.057 | 3.77E-02 | −0.034 | 8.72E-02 | 0.000 | 9.66E-01 | −0.008 | 7.29E-01 | −0.001 | 9.41E-01 | MOBP | 0.73 | 0.67–0.78 | 5.3×10−17 |
Seven SNPs near six PSP candidate risk genes from a recent PSP GWAS [27] were tested for transcript associations in cis in our cerebellar (CER) eGWAS and temporal cortex replications. The chromosome (CHR), SNP, Probe, Gene Symbol (SYMBOL) of these associations are depicted. The uncorrected (P) and Beta coefficient of association are shown for the combined (All), PSP, AD analyses in the cerebellar eGWAS and the temporal cortex replication study. Regression coefficients are based on the SNP minor allele using an additive model. NA: Not available. a. Though a SNP is present in the sequence of probe ILMN_2298727 (rs73314997), this is essentially monomorphic in the eGWAS subjects. b. The odds ratios (OR), confidence intervals and P values of disease risk association from the PSP GWAS are also shown using results from Supplementary Table 2 in Dataset S1 of this study [27].