Table 2.
Fine-mapping results based on TWAS-identified genes for AD risk
| Region | Tx Start | Tx End | Tissue | OR (95% CI) | TWAS P value | Focusa | |
|---|---|---|---|---|---|---|---|
| 1q23.3 | NDUFS2 | 161166894 | 161184185 | Brain caudate basal ganglia | 0.96 (0.95–0.97) | 1.83 × 10−9 | 0.96 |
| Brain anterior cingulate cortex BA24 | 0.95 (0.93–0.96) | 6.79 × 10−10 | 1 | ||||
| Brain hippocampus | 0.94 (0.92–0.96) | 3.29 × 10−10 | 1 | ||||
| FCER1G | 161185024 | 161190489 | Brain hypothalamus | 0.92 (0.89–0.94) | 1.44 × 10−9 | 0.97 | |
| 1q32.2 | CR1 | 207669492 | 207813992 | Brain hypothalamus | 1.20 (1.15–1.25) | 1.00 × 10−16 | 1 |
| Brain nucleus accumbens basal ganglia | 1.17 (1.13–1.21) | 1.44 × 10−17 | 1 | ||||
| Brain anterior cingulate cortex BA24 | 1.13 (1.10–1.16) | 2.47 × 10−17 | 1 | ||||
| Brain caudate basal ganglia | 1.13 (1.10–1.16) | 1.22 × 10−17 | 1 | ||||
| Brain hippocampus | 1.12 (1.09–1.15) | 6.76 × 10−17 | 1 | ||||
| Brain amygdala | 1.12 (1.09–1.15) | 2.60 × 10−17 | 1 | ||||
| Brain substantia nigra | 1.12 (1.09–1.15) | 2.28 × 10−17 | 1 | ||||
| Brain cortex | 1.11 (1.09–1.14) | 7.96 × 10−18 | 1 | ||||
| Brain putamen basal ganglia | 1.11 (1.09–1.14) | 1.41 × 10−17 | 1 | ||||
| 6p21.32 | BTNL2 | 32361740 | 32374905 | Brain caudate basal ganglia | 1.07 (1.05–1.10) | 5.09 × 10−12 | 1 |
| Brain cortex | 1.05 (1.03–1.07) | 1.10 × 10−6 | 0.91 | ||||
| 7q22.1 | AC004522.3 | 99527015 | 99546243 | Brain amygdala | 0.96 (0.94–0.97) | 2.63 × 10−8 | 0.93 |
| GPC2 | 99767229 | 99774995 | Brain putamen basal ganglia | 1.04 (1.02–1.05) | 1.71 × 10−6 | 0.96 | |
| PVRIG | 99815864 | 99819113 | Brain hippocampus | 0.98 (0.97–0.99) | 9.74 × 10−9 | 0.93 | |
| NYAP1 | 100081550 | 100092422 | Brain hypothalamus | 0.86 (0.82–0.91) | 2.72 × 10−9 | 1 | |
| 8p21.1 | CLU | 27454434 | 27472548 | Brain putamen basal ganglia | 0.92 (0.90–0.94) | 3.77 × 10−13 | 1 |
| 16p11.2 | KAT8 | 31127075 | 31142714 | Pituitary | 0.98 (0.97–0.99) | 1.28 × 10−9 | 0.98 |
| Brain hippocampus | 0.98 (0.97–0.98) | 4.90 × 10−10 | 0.96 | ||||
| Brain caudate basal ganglia | 0.98 (0.97–0.98) | 1.43 × 10−9 | 0.93 | ||||
| Brain amygdala | 0.98 (0.97–0.98) | 1.16 × 10−9 | 0.93 | ||||
| Brain substantia nigra | 0.97 (0.97–0.98) | 1.64 × 10−9 | 1 | ||||
| Brain anterior cingulate cortex BA24 | 0.97 (0.96–0.98) | 3.59 × 10−10 | 0.98 | ||||
| 17p13.2 | AC012146.1 | 5014763 | 5017674 | Brain caudate basal ganglia | 0.97 (0.97–0.98) | 5.29 × 10−8 | 0.96 |
| Brain hippocampus | 0.97 (0.97–0.98) | 1.98 × 10−7 | 0.96 | ||||
| Brain amygdala | 0.97 (0.96–0.98) | 4.12 × 10−8 | 0.97 | ||||
| 17q23.3 | ACE | 61554422 | 61599205 | Brain anterior cingulate cortex BA24 | 0.97 (0.96–0.98) | 5.18 × 10−8 | 0.99 |
| 19q13.31-13.32 | AC243964.3 | 45135500 | 45222031 | Brain amygdala | 1.04 (1.03–1.05) | 1.78 × 10−25 | 1 |
| Brain anterior cingulate cortex BA24 | 1.03 (1.03–1.04) | 6.17 × 10−25 | 1 | ||||
| Brain putamen basal ganglia | 1.03 (1.02–1.03) | 8.54 × 10−25 | 1 | ||||
| Pituitary | 1.03 (1.02–1.03) | 1.17 × 10−24 | 1 | ||||
| 19q13.31 | CEACAM19 | 45165545 | 45187631 | Brain amygdala | 1.05 (1.04–1.06) | 5.36 × 10−20 | 1 |
| Brain anterior cingulate cortex BA24 | 1.04 (1.03–1.05) | 1.66 × 10−15 | 0.99 | ||||
| 19q13.32 | NECTIN2 | 45349432 | 45392485 | Brain substantia nigra | 0.92 (0.90–0.93) | 2.67 × 10−27 | 1 |
| Pituitary | 0.98 (0.96–0.99) | 4.62 × 10−3 | 1 | ||||
| TOMM40 | 45393826 | 45406946 | Pituitary | 9.05 (8.19–9.99) | 0 | 1 | |
| APOE | 45409011 | 45412650 | Brain substantia nigra | 1.42 (1.38–1.46) | 7.92 × 10−135 | 1 | |
| Pituitary | 0.86 (0.84–0.89) | 4.89 × 10−24 | 1 | ||||
| APOC4 | 45445495 | 45452820 | Brain putamen basal ganglia | 0.98 (0.98–0.99) | 2.65 × 10−12 | 1 | |
| APOC2 | 45449243 | 45452822 | Brain anterior cingulate cortex BA24 | 1.08 (1.06–1.11) | 7.84 × 10−12 | 1 | |
| Brain putamen basal ganglia | 1.03 (1.02–1.04) | 2.77 × 10−8 | 1 | ||||
| Pituitary | 0.95 (0.93–0.97) | 1.33 × 10−5 | 1 | ||||
| ZNF296 | 45574758 | 45579846 | Brain amygdala | 0.89 (0.86–0.92) | 2.90 × 10−12 | 1 | |
| KLC3 | 45836692 | 45854778 | Brain amygdala | 0.94 (0.92–0.97) | 1.49 × 10−6 | 0.94 |
aThe posterior probabilities of FOCUS