Table 1.
Associations between CpGs or index SNPs and NP burden and AD diagnosis
| SNP | Position | Gene | SNP to NP association | SNP to AD association |
|---|---|---|---|---|
| P-value | P-value | |||
| rs6656401 | 1:207692049 | CR1 | 0.0169 | 1.1E-04 |
| rs744373 | 2:127894615 | BIN1 | 0.1790 | 0.2243 |
| rs9349407 | 6:47453378 | CD2AP | 0.4393 | 0.6703 |
| rs11767557 | 7:143109139 | EPHA1 | 0.4565 | 0.6931 |
| rs11136000 | 8:27464519 | CLU | 0.4878 | 0.4364 |
| rs610932 | 11:59939307 | MS4A6A | 0.7040 | 0.8746 |
| rs4938933 | 11:60034429 | MS4A4A | 0.9301 | 0.9305 |
| rs7110631 | 11:85856187 | PICALM | 0.3863 | 0.5214 |
| rs3752246 | 19:1056492 | ABCA7 | 0.2102 | 0.6958 |
| anye4 | APOE | 3.8E-23 | 1.6E-13 | |
| rs3865444 | 19:51727962 | CD33 | 0.1233 | 0.0951 |
| BIN1 (53 tested) | Position | Chromatin state | CpG to NP association | CpG to AD association | ||
|---|---|---|---|---|---|---|
| P-value | Direction* | P-value | Direction* | |||
| cg22883290 | 127800646 | Weak transcribed/low signal proximal to active regions | 3.7E-08 | + | 1.5E-05 | + |
| cg19153828 | 127782651 | Strong promoter | 0.0002 | + | 0.0012 | + |
| cg04019522 | 127852450 | Active enhancer | 0.0002 | + | 1.1E-04 | + |
| cg09006514 | 127800616 | Weak transcribed/low signal proximal to active regions | 0.0013 | + | 0.0060 | + |
| cg18981277 | 127805910 | Strong transcription | 0.0022 | − | 0.0232 | − |
| Position | Chromatin state | CpG to NP | CpG to AD | |||
|---|---|---|---|---|---|---|
| CD2AP (20 tested) | ||||||
| cg20172563 | 47487173 | Low signal | 7.5E-06 | + | 0.0043 | + |
| CLU (40 tested) | ||||||
| cg16292768 | 27467783 | Active TSS flanking | 3.7E-05 | − | 0.0003 | − |
| cg08594681 | 27468684 | Active TSS flanking | 8.4E-04 | − | 0.0847 | − |
| cg11783834 | 27469331 | Active TSS flanking | 0.0029 | − | 0.0976 | − |
| cg13488078 | 27469338 | Active TSS flanking | 0.0029 | − | 0.0034 | − |
| cg20918219 | 27493854 | Weak enhancer | 0.0035 | + | 0.0025 | + |
| MS4A6A (12 tested) | ||||||
| cg03055440 | 59950405 | Low signal | 0.0015 | − | 0.0012 | − |
| cg07170641 | 59950068 | Low signal | 0.0016 | − | 0.0161 | − |
| cg18159934 | 59942032 | Low signal | 0.0030 | + | 0.0583 | + |
| ABCA7 (91 tested) | ||||||
| cg02308560 | 1071176 | PC repressed | 3.1E-08 | + | 5.0E-06 | + |
| cg04587220 | 1071208 | PC repressed | 5.0E-06 | + | 2.3E-04 | + |
| APOE (41 tested) | ||||||
| cg18799241 | 45412599 | Weak transcribed/low signal proximal to active regions | 6.2E-04 | + | 0.0241 | + |
Only those features meeting a Benjamini-Hochberg threshold of significance are presented. All models are adjusted for age at death, sex, study,batch effect, and bisulfide conversion QC probes. CR1 (31 CpGs), EPHA1 (60 CpGs), MS4A4A (11 CpGs), PICALM (25 CpGs) and CD33 (12 CpGs) showed no CpGs that met multiple comparisons cutoff.
*
“+” means more methylation is associated with more pathology or increased odds of AD, “−” means more methylation is assoicated with less pathology or decreased odds of AD.