|
SNP (coordinates, proximate gene)
|
Genes
|
NeuN- non-neuronal
|
HPCA-annotated astrocytes
|
HPCA-annotated microglia
|
|---|
|
Mean log (FC)
|
Adjusted p value
|
Mean log (FC)
|
Adjusted p value
|
Mean log (FC)
|
Adjusted p value
|
|---|
|
rs7920721 (chr10:11,678,309, ECHDC3)
|
CELF2
|
0.087
|
1
|
−0.090
|
1
|
0.47
|
4.90 × 10−16
|
|
USP6NL
|
0.12
|
0.32
|
−0.022
|
1
|
0.29
|
1
|
|
ECHDC3
|
0.067
|
1
|
0.016
|
1
|
0.31
|
1
|
|
UPF2
|
−0.34
|
0.00042
|
−0.31
|
1
|
−0.48
|
1
|
|
DHTKD1
|
−0.16
|
1
|
−0.23
|
1
|
0.011
|
1
|
|
SEC61A2
|
0.028
|
1
|
−0.028
|
1
|
0.15
|
1
|
|
NUDT5
|
−0.032
|
1
|
−0.097
|
1
|
0.21
|
1
|
|
rs3752246 (chr19:1,056,493, ABCA7)
|
BSG
|
0.035
|
1
|
0.10
|
0.32
|
−0.11
|
1
|
|
POLRMT
|
−0.047
|
1
|
−0.030
|
1
|
0.061
|
1
|
|
FSTL3
|
−0.12
|
0.065
|
−0.13
|
1
|
0.047
|
1
|
|
PALM
|
−0.071
|
1
|
0.010
|
1
|
−0.25
|
1
|
|
PTBP1
|
−0.034
|
1
|
−0.053
|
1
|
0.065
|
1
|
|
AZU1
|
−0.012
|
1
|
−0.015
|
1
|
−0.039
|
1
|
|
MED16
|
−0.036
|
1
|
−0.051
|
1
|
−0.19
|
1
|
|
ARID3A
|
0.089
|
0.97
|
0.047
|
1
|
0.12
|
1
|
|
TMEM259
|
0.050
|
1
|
0.089
|
1
|
−0.11
|
1
|
|
ABCA7
|
−0.013
|
1
|
−0.022
|
1
|
0.075
|
1
|
|
STK11
|
−0.024
|
1
|
−0.041
|
1
|
−0.13
|
1
|
|
CBARP
|
0.013
|
1
|
0.017
|
1
|
0.026
|
1
|
|
ATP5F1D
|
0.040
|
1
|
0.11
|
1
|
−0.032
|
1
|
|
MIDN
|
0.042
|
1
|
−0.073
|
1
|
0.14
|
1
|
|
CIRBP
|
−0.71
|
1.52 × 10−57
|
−0.80
|
1.27 × 10−42
|
−0.51
|
1
|
|
C19orf24
|
0.033
|
1
|
0.014
|
1
|
0.12
|
1
|
|
NDUFS7
|
0.083
|
0.016
|
0.11
|
0.0014
|
−0.014
|
1
|
|
GAMT
|
− 0.10
|
1
|
− 0.065
|
1
|
− 0.28
|
1
|
|
RPS15
|
−0.14
|
1
|
−0.19
|
0.66
|
0.088
|
1
|
|
APC2
|
−0.027
|
1
|
0.022
|
1
|
−0.14
|
1
|
|
PCSK4
|
−0.033
|
1
|
−0.025
|
1
|
−0.10
|
1
|
- Negative mean log (FC) values indicate down-regulation in LOAD and positive values indicate up-regulation in LOAD. Significant adjusted p values are bolded and mean log (FC) values consistent with ATAC-seq data are underlined. FC = fold change. Genes that were not detected or that had mean log (FC) values below 0.01 for any of the three groups were excluded from the table. Refer to detailed genomic structure presented in Supplemental Fig. 9
