Table 3 Differential snRNA-seq expression from level 3 female glia controls vs cases that are within 500 kb of LOAD-GWAS SNPs at loci found to be more accessible (rs7920721) or less accessible (rs3752246) in LOAD by ATAC-seq
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 | |