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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

From: Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains

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
  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