Table 3.
Differentially accessible peaks in Astrocyte cluster 1 in Alzheimer disease GWAS candidate genes.
| Gene | Chr. | Peak location | Cell cluster | Distance to TSS | SnATAC FC | SnATAC FDR | SnRNA FC | SnRNA FDR | Region |
|---|---|---|---|---|---|---|---|---|---|
| PTK2B | chr8 | 27340471 | Astrocyte 1 | 29239 | 2.327 | 0.026 | −1.05 | 4.67E-13 | intron |
| CLU | chr8 | 27596089 | Astrocyte 1 | 18692 | 4.235 | 0.019 | −1.15 | 3.39E-73 | intergenic |
| CLU | chr8 | 27597084 | Astrocyte 1 | 17697 | 2.556 | 0.035 | −1.15 | 3.39E-73 | exon |
| CLU | chr8 | 27597084 | Astrocyte 1 | 17697 | 2.556 | 0.035 | −1.15 | 3.39E-73 | intron |
| CLU | chr8 | 27597917 | Astrocyte 1 | 16864 | 18.113 | 0.008 | −1.15 | 3.39E-73 | exon |
| CLU | chr8 | 27597917 | Astrocyte 1 | 16864 | 18.113 | 0.008 | −1.15 | 3.39E-73 | intron |
| CLU | chr8 | 27607577 | Astrocyte 1 | 7204 | 6.695 | 0.032 | −1.15 | 3.39E-73 | intron |
| ACER3 | chr11 | 76799174 | Astrocyte 1 | −61449 | 2.41 | 0.008 | 1.04 | 1.12E-30 | intergenic |
| SORL1 | chr11 | 121566449 | Astrocyte 1 | 114496 | 3.538 | 0.044 | −1.05 | 4.51E-53 | exon |
| SORL1 | chr11 | 121566449 | Astrocyte 1 | 114496 | 3.538 | 0.044 | −1.05 | 4.51E-53 | intron |
| SORL1 | chr11 | 121566449 | Astrocyte 1 | −26 | 3.538 | 0.044 | −1.05 | 4.51E-53 | promoter-TSS |
| SORL1 | chr11 | 121591362 | Astrocyte 1 | 139409 | 7.332 | 0.011 | −1.05 | 4.51E-53 | intron |
| SORL1 | chr11 | 121591362 | Astrocyte 1 | 1193 | 7.332 | 0.011 | −1.05 | 4.51E-53 | promoter-TSS |
| SORL1 | chr11 | 121596337 | Astrocyte 1 | 6168 | 6.485 | 0.046 | −1.05 | 4.51E-53 | intron |
| SORL1 | chr11 | 121596337 | Astrocyte 1 | 144384 | 6.485 | 0.046 | −1.05 | 4.51E-53 | intron |
| SORL1 | chr11 | 121695992 | Astrocyte 1 | 105823 | 3.063 | 0.039 | −1.05 | 4.51E-53 | intergenic |
| SORL1 | chr11 | 121695992 | Astrocyte 1 | 244039 | 3.063 | 0.039 | −1.05 | 4.51E-53 | intergenic |
| SORL1 | chr11 | 121795198 | Astrocyte 1 | 205029 | 3.099 | 0.027 | −1.05 | 4.51E-53 | intergenic |
| SORL1 | chr11 | 121795198 | Astrocyte 1 | 343245 | 3.099 | 0.027 | −1.05 | 4.51E-53 | intergenic |
| SORL1 | chr11 | 121929505 | Astrocyte 1 | 477552 | 3.494 | 0.004 | −1.05 | 4.51E-53 | intergenic |
| SORL1 | chr11 | 121932043 | Astrocyte 1 | 480090 | 11.926 | 0.031 | −1.05 | 4.51E-53 | intergenic |
| SPHK1 | chr17 | 76397939 | Astrocyte 1 | 13539 | 4.176 | 0.041 | −1.01 | 9.98E-43 | intergenic |
| SPHK1 | chr17 | 76397939 | Astrocyte 1 | 12897 | 4.176 | 0.041 | −1.01 | 9.98E-43 | intron |
| SPHK1 | chr17 | 76414406 | Astrocyte 1 | 30006 | 15.903 | 0 | −1.01 | 9.98E-43 | intergenic |
| ABCA7 | chr19 | 1039766 | Astrocyte 1 | −87 | 2.429 | 0.001 | 1.09 | 2.95E-21 | promoter-TSS |
| ABCA7 | chr19 | 1040877 | Astrocyte 1 | −119 | 4.091 | 0.002 | 1.09 | 2.95E-21 | promoter-TSS |
| ABCA7 | chr19 | 1040877 | Astrocyte 1 | 1024 | 4.091 | 0.002 | 1.09 | 2.95E-21 | promoter-TSS |
| VRK3 | chr19 | 50024717 | Astrocyte 1 | 360 | 5.864 | 0.043 | 1.09 | 4.88E-24 | promoter-TSS |
| VRK3 | chr19 | 50024717 | Astrocyte 1 | 979 | 5.864 | 0.043 | 1.09 | 4.88E-24 | promoter-TSS |
| VRK3 | chr19 | 50025268 | Astrocyte 1 | −116 | 3.408 | 0.002 | 1.09 | 4.88E-24 | promoter-TSS |
| VRK3 | chr19 | 50025268 | Astrocyte 1 | 428 | 3.408 | 0.002 | 1.09 | 4.88E-24 | promoter-TSS |
| VRK3 | chr19 | 50050285 | Astrocyte 1 | −24589 | 5.267 | 0.002 | 1.09 | 4.88E-24 | intergenic |
FC: Chr.: Chromosome; FC:Fold change; TSS: Transcription Starting Site; Negative value in Distance to TSS reflects peaks falling upstream of TSS