Transcription factors with Perturb-seq knockdown data for HMGA2-AS1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = HMGA2-AS1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HMGA2-AS1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr12:65,566,010–65,566,599 | 315.7 kb | Distal (>10kb) Multiome HiCAR | 314 | |
| chr12:65,638,328–65,638,825 | 243.5 kb | Distal (>10kb) Multiome | 85 | |
| chr12:65,740,801–65,742,990 | 139.5 kb | Distal (>10kb) Multiome | 695 | |
| chr12:65,754,735–65,755,896 | 126.8 kb | Distal (>10kb) Multiome | 173 | |
| chr12:65,817,596–65,818,266 | 64.0 kb | Distal (>10kb) Multiome | 138 | |
| chr12:65,823,815–65,826,447 | 57.6 kb | Distal (>10kb) Multiome | 894 | |
| chr12:65,845,814–65,846,311 | 36.0 kb | Distal (>10kb) Multiome | 145 | |
| chr12:65,876,859–65,877,428 | 4.6 kb | Proximal (<10kb) | 171 | |
| chr12:65,878,668–65,878,811 | 3.2 kb | Proximal (<10kb) | 106 | |
| chr12:65,881,668–65,882,208 | at TSS | At TSS | 153 | |
| chr12:65,883,008–65,883,609 | 967 bp | At TSS | 61 | |
| chr12:65,897,482–65,897,992 | 15.7 kb | Distal (>10kb) Multiome | 129 | |
| chr12:65,925,832–65,927,041 | 44.3 kb | Distal (>10kb) Multiome | 384 | |
| chr12:66,061,688–66,062,514 | 180.1 kb | Distal (>10kb) Multiome | 137 | |
| chr12:66,169,293–66,170,152 | 287.7 kb | Distal (>10kb) Multiome | 1068 |
Genomic view of the HMGA2-AS1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.