Transcription factors with Perturb-seq knockdown data for THUMPD3-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 = THUMPD3-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 THUMPD3-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 |
|---|---|---|---|---|
| chr3:9,101,985–9,102,991 | 294.1 kb | Distal (>10kb) Multiome | 210 | |
| chr3:9,135,686–9,136,655 | 260.4 kb | Distal (>10kb) Multiome | 201 | |
| chr3:9,158,726–9,159,822 | 237.3 kb | Distal (>10kb) Multiome | 115 | |
| chr3:9,204,163–9,205,101 | 192.1 kb | Distal (>10kb) Multiome | 389 | |
| chr3:9,249,284–9,250,085 | 147.0 kb | Distal (>10kb) Multiome | 452 | |
| chr3:9,302,190–9,302,888 | 94.0 kb | Distal (>10kb) Multiome | 416 | |
| chr3:9,362,788–9,363,525 | 33.5 kb | Distal (>10kb) Multiome | 988 | |
| chr3:9,395,817–9,398,659 | at TSS | At TSS | 1141 | |
| chr3:9,399,820–9,400,096 | 3.1 kb | Proximal (<10kb) | 394 | |
| chr3:9,402,915–9,403,144 | 6.2 kb | Proximal (<10kb) | 432 | |
| chr3:9,499,948–9,500,976 | 104.0 kb | Distal (>10kb) Multiome | 320 | |
| chr3:9,552,048–9,552,879 | 155.8 kb | Distal (>10kb) Multiome | 372 | |
| chr3:9,553,391–9,554,161 | 157.2 kb | Distal (>10kb) Multiome | 128 | |
| chr3:9,649,068–9,649,746 | 252.7 kb | Distal (>10kb) Multiome | 793 |
Genomic view of the THUMPD3-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.