Transcription factors with Perturb-seq knockdown data for VPS9D1-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 = VPS9D1-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 VPS9D1-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 |
|---|---|---|---|---|
| chr16:89,489,154–89,489,850 | 222.5 kb | Distal (>10kb) Multiome | 596 | |
| chr16:89,490,254–89,491,281 | 221.1 kb | Distal (>10kb) Multiome | 817 | |
| chr16:89,507,395–89,509,159 | 203.6 kb | Distal (>10kb) Multiome | 987 | |
| chr16:89,560,298–89,561,204 | 151.2 kb | Distal (>10kb) Multiome | 1030 | |
| chr16:89,564,633–89,566,356 | 146.8 kb | Distal (>10kb) Multiome | 894 | |
| chr16:89,574,359–89,574,949 | 137.1 kb | Distal (>10kb) Multiome | 373 | |
| chr16:89,657,432–89,658,521 | 54.0 kb | Distal (>10kb) Multiome | 859 | |
| chr16:89,686,359–89,687,641 | 25.0 kb | Distal (>10kb) Multiome | 1006 | |
| chr16:89,699,933–89,702,566 | 11.6 kb | Distal (>10kb) Multiome | 1079 | |
| chr16:89,705,986–89,706,232 | 5.6 kb | Proximal (<10kb) | 414 | |
| chr16:89,711,278–89,712,334 | 98 bp | At TSS Multiome | 443 | |
| chr16:89,720,440–89,722,486 | 9.5 kb | Proximal (<10kb) Multiome | 1048 | |
| chr16:89,816,022–89,817,100 | 104.9 kb | Distal (>10kb) Multiome | 995 | |
| chr16:89,827,667–89,829,190 | 116.6 kb | Distal (>10kb) Multiome | 784 | |
| chr16:89,872,618–89,874,723 | 162.3 kb | Distal (>10kb) Multiome | 1046 | |
| chr16:89,917,809–89,919,023 | 206.8 kb | Distal (>10kb) Multiome | 986 | |
| chr16:89,921,530–89,925,204 | 211.3 kb | Distal (>10kb) Multiome | 1006 | |
| chr16:89,925,437–89,926,738 | 214.4 kb | Distal (>10kb) Multiome | 654 | |
| chr16:89,972,039–89,973,313 | 260.8 kb | Distal (>10kb) Multiome | 965 |
Genomic view of the VPS9D1-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.