Transcription factors with Perturb-seq knockdown data for NEPRO-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 = NEPRO-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 NEPRO-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 |
|---|---|---|---|---|
| chr3:112,560,905–112,563,207 | 457.5 kb | Distal (>10kb) Multiome HiCAR | 967 | |
| chr3:112,785,378–112,786,966 | 233.3 kb | Distal (>10kb) Multiome | 290 | |
| chr3:112,990,506–112,991,646 | 28.5 kb | Distal (>10kb) Multiome | 925 | |
| chr3:113,018,819–113,020,010 | 52 bp | At TSS Multiome | 965 | |
| chr3:113,210,367–113,212,837 | 192.4 kb | Distal (>10kb) Multiome | 482 | |
| chr3:113,240,837–113,244,224 | 222.2 kb | Distal (>10kb) Multiome | 545 |
Genomic view of the NEPRO-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.