Transcription factors with Perturb-seq knockdown data for NNT-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 = NNT-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 NNT-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 |
|---|---|---|---|---|
| chr5:43,312,549–43,314,340 | 289.5 kb | Distal (>10kb) Multiome | 954 | |
| chr5:43,348,196–43,348,656 | 254.7 kb | Distal (>10kb) Multiome | 141 | |
| chr5:43,396,804–43,397,322 | 206.0 kb | Distal (>10kb) Multiome | 340 | |
| chr5:43,416,225–43,416,784 | 186.7 kb | Distal (>10kb) Multiome | 263 | |
| chr5:43,483,333–43,484,741 | 119.2 kb | Distal (>10kb) Multiome | 1033 | |
| chr5:43,514,568–43,515,502 | 88.0 kb | Distal (>10kb) Multiome | 817 | |
| chr5:43,555,878–43,557,718 | 46.2 kb | Distal (>10kb) Multiome | 936 | |
| chr5:43,602,369–43,604,281 | 3 bp | At TSS Multiome | 912 | |
| chr5:43,607,002–43,607,875 | 4.0 kb | Proximal (<10kb) | 24 | |
| chr5:44,506,221–44,506,892 | 903.6 kb | Distal (>10kb) Multiome HiCAR | 207 | |
| chr5:44,638,090–44,639,138 | 1035.5 kb | Distal (>10kb) Multiome HiCAR | 164 |
Genomic view of the NNT-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.