Transcription factors with Perturb-seq knockdown data for LINC01138. 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 = LINC01138 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 LINC01138, 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 |
|---|---|---|---|---|
| chr1:148,038,392–148,038,981 | 296.3 kb | Distal (>10kb) Multiome HiCAR | 522 | |
| chr1:148,263,120–148,264,484 | 71.4 kb | Distal (>10kb) Multiome | 872 | |
| chr1:148,264,619–148,265,210 | 69.9 kb | Distal (>10kb) Multiome | 447 | |
| chr1:148,280,452–148,280,755 | at TSS | At TSS | 126 | |
| chr1:148,303,450–148,304,082 | 31.3 kb | Distal (>10kb) Multiome | 89 | |
| chr1:148,333,992–148,335,292 | 203 bp | At TSS Multiome | 1026 | |
| chr1:148,353,276–148,354,139 | 18.7 kb | Distal (>10kb) Multiome | 234 | |
| chr1:148,384,953–148,386,164 | 50.7 kb | Distal (>10kb) Multiome | 88 | |
| chr1:148,388,031–148,389,108 | 53.8 kb | Distal (>10kb) Multiome | 719 | |
| chr1:148,402,223–148,402,924 | 67.5 kb | Distal (>10kb) Multiome | 457 | |
| chr1:148,522,518–148,523,224 | 187.7 kb | Distal (>10kb) Multiome | 832 |
Genomic view of the LINC01138 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.