Transcription factors with Perturb-seq knockdown data for ALMS1-IT1. 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 = ALMS1-IT1 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 ALMS1-IT1, 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 |
|---|---|---|---|---|
| chr2:73,156,488–73,157,075 | 300.0 kb | Distal (>10kb) Multiome | 419 | |
| chr2:73,175,306–73,176,433 | 281.0 kb | Distal (>10kb) Multiome | 499 | |
| chr2:73,176,845–73,177,711 | 279.2 kb | Distal (>10kb) Multiome | 779 | |
| chr2:73,202,161–73,203,581 | 254.2 kb | Distal (>10kb) Multiome | 227 | |
| chr2:73,214,088–73,214,797 | 242.4 kb | Distal (>10kb) Multiome | 870 | |
| chr2:73,232,770–73,234,882 | 222.3 kb | Distal (>10kb) Multiome | 1129 | |
| chr2:73,268,616–73,269,882 | 187.6 kb | Distal (>10kb) Multiome | 384 | |
| chr2:73,283,511–73,285,190 | 172.2 kb | Distal (>10kb) Multiome | 734 | |
| chr2:73,291,197–73,292,186 | 165.3 kb | Distal (>10kb) Multiome | 609 | |
| chr2:73,293,075–73,294,022 | 163.1 kb | Distal (>10kb) Multiome | 382 | |
| chr2:73,385,262–73,386,724 | 70.9 kb | Distal (>10kb) Multiome | 893 | |
| chr2:73,736,841–73,737,678 | 280.7 kb | Distal (>10kb) Multiome | 952 |
Genomic view of the ALMS1-IT1 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.