Transcription factors with Perturb-seq knockdown data for LNCRNA-IUR. 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 = LNCRNA-IUR 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 LNCRNA-IUR, 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 |
|---|---|---|---|---|
| chr11:94,866,030–94,867,452 | 283.9 kb | Distal (>10kb) Multiome | 112 | |
| chr11:94,973,096–94,974,006 | 176.9 kb | Distal (>10kb) Multiome | 740 | |
| chr11:95,066,821–95,068,191 | 83.2 kb | Distal (>10kb) Multiome | 721 | |
| chr11:95,089,389–95,090,696 | 60.7 kb | Distal (>10kb) Multiome | 660 | |
| chr11:95,107,207–95,108,126 | 42.9 kb | Distal (>10kb) Multiome | 232 | |
| chr11:95,144,387–95,145,222 | 5.7 kb | Proximal (<10kb) Multiome | 127 | |
| chr11:95,149,652–95,152,295 | 653 bp | At TSS Multiome | 685 | |
| chr11:95,154,569–95,154,793 | 2.9 kb | Proximal (<10kb) | 136 | |
| chr11:95,158,839–95,159,031 | 7.1 kb | Proximal (<10kb) | 64 | |
| chr11:95,229,933–95,232,611 | 80.8 kb | Distal (>10kb) Multiome | 696 | |
| chr11:95,232,733–95,233,136 | 1.5 kb | Proximal (<10kb) | 73 | |
| chr11:95,235,300–95,235,760 | 4.0 kb | Proximal (<10kb) | 110 | |
| chr11:95,788,868–95,791,310 | 639.2 kb | Distal (>10kb) Multiome HiCAR | 1058 | |
| chr11:96,389,261–96,390,676 | 1239.4 kb | Distal (>10kb) Multiome HiCAR | 898 |
Genomic view of the LNCRNA-IUR 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.