Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]
Transcription factors with Perturb-seq knockdown data for KDM1B. 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 = KDM1B 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 KDM1B, 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 |
|---|---|---|---|---|
| chr6:17,939,336–17,940,066 | 215.7 kb | Distal (>10kb) Multiome | 164 | |
| chr6:17,986,741–17,988,454 | 167.7 kb | Distal (>10kb) Multiome | 815 | |
| chr6:18,022,711–18,023,230 | 132.4 kb | Distal (>10kb) Multiome | 195 | |
| chr6:18,122,030–18,123,058 | 32.7 kb | Distal (>10kb) Multiome | 824 | |
| chr6:18,141,867–18,142,341 | 13.4 kb | Distal (>10kb) Multiome | 113 | |
| chr6:18,152,627–18,153,245 | 2.6 kb | Proximal (<10kb) Multiome | 199 | |
| chr6:18,154,608–18,156,434 | 158 bp | At TSS Multiome | 937 | |
| chr6:18,185,739–18,186,332 | 30.7 kb | Distal (>10kb) Multiome | 189 | |
| chr6:18,263,804–18,265,203 | 109.1 kb | Distal (>10kb) Multiome | 869 | |
| chr6:18,312,094–18,312,753 | 157.1 kb | Distal (>10kb) Multiome | 104 | |
| chr6:18,386,971–18,387,968 | 232.0 kb | Distal (>10kb) Multiome | 780 | |
| chr6:18,394,997–18,395,808 | 240.0 kb | Distal (>10kb) Multiome | 134 |
Genomic view of the KDM1B 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.