This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Transcription factors with Perturb-seq knockdown data for KDM5B. 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 = KDM5B 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 KDM5B, 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 |
|---|---|---|---|---|
| chr1:202,638,017–202,638,513 | 170.1 kb | Distal (>10kb) Multiome | 19 | |
| chr1:202,643,050–202,644,080 | 164.6 kb | Distal (>10kb) Multiome | 115 | |
| chr1:202,709,842–202,710,859 | 98.0 kb | Distal (>10kb) Multiome | 255 | |
| chr1:202,806,787–202,808,806 | 2 bp | At TSS Multiome | 869 | |
| chr1:202,810,279–202,811,748 | 2.4 kb | Proximal (<10kb) Multiome | 933 | |
| chr1:202,818,850–202,819,302 | 10.5 kb | Distal (>10kb) Multiome | 40 | |
| chr1:202,860,760–202,862,216 | 53.2 kb | Distal (>10kb) Multiome | 695 | |
| chr1:202,888,353–202,889,540 | 80.5 kb | Distal (>10kb) Multiome | 894 | |
| chr1:202,926,591–202,927,689 | 118.7 kb | Distal (>10kb) Multiome | 1072 | |
| chr1:202,957,716–202,958,953 | 149.9 kb | Distal (>10kb) Multiome | 787 | |
| chr1:202,966,422–202,967,948 | 158.9 kb | Distal (>10kb) Multiome | 536 | |
| chr1:203,005,211–203,007,890 | 197.1 kb | Distal (>10kb) Multiome | 874 | |
| chr1:203,026,091–203,027,571 | 218.0 kb | Distal (>10kb) Multiome | 771 | |
| chr1:203,075,525–203,076,284 | 267.5 kb | Distal (>10kb) Multiome | 165 |
Genomic view of the KDM5B 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.