This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
Transcription factors with Perturb-seq knockdown data for KDM5A. 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 = KDM5A 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 KDM5A, 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 |
|---|---|---|---|---|
| chr12:114,410–115,115 | 274.5 kb | Distal (>10kb) Multiome | 103 | |
| chr12:188,514–189,385 | 200.1 kb | Distal (>10kb) Multiome | 399 | |
| chr12:203,433–204,150 | 185.5 kb | Distal (>10kb) Multiome | 173 | |
| chr12:219,759–220,243 | 169.2 kb | Distal (>10kb) Multiome | 454 | |
| chr12:253,958–254,560 | 135.0 kb | Distal (>10kb) Multiome | 30 | |
| chr12:459,530–460,568 | 70.6 kb | Distal (>10kb) Multiome | 338 | |
| chr12:509,461–510,940 | 121.1 kb | Distal (>10kb) Multiome | 399 | |
| chr12:569,602–571,188 | 180.6 kb | Distal (>10kb) Multiome | 800 | |
| chr12:642,622–643,509 | 253.7 kb | Distal (>10kb) Multiome | 556 | |
| chr12:669,635–670,134 | 280.5 kb | Distal (>10kb) Multiome | 33 |
Genomic view of the KDM5A 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.