This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]
Transcription factors with Perturb-seq knockdown data for KDM4A. 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 = KDM4A 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 KDM4A, 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 |
|---|---|---|---|---|
| chr1:43,358,112–43,359,560 | 291.3 kb | Distal (>10kb) Multiome | 818 | |
| chr1:43,366,277–43,366,800 | 283.7 kb | Distal (>10kb) Multiome | 226 | |
| chr1:43,366,988–43,368,619 | 282.0 kb | Distal (>10kb) Multiome | 991 | |
| chr1:43,389,284–43,390,213 | 260.3 kb | Distal (>10kb) Multiome | 905 | |
| chr1:43,452,851–43,454,257 | 196.8 kb | Distal (>10kb) Multiome | 455 | |
| chr1:43,454,433–43,454,997 | 195.4 kb | Distal (>10kb) Multiome | 267 | |
| chr1:43,530,512–43,532,007 | 119.2 kb | Distal (>10kb) Multiome | 520 | |
| chr1:43,545,657–43,546,353 | 104.1 kb | Distal (>10kb) Multiome | 445 | |
| chr1:43,549,934–43,550,659 | 99.9 kb | Distal (>10kb) Multiome | 343 | |
| chr1:43,565,502–43,566,158 | 84.3 kb | Distal (>10kb) Multiome | 173 | |
| chr1:43,649,463–43,650,795 | 17 bp | At TSS Multiome | 997 | |
| chr1:43,707,108–43,708,162 | 57.4 kb | Distal (>10kb) Multiome | 937 | |
| chr1:43,933,385–43,935,511 | 284.8 kb | Distal (>10kb) Multiome | 565 | |
| chr1:43,935,659–43,937,001 | 286.6 kb | Distal (>10kb) Multiome | 359 | |
| chr1:43,946,199–43,947,337 | 296.5 kb | Distal (>10kb) Multiome | 1003 |
Genomic view of the KDM4A 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.