This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine oxidase domain. This protein is a component of several histone deacetylase complexes, though it silences genes by functioning as a histone demethylase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Transcription factors with Perturb-seq knockdown data for KDM1A. 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 = KDM1A 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 KDM1A, 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 |
|---|---|---|---|---|
| chr1:22,741,075–22,741,547 | 278.2 kb | Distal (>10kb) Multiome | 33 | |
| chr1:22,976,445–22,976,936 | 42.8 kb | Distal (>10kb) Multiome | 351 | |
| chr1:23,019,210–23,020,140 | 30 bp | At TSS Multiome | 1023 | |
| chr1:23,168,432–23,169,217 | 149.4 kb | Distal (>10kb) Multiome | 673 | |
| chr1:23,177,510–23,178,128 | 158.3 kb | Distal (>10kb) Multiome | 628 | |
| chr1:23,216,791–23,217,828 | 197.6 kb | Distal (>10kb) Multiome | 415 | |
| chr1:23,343,731–23,344,999 | 325.0 kb | Distal (>10kb) Multiome | 939 |
Genomic view of the KDM1A 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.