The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defects in this gene have been associated with familial exudative vitreoretinopathy (FEVR) and retinitis pigmentosa (RP). [provided by RefSeq, Dec 2016]
Transcription factors with Perturb-seq knockdown data for ZNF408. 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 = ZNF408 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 ZNF408, 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 |
|---|---|---|---|---|
| chr11:46,593,562–46,594,345 | 107.1 kb | Distal (>10kb) Multiome | 845 | |
| chr11:46,616,855–46,618,064 | 83.7 kb | Distal (>10kb) Multiome | 823 | |
| chr11:46,674,791–46,675,556 | 26.0 kb | Distal (>10kb) Multiome | 308 | |
| chr11:46,700,262–46,701,275 | 314 bp | At TSS Multiome | 997 | |
| chr11:46,826,562–46,827,053 | 125.9 kb | Distal (>10kb) Multiome | 529 | |
| chr11:46,845,538–46,846,680 | 145.2 kb | Distal (>10kb) Multiome | 879 | |
| chr11:46,912,540–46,913,271 | 211.8 kb | Distal (>10kb) Multiome | 252 | |
| chr11:46,917,991–46,919,090 | 217.6 kb | Distal (>10kb) Multiome | 405 | |
| chr11:46,936,572–46,937,187 | 235.8 kb | Distal (>10kb) Multiome | 744 |
Genomic view of the ZNF408 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.