This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This protein functions as a transcriptional repressor and may regulate tissue specific expression of dopamine receptor D1. Expansion of an alanine repeat in the C-terminus of the encoded protein and other mutations in this gene cause holoprosencephaly type 5. Holoprosencephaly is the most common structural anomaly of the human brain. A polyhistidine tract polymorphism in this gene may be associated with increased risk of neural tube defects. This gene is closely linked to a gene encoding zinc finger protein of the cerebellum 5, a related family member on chromosome 13. [provided by RefSeq, Jul 2016]
Transcription factors with Perturb-seq knockdown data for ZIC2. 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 = ZIC2 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 ZIC2, 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 |
|---|---|---|---|---|
| chr13:99,657,854–99,658,963 | 323.3 kb | Distal (>10kb) Multiome HiCAR | 252 | |
| chr13:99,686,744–99,688,098 | 294.6 kb | Distal (>10kb) Multiome | 332 | |
| chr13:99,818,120–99,818,590 | 163.5 kb | Distal (>10kb) Multiome | 93 | |
| chr13:99,955,497–99,958,187 | 24.1 kb | Distal (>10kb) Multiome | 501 | |
| chr13:99,970,037–99,972,702 | 9.9 kb | Proximal (<10kb) Multiome | 629 | |
| chr13:99,974,409–99,974,618 | 7.2 kb | Proximal (<10kb) | 53 | |
| chr13:99,974,729–99,975,144 | 6.6 kb | Proximal (<10kb) | 81 | |
| chr13:99,978,424–99,982,746 | 2.6 kb | Proximal (<10kb) Multiome | 812 | |
| chr13:99,983,558–99,984,579 | 1.8 kb | Proximal (<10kb) | 323 | |
| chr13:99,984,710–99,985,546 | 2.9 kb | Proximal (<10kb) | 213 | |
| chr13:99,987,300–99,988,293 | 5.5 kb | Proximal (<10kb) | 156 | |
| chr13:99,988,365–99,990,011 | 6.6 kb | Proximal (<10kb) | 245 | |
| chr13:99,990,093–99,992,597 | 10.1 kb | Distal (>10kb) Multiome | 378 | |
| chr13:99,996,965–99,998,156 | 15.7 kb | Distal (>10kb) Multiome | 258 | |
| chr13:100,050,037–100,051,771 | 69.4 kb | Distal (>10kb) Multiome | 289 | |
| chr13:100,088,371–100,089,589 | 107.2 kb | Distal (>10kb) Multiome HiCAR | 925 | |
| chr13:100,510,174–100,511,130 | 528.7 kb | Distal (>10kb) Multiome HiCAR | 264 | |
| chr13:100,588,327–100,589,133 | 607.0 kb | Distal (>10kb) Multiome HiCAR | 783 |
Genomic view of the ZIC2 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.