Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; regulation of cytokine production; and regulation of immune system process. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
Modules significantly affected by knockdown. ↑ Up = module upregulated upon KD; ↓ Down = module downregulated upon KD.
| Module | Dir | NES | #gRNA | padj | Bind | OR | padj (bind) |
|---|
| Submodule | Module | Dir | NES | #gRNA | Bind | OR | padj (bind) |
|---|
Genes likely regulated by HIC2 through linked binding evidence in open chromatin. The chart ranks TF-linked genes by their mean Perturb-seq response to HIC2 knockdown, with negative coefficients indicating downregulation and positive coefficients indicating upregulation upon knockdown.
Open chromatin elements (ATAC-seq) where HIC2 has ChIP-seq or motif footprint binding evidence and which are linked to at least one target gene region.
| Element | Size | Linked genes |
|---|
Transcription factors with Perturb-seq knockdown data for HIC2. 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 = HIC2 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 HIC2, 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 |
|---|---|---|---|---|
| chr22:20,020,662–20,021,745 | 1396.3 kb | Distal (>10kb) Multiome HiCAR | 718 | |
| chr22:20,243,636–20,244,300 | 1173.4 kb | Distal (>10kb) Multiome HiCAR | 251 | |
| chr22:20,418,190–20,418,662 | 999.0 kb | Distal (>10kb) Multiome HiCAR | 594 | |
| chr22:20,857,959–20,859,512 | 558.6 kb | Distal (>10kb) Multiome HiCAR | 901 | |
| chr22:21,567,510–21,568,436 | 150.3 kb | Distal (>10kb) Multiome | 951 | |
| chr22:21,628,821–21,630,259 | 212.7 kb | Distal (>10kb) Multiome HiCAR | 1055 | |
| chr22:21,641,511–21,643,313 | 224.8 kb | Distal (>10kb) Multiome HiCAR | 754 | |
| chr22:21,651,622–21,652,445 | 234.8 kb | Distal (>10kb) Multiome HiCAR | 719 | |
| chr22:21,657,073–21,658,429 | 240.3 kb | Distal (>10kb) Multiome HiCAR | 802 | |
| chr22:21,665,721–21,666,577 | 248.8 kb | Distal (>10kb) Multiome | 893 | |
| chr22:21,938,040–21,938,786 | 520.9 kb | Distal (>10kb) Multiome HiCAR | 871 | |
| chr22:21,951,964–21,953,251 | 535.5 kb | Distal (>10kb) Multiome HiCAR | 645 |
Genomic view of the HIC2 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.