The protein encoded by this gene is a membrane protein involved in the regulation of planar cell polarity, especially in the stereociliary bundles of the cochlea. The encoded protein transmits directional signals to individual cells or groups of cells in epithelial sheets. This protein is also involved in the development of the neural plate. [provided by RefSeq, Sep 2011]
Transcription factors with Perturb-seq knockdown data for VANGL2. 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 = VANGL2 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 VANGL2, 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 |
|---|---|---|---|---|
| chr1:160,100,845–160,101,543 | 299.4 kb | Distal (>10kb) Multiome | 530 | |
| chr1:160,169,049–160,170,141 | 230.9 kb | Distal (>10kb) Multiome | 330 | |
| chr1:160,192,913–160,193,769 | 207.3 kb | Distal (>10kb) Multiome | 551 | |
| chr1:160,204,860–160,206,035 | 195.1 kb | Distal (>10kb) Multiome | 637 | |
| chr1:160,261,515–160,263,143 | 138.1 kb | Distal (>10kb) Multiome | 992 | |
| chr1:160,284,609–160,285,332 | 115.4 kb | Distal (>10kb) Multiome | 638 | |
| chr1:160,342,945–160,343,700 | 57.3 kb | Distal (>10kb) Multiome | 868 | |
| chr1:160,399,764–160,401,441 | 137 bp | At TSS Multiome | 590 | |
| chr1:160,403,360–160,403,555 | 2.8 kb | Proximal (<10kb) | 22 | |
| chr1:160,539,925–160,540,644 | 139.7 kb | Distal (>10kb) Multiome | 479 | |
| chr1:160,619,659–160,620,443 | 219.5 kb | Distal (>10kb) Multiome HiCAR | 187 | |
| chr1:160,651,647–160,653,226 | 252.0 kb | Distal (>10kb) Multiome HiCAR | 296 | |
| chr1:160,658,117–160,659,135 | 258.0 kb | Distal (>10kb) Multiome HiCAR | 111 | |
| chr1:160,665,307–160,666,295 | 265.2 kb | Distal (>10kb) Multiome | 417 | |
| chr1:160,674,985–160,675,879 | 275.0 kb | Distal (>10kb) Multiome HiCAR | 258 | |
| chr1:160,681,274–160,681,823 | 281.0 kb | Distal (>10kb) Multiome HiCAR | 237 |
Genomic view of the VANGL2 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.