This gene encodes a member of the tretraspanin family. The encoded protein may be involved in mediating intestinal trefoil factor induced wound healing in the intestinal mucosa. Mutations in this gene are associated with neural tube defects. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
Transcription factors with Perturb-seq knockdown data for VANGL1. 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 = VANGL1 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 VANGL1, 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 |
|---|---|---|---|---|
| chr1:115,536,244–115,536,776 | 105.5 kb | Distal (>10kb) Multiome | 29 | |
| chr1:115,593,347–115,594,339 | 48.2 kb | Distal (>10kb) Multiome | 81 | |
| chr1:115,632,646–115,633,035 | 9.0 kb | Proximal (<10kb) | 51 | |
| chr1:115,641,554–115,643,092 | 102 bp | At TSS Multiome | 748 | |
| chr1:115,647,204–115,647,416 | 5.2 kb | Proximal (<10kb) | 94 | |
| chr1:115,647,538–115,647,746 | 5.5 kb | Proximal (<10kb) | 66 | |
| chr1:115,648,738–115,649,618 | 6.7 kb | Proximal (<10kb) | 296 | |
| chr1:115,649,832–115,650,363 | 8.1 kb | Proximal (<10kb) Multiome | 246 | |
| chr1:115,650,914–115,651,221 | 8.9 kb | Proximal (<10kb) | 63 | |
| chr1:115,771,492–115,772,197 | 129.9 kb | Distal (>10kb) Multiome | 355 | |
| chr1:115,828,121–115,829,682 | 186.7 kb | Distal (>10kb) Multiome | 408 | |
| chr1:115,837,650–115,839,828 | 196.0 kb | Distal (>10kb) Multiome | 304 | |
| chr1:115,924,342–115,925,363 | 282.9 kb | Distal (>10kb) Multiome | 172 |
Genomic view of the VANGL1 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.