Involved in endosome to lysosome transport and intracellular protein transport. Acts upstream of or within collagen metabolic process and peptidyl-lysine hydroxylation. Located in Golgi apparatus and endosome. Part of vesicle tethering complex. Implicated in arthrogryposis, renal dysfunction, and cholestasis 2. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for VIPAS39. 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 = VIPAS39 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 VIPAS39, 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 |
|---|---|---|---|---|
| chr14:77,181,185–77,182,207 | 275.9 kb | Distal (>10kb) Multiome | 485 | |
| chr14:77,270,588–77,271,586 | 186.4 kb | Distal (>10kb) Multiome | 147 | |
| chr14:77,320,198–77,322,121 | 136.4 kb | Distal (>10kb) Multiome HiCAR | 915 | |
| chr14:77,376,423–77,377,683 | 80.4 kb | Distal (>10kb) Multiome | 630 | |
| chr14:77,456,961–77,458,831 | 151 bp | At TSS Multiome | 878 | |
| chr14:77,498,012–77,499,509 | 41.3 kb | Distal (>10kb) Multiome | 599 | |
| chr14:77,615,862–77,617,380 | 159.3 kb | Distal (>10kb) Multiome | 892 | |
| chr14:77,654,873–77,655,664 | 197.7 kb | Distal (>10kb) Multiome | 287 | |
| chr14:77,707,585–77,708,371 | 250.5 kb | Distal (>10kb) Multiome | 744 |
Genomic view of the VIPAS39 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.