This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]
Transcription factors with Perturb-seq knockdown data for VARS2. 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 = VARS2 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 VARS2, 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 |
|---|---|---|---|---|
| chr6:30,614,393–30,615,939 | 299.0 kb | Distal (>10kb) Multiome | 837 | |
| chr6:30,616,770–30,618,155 | 296.7 kb | Distal (>10kb) Multiome | 1072 | |
| chr6:30,626,560–30,627,206 | 287.4 kb | Distal (>10kb) Multiome | 802 | |
| chr6:30,646,505–30,648,035 | 266.9 kb | Distal (>10kb) Multiome | 961 | |
| chr6:30,672,571–30,673,266 | 241.2 kb | Distal (>10kb) Multiome | 812 | |
| chr6:30,679,032–30,679,479 | 235.0 kb | Distal (>10kb) Multiome | 603 | |
| chr6:30,686,268–30,688,032 | 227.0 kb | Distal (>10kb) Multiome | 801 | |
| chr6:30,690,445–30,691,240 | 223.3 kb | Distal (>10kb) Multiome | 644 | |
| chr6:30,716,986–30,717,874 | 196.7 kb | Distal (>10kb) Multiome | 1059 | |
| chr6:30,719,428–30,720,577 | 194.0 kb | Distal (>10kb) Multiome | 724 | |
| chr6:30,721,307–30,722,103 | 192.7 kb | Distal (>10kb) Multiome | 872 | |
| chr6:30,725,731–30,726,564 | 188.0 kb | Distal (>10kb) Multiome | 478 | |
| chr6:30,740,996–30,745,094 | 171.5 kb | Distal (>10kb) Multiome | 1233 | |
| chr6:30,763,647–30,765,193 | 149.8 kb | Distal (>10kb) Multiome | 850 | |
| chr6:30,880,638–30,881,295 | 33.3 kb | Distal (>10kb) Multiome | 124 | |
| chr6:30,882,560–30,883,422 | 31.3 kb | Distal (>10kb) Multiome | 308 | |
| chr6:30,883,625–30,885,122 | 29.8 kb | Distal (>10kb) Multiome | 538 | |
| chr6:30,907,770–30,908,494 | 6.1 kb | Proximal (<10kb) Multiome | 1005 | |
| chr6:30,913,674–30,914,800 | 13 bp | At TSS Multiome | 944 | |
| chr6:30,915,583–30,915,794 | 1.4 kb | Proximal (<10kb) | 146 | |
| chr6:30,942,475–30,943,087 | 28.6 kb | Distal (>10kb) Multiome | 300 | |
| chr6:30,955,192–30,955,975 | 41.5 kb | Distal (>10kb) Multiome | 524 | |
| chr6:31,157,467–31,159,255 | 244.2 kb | Distal (>10kb) Multiome | 740 | |
| chr6:31,171,796–31,173,419 | 257.8 kb | Distal (>10kb) Multiome | 178 |
Genomic view of the VARS2 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.