NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]
Transcription factors with Perturb-seq knockdown data for NIPSNAP3A. 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 = NIPSNAP3A 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 NIPSNAP3A, 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 |
|---|---|---|---|---|
| chr9:104,738,557–104,738,925 | 8.8 kb | Proximal (<10kb) | 21 | |
| chr9:104,743,482–104,743,733 | 3.9 kb | Proximal (<10kb) | 119 | |
| chr9:104,745,695–104,746,363 | 1.3 kb | Proximal (<10kb) | 152 | |
| chr9:104,747,331–104,748,817 | 178 bp | At TSS Multiome | 758 | |
| chr9:104,763,613–104,764,841 | 16.6 kb | Distal (>10kb) Multiome | 645 | |
| chr9:104,778,305–104,779,370 | 31.2 kb | Distal (>10kb) Multiome | 109 | |
| chr9:104,868,780–104,869,418 | 121.4 kb | Distal (>10kb) Multiome | 308 | |
| chr9:104,885,889–104,886,798 | 138.6 kb | Distal (>10kb) Multiome | 467 | |
| chr9:104,926,377–104,928,757 | 179.0 kb | Distal (>10kb) Multiome | 898 | |
| chr9:104,961,289–104,961,961 | 213.8 kb | Distal (>10kb) Multiome | 296 | |
| chr9:104,967,924–104,969,360 | 220.8 kb | Distal (>10kb) Multiome | 657 | |
| chr9:104,990,922–104,992,163 | 244.1 kb | Distal (>10kb) Multiome | 685 | |
| chr9:104,993,121–104,994,152 | 245.9 kb | Distal (>10kb) Multiome | 314 |
Genomic view of the NIPSNAP3A 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.