This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
Transcription factors with Perturb-seq knockdown data for SCN9A. 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 = SCN9A 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 SCN9A, 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 |
|---|---|---|---|---|
| chr2:166,365,989–166,366,823 | 9.1 kb | Proximal (<10kb) | 104 | |
| chr2:166,372,803–166,373,404 | 2.5 kb | Proximal (<10kb) | 122 | |
| chr2:166,374,047–166,374,235 | 1.7 kb | Proximal (<10kb) | 199 | |
| chr2:166,375,161–166,377,020 | 141 bp | At TSS Multiome | 941 | |
| chr2:166,382,580–166,382,818 | 6.6 kb | Proximal (<10kb) | 3 |
Genomic view of the SCN9A 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.