This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
Transcription factors with Perturb-seq knockdown data for CHRNA3. 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 = CHRNA3 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 CHRNA3, 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 |
|---|---|---|---|---|
| chr15:78,340,100–78,340,745 | 280.7 kb | Distal (>10kb) Multiome | 194 | |
| chr15:78,437,554–78,438,897 | 182.8 kb | Distal (>10kb) Multiome | 918 | |
| chr15:78,506,965–78,508,087 | 113.5 kb | Distal (>10kb) Multiome | 674 | |
| chr15:78,539,941–78,541,020 | 80.5 kb | Distal (>10kb) Multiome | 773 | |
| chr15:78,564,790–78,566,388 | 55.5 kb | Distal (>10kb) Multiome | 618 | |
| chr15:78,618,487–78,618,677 | 2.3 kb | Proximal (<10kb) | 205 | |
| chr15:78,619,950–78,621,461 | 693 bp | At TSS Multiome | 274 | |
| chr15:78,640,579–78,641,869 | 20.4 kb | Distal (>10kb) Multiome | 406 | |
| chr15:78,671,569–78,672,301 | 50.8 kb | Distal (>10kb) Multiome | 254 | |
| chr15:78,810,245–78,812,147 | 190.6 kb | Distal (>10kb) Multiome | 505 | |
| chr15:78,872,212–78,873,881 | 251.8 kb | Distal (>10kb) Multiome | 950 |
Genomic view of the CHRNA3 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.