This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. AT-hook transcription factor AKNA is reported to coordinately regulate the expression of this receptor and its ligand, which may be important for homotypic cell interactions. Adaptor protein TNFR2 interacts with this receptor and serves as a mediator of the signal transduction. The interaction of this receptor and its ligand is found to be necessary for amyloid-beta-induced microglial activation, and thus is thought to be an early event in Alzheimer disease pathogenesis. Mutations affecting this gene are the cause of autosomal recessive hyper-IgM immunodeficiency type 3 (HIGM3). Multiple alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Nov 2014]
Transcription factors with Perturb-seq knockdown data for CD40. 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 = CD40 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 CD40, 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 |
|---|---|---|---|---|
| chr20:45,833,493–45,834,622 | 284.3 kb | Distal (>10kb) Multiome | 833 | |
| chr20:45,856,871–45,858,137 | 260.8 kb | Distal (>10kb) Multiome | 884 | |
| chr20:45,880,796–45,881,524 | 237.1 kb | Distal (>10kb) Multiome | 738 | |
| chr20:45,890,127–45,891,800 | 226.9 kb | Distal (>10kb) Multiome | 1095 | |
| chr20:45,910,538–45,912,397 | 206.0 kb | Distal (>10kb) Multiome | 713 | |
| chr20:45,933,591–45,935,780 | 183.2 kb | Distal (>10kb) Multiome | 1195 | |
| chr20:45,971,553–45,972,790 | 146.1 kb | Distal (>10kb) Multiome | 1206 | |
| chr20:46,004,647–46,005,315 | 113.3 kb | Distal (>10kb) Multiome | 207 | |
| chr20:46,011,604–46,012,166 | 106.4 kb | Distal (>10kb) Multiome | 239 | |
| chr20:46,013,565–46,014,586 | 104.2 kb | Distal (>10kb) Multiome | 735 | |
| chr20:46,021,209–46,023,166 | 96.3 kb | Distal (>10kb) Multiome | 679 | |
| chr20:46,031,750–46,032,261 | 86.2 kb | Distal (>10kb) Multiome | 227 | |
| chr20:46,058,408–46,058,983 | 59.5 kb | Distal (>10kb) Multiome | 123 | |
| chr20:46,089,092–46,090,355 | 28.4 kb | Distal (>10kb) Multiome | 1047 | |
| chr20:46,091,736–46,092,300 | 26.1 kb | Distal (>10kb) Multiome | 38 | |
| chr20:46,117,897–46,118,755 | 8 bp | At TSS Multiome | 376 | |
| chr20:46,174,457–46,175,011 | 56.4 kb | Distal (>10kb) Multiome | 277 | |
| chr20:46,268,041–46,268,560 | 150.0 kb | Distal (>10kb) Multiome | 82 | |
| chr20:46,307,134–46,307,979 | 189.0 kb | Distal (>10kb) Multiome HiCAR | 455 | |
| chr20:46,308,245–46,308,857 | 190.3 kb | Distal (>10kb) Multiome HiCAR | 287 | |
| chr20:46,363,898–46,364,657 | 246.1 kb | Distal (>10kb) Multiome | 983 | |
| chr20:46,405,903–46,407,320 | 288.3 kb | Distal (>10kb) Multiome | 946 |
Genomic view of the CD40 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.