The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders. Alternate splicing results in two transcript variants that encode different proteins. [provided by RefSeq, Mar 2012]
Transcription factors with Perturb-seq knockdown data for CLCN4. 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 = CLCN4 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 CLCN4, 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 |
|---|---|---|---|---|
| chrX:10,014,411–10,016,412 | 141.9 kb | Distal (>10kb) Multiome | 486 | |
| chrX:10,156,631–10,157,191 | at TSS | At TSS | 376 | |
| chrX:10,158,328–10,158,620 | 1.4 kb | Proximal (<10kb) | 131 | |
| chrX:10,159,942–10,160,198 | 3.0 kb | Proximal (<10kb) | 21 | |
| chrX:10,173,123–10,173,911 | 16.6 kb | Distal (>10kb) Multiome | 271 | |
| chrX:11,111,059–11,111,867 | 954.3 kb | Distal (>10kb) Multiome HiCAR | 546 |
Genomic view of the CLCN4 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.