This gene encodes a voltage-gated chloride channel. The encoded protein is a transmembrane protein that maintains chloride ion homeostasis in various cells. Defects in this gene may be a cause of certain epilepsies. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
Transcription factors with Perturb-seq knockdown data for CLCN2. 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 = CLCN2 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 CLCN2, 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 |
|---|---|---|---|---|
| chr3:184,134,086–184,134,568 | 227.5 kb | Distal (>10kb) Multiome | 732 | |
| chr3:184,134,801–184,135,887 | 226.2 kb | Distal (>10kb) Multiome | 941 | |
| chr3:184,154,967–184,155,880 | 206.3 kb | Distal (>10kb) Multiome | 580 | |
| chr3:184,174,432–184,175,524 | 186.9 kb | Distal (>10kb) Multiome | 765 | |
| chr3:184,176,129–184,177,706 | 184.9 kb | Distal (>10kb) Multiome | 480 | |
| chr3:184,185,411–184,187,065 | 175.6 kb | Distal (>10kb) Multiome | 878 | |
| chr3:184,229,229–184,229,859 | 132.1 kb | Distal (>10kb) Multiome | 409 | |
| chr3:184,236,026–184,236,474 | 125.4 kb | Distal (>10kb) Multiome | 41 | |
| chr3:184,241,140–184,242,189 | 119.9 kb | Distal (>10kb) Multiome | 700 | |
| chr3:184,248,652–184,250,567 | 112.0 kb | Distal (>10kb) Multiome | 1061 | |
| chr3:184,259,723–184,260,497 | 101.6 kb | Distal (>10kb) Multiome | 318 | |
| chr3:184,260,815–184,262,571 | 100.0 kb | Distal (>10kb) Multiome | 511 | |
| chr3:184,298,591–184,299,718 | 62.5 kb | Distal (>10kb) Multiome | 768 | |
| chr3:184,314,169–184,315,514 | 47.0 kb | Distal (>10kb) Multiome | 761 | |
| chr3:184,335,265–184,337,276 | 25.7 kb | Distal (>10kb) Multiome | 796 | |
| chr3:184,338,471–184,338,964 | 22.9 kb | Distal (>10kb) Multiome | 203 | |
| chr3:184,354,371–184,354,570 | 7.1 kb | Proximal (<10kb) | 187 | |
| chr3:184,360,146–184,360,404 | 1.2 kb | Proximal (<10kb) | 52 | |
| chr3:184,361,172–184,363,709 | 1.6 kb | Proximal (<10kb) Multiome | 1034 | |
| chr3:184,371,554–184,371,991 | 9.9 kb | Proximal (<10kb) | 469 | |
| chr3:184,379,849–184,380,935 | 18.6 kb | Distal (>10kb) Multiome | 242 | |
| chr3:184,513,458–184,514,228 | 152.2 kb | Distal (>10kb) Multiome | 391 | |
| chr3:184,525,317–184,526,423 | 164.4 kb | Distal (>10kb) Multiome HiCAR | 281 | |
| chr3:184,558,752–184,559,234 | 197.3 kb | Distal (>10kb) Multiome | 58 | |
| chr3:184,561,059–184,562,613 | 200.0 kb | Distal (>10kb) Multiome | 671 | |
| chr3:184,568,694–184,569,481 | 207.5 kb | Distal (>10kb) Multiome | 342 | |
| chr3:184,574,449–184,575,341 | 213.3 kb | Distal (>10kb) Multiome | 164 | |
| chr3:184,583,141–184,585,336 | 223.1 kb | Distal (>10kb) Multiome | 270 | |
| chr3:184,601,537–184,603,254 | 240.6 kb | Distal (>10kb) Multiome | 179 | |
| chr3:184,603,592–184,605,089 | 243.0 kb | Distal (>10kb) Multiome | 321 | |
| chr3:184,629,636–184,630,157 | 268.2 kb | Distal (>10kb) Multiome | 71 | |
| chr3:184,642,851–184,643,762 | 281.6 kb | Distal (>10kb) Multiome | 135 | |
| chr3:184,645,190–184,645,870 | 283.9 kb | Distal (>10kb) Multiome | 234 |
Genomic view of the CLCN2 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.