This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]
Transcription factors with Perturb-seq knockdown data for CLN6. 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 = CLN6 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 CLN6, 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 |
|---|---|---|---|---|
| chr15:67,839,939–67,840,842 | 389.2 kb | Distal (>10kb) Multiome HiCAR | 902 | |
| chr15:67,967,988–67,968,440 | 261.3 kb | Distal (>10kb) Multiome | 234 | |
| chr15:68,053,850–68,055,256 | 175.2 kb | Distal (>10kb) Multiome | 832 | |
| chr15:68,229,045–68,230,269 | 184 bp | At TSS Multiome | 889 | |
| chr15:68,256,694–68,257,399 | 27.6 kb | Distal (>10kb) Multiome | 551 | |
| chr15:68,277,201–68,278,718 | 48.4 kb | Distal (>10kb) Multiome | 1100 | |
| chr15:68,431,141–68,432,391 | 202.7 kb | Distal (>10kb) Multiome | 295 | |
| chr15:68,542,811–68,543,454 | 313.6 kb | Distal (>10kb) Multiome | 155 |
Genomic view of the CLN6 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.