This gene encodes a sodium-hydrogen exchanger that is amember of the solute carrier family 9. The encoded protein localizes to early and recycling endosomes and may be involved in regulating endosomal pH and volume. Defects in this gene are associated with X-linked syndromic cognitive disability, Christianson type. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
Transcription factors with Perturb-seq knockdown data for SLC9A6. 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 = SLC9A6 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 SLC9A6, 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:135,973,479–135,974,209 | 11.2 kb | Distal (>10kb) Multiome | 624 | |
| chrX:135,974,362–135,974,748 | 522 bp | At TSS | 65 | |
| chrX:135,985,105–135,985,952 | 30 bp | At TSS Multiome | 442 | |
| chrX:136,146,916–136,147,890 | 162.0 kb | Distal (>10kb) Multiome | 231 | |
| chrX:136,250,770–136,251,801 | 265.9 kb | Distal (>10kb) Multiome | 399 |
Genomic view of the SLC9A6 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.