The WNT gene family consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is expressed in gastric cancer cell lines. The protein encoded by this gene shows 75% amino acid identity to chicken Wnt14, which has been shown to play a central role in initiating synovial joint formation in the chick limb. This gene is clustered with another family member, WNT3A, in the chromosome 1q42 region. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for WNT9A. 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 = WNT9A 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 WNT9A, 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 |
|---|---|---|---|---|
| chr1:227,728,086–227,729,232 | 219.5 kb | Distal (>10kb) Multiome | 590 | |
| chr1:227,730,363–227,730,812 | 217.3 kb | Distal (>10kb) Multiome HiCAR | 276 | |
| chr1:227,734,745–227,735,925 | 212.6 kb | Distal (>10kb) Multiome HiCAR | 1052 | |
| chr1:227,787,209–227,789,037 | 159.7 kb | Distal (>10kb) Multiome HiCAR | 579 | |
| chr1:227,946,348–227,948,809 | 1.2 kb | Proximal (<10kb) Multiome | 645 | |
| chr1:227,953,965–227,954,186 | 6.0 kb | Proximal (<10kb) | 255 | |
| chr1:228,004,351–228,004,883 | 56.7 kb | Distal (>10kb) Multiome | 154 | |
| chr1:228,058,680–228,061,126 | 111.9 kb | Distal (>10kb) Multiome | 377 | |
| chr1:228,081,634–228,083,952 | 134.7 kb | Distal (>10kb) Multiome | 942 | |
| chr1:228,101,882–228,103,743 | 155.4 kb | Distal (>10kb) Multiome | 929 | |
| chr1:228,108,924–228,110,105 | 161.5 kb | Distal (>10kb) Multiome | 958 | |
| chr1:228,130,684–228,131,457 | 183.1 kb | Distal (>10kb) Multiome | 488 | |
| chr1:228,139,579–228,140,870 | 192.2 kb | Distal (>10kb) Multiome | 931 | |
| chr1:228,164,898–228,166,840 | 217.8 kb | Distal (>10kb) Multiome | 1011 | |
| chr1:228,174,477–228,174,893 | 226.7 kb | Distal (>10kb) Multiome | 254 | |
| chr1:228,212,247–228,214,390 | 265.2 kb | Distal (>10kb) Multiome | 604 |
Genomic view of the WNT9A 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.