Synovial sarcomas occur most frequently in the extremities around large joints. More than 90% of cases have a recurrent and specific chromosomal translocation, t(X;18)(p11.2;q11.2), in which the 5-prime end of the SS18 gene (MIM 600192) is fused in-frame to the 3-prime end of the SSX1 (MIM 312820), SSX2 (MIM 300192), or SSX4 (MIM 300326) gene. The SS18L2 gene is homologous to SS18.[supplied by OMIM, Jul 2002]
Transcription factors with Perturb-seq knockdown data for SS18L2. 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 = SS18L2 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 SS18L2, 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 |
|---|---|---|---|---|
| chr3:42,349,668–42,350,325 | 240.9 kb | Distal (>10kb) Multiome | 246 | |
| chr3:42,446,025–42,446,484 | 144.6 kb | Distal (>10kb) Multiome | 27 | |
| chr3:42,501,285–42,503,228 | 88.3 kb | Distal (>10kb) Multiome | 508 | |
| chr3:42,539,796–42,540,344 | 50.8 kb | Distal (>10kb) Multiome | 180 | |
| chr3:42,581,475–42,582,842 | 8.8 kb | Proximal (<10kb) Multiome | 889 | |
| chr3:42,590,205–42,591,365 | 114 bp | At TSS Multiome | 646 | |
| chr3:42,595,713–42,595,988 | 4.9 kb | Proximal (<10kb) | 30 | |
| chr3:42,600,083–42,601,438 | 9.8 kb | Proximal (<10kb) Multiome | 914 | |
| chr3:42,653,440–42,655,446 | 63.8 kb | Distal (>10kb) Multiome | 631 | |
| chr3:42,772,623–42,773,428 | 182.4 kb | Distal (>10kb) Multiome | 446 | |
| chr3:42,803,822–42,804,944 | 213.7 kb | Distal (>10kb) Multiome | 881 | |
| chr3:42,805,298–42,806,226 | 215.1 kb | Distal (>10kb) Multiome | 381 | |
| chr3:42,880,478–42,881,506 | 290.3 kb | Distal (>10kb) Multiome | 685 | |
| chr3:42,884,409–42,884,926 | 293.7 kb | Distal (>10kb) Multiome | 59 |
Genomic view of the SS18L2 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.