This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
Transcription factors with Perturb-seq knockdown data for MSH2. 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 = MSH2 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 MSH2, 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 |
|---|---|---|---|---|
| chr2:47,174,954–47,177,223 | 226.4 kb | Distal (>10kb) Multiome | 1239 | |
| chr2:47,272,083–47,272,830 | 130.6 kb | Distal (>10kb) Multiome | 744 | |
| chr2:47,309,704–47,310,671 | 93.0 kb | Distal (>10kb) Multiome | 599 | |
| chr2:47,344,928–47,345,791 | 57.9 kb | Distal (>10kb) Multiome | 714 | |
| chr2:47,357,404–47,357,893 | 45.5 kb | Distal (>10kb) Multiome | 106 | |
| chr2:47,368,887–47,370,156 | 33.9 kb | Distal (>10kb) Multiome | 897 | |
| chr2:47,401,975–47,403,688 | 114 bp | At TSS Multiome | 1037 | |
| chr2:47,569,846–47,572,135 | 168.1 kb | Distal (>10kb) Multiome | 861 | |
| chr2:47,687,986–47,688,838 | 285.2 kb | Distal (>10kb) Multiome | 108 | |
| chr2:47,695,400–47,699,248 | 295.6 kb | Distal (>10kb) Multiome | 441 | |
| chr2:47,759,506–47,760,474 | 356.9 kb | Distal (>10kb) Multiome HiCAR | 166 | |
| chr2:47,782,231–47,784,581 | 380.9 kb | Distal (>10kb) Multiome HiCAR | 1079 |
Genomic view of the MSH2 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.