This gene encodes a chromatin-associated protein involved in the regulation of gene transcription, integration of retroviruses into chromosomes, and the metastatic progression of cancer cells. The encoded protein preferentially binds to the minor groove of AT-rich regions in double-stranded DNA. Multiple transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene have been identified on multiple chromosomes. [provided by RefSeq, Jan 2016]
Transcription factors with Perturb-seq knockdown data for HMGA1. 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 = HMGA1 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 HMGA1, 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 |
|---|---|---|---|---|
| chr6:33,950,527–33,951,235 | 286.1 kb | Distal (>10kb) Multiome | 82 | |
| chr6:34,052,159–34,053,582 | 183.7 kb | Distal (>10kb) Multiome | 133 | |
| chr6:34,056,249–34,056,753 | 180.4 kb | Distal (>10kb) Multiome | 192 | |
| chr6:34,143,812–34,144,483 | 92.7 kb | Distal (>10kb) Multiome | 304 | |
| chr6:34,144,948–34,146,170 | 91.3 kb | Distal (>10kb) Multiome | 310 | |
| chr6:34,196,308–34,196,855 | 40.5 kb | Distal (>10kb) Multiome | 723 | |
| chr6:34,202,245–34,203,164 | 34.1 kb | Distal (>10kb) Multiome | 90 | |
| chr6:34,223,440–34,224,542 | 12.9 kb | Distal (>10kb) Multiome | 795 | |
| chr6:34,227,295–34,227,501 | 9.4 kb | Proximal (<10kb) | 156 | |
| chr6:34,234,536–34,237,980 | 36 bp | At TSS Multiome | 1100 | |
| chr6:34,238,090–34,238,354 | 1.2 kb | Proximal (<10kb) | 881 | |
| chr6:34,246,464–34,249,721 | 12.3 kb | Distal (>10kb) Multiome | 1030 | |
| chr6:34,391,718–34,393,315 | 155.8 kb | Distal (>10kb) Multiome | 1033 | |
| chr6:34,425,555–34,426,314 | 189.2 kb | Distal (>10kb) Multiome | 859 | |
| chr6:34,457,890–34,458,608 | 221.3 kb | Distal (>10kb) Multiome | 192 | |
| chr6:34,465,686–34,466,203 | 229.1 kb | Distal (>10kb) Multiome HiCAR | 319 | |
| chr6:34,527,078–34,527,644 | 290.4 kb | Distal (>10kb) Multiome | 606 | |
| chr6:34,531,348–34,532,578 | 295.1 kb | Distal (>10kb) Multiome | 150 |
Genomic view of the HMGA1 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.