Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]
Transcription factors with Perturb-seq knockdown data for H2BC9. 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 = H2BC9 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 H2BC9, 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 |
|---|---|---|---|---|
| chr6:25,992,391–25,993,479 | 258.9 kb | Distal (>10kb) Multiome | 1012 | |
| chr6:26,020,104–26,022,401 | 231.2 kb | Distal (>10kb) Multiome | 920 | |
| chr6:26,025,866–26,027,859 | 225.3 kb | Distal (>10kb) Multiome | 1194 | |
| chr6:26,031,341–26,032,990 | 219.5 kb | Distal (>10kb) Multiome | 1083 | |
| chr6:26,033,113–26,034,309 | 217.9 kb | Distal (>10kb) Multiome | 800 | |
| chr6:26,054,926–26,057,287 | 196.3 kb | Distal (>10kb) Multiome | 1174 | |
| chr6:26,087,383–26,088,017 | 163.9 kb | Distal (>10kb) Multiome | 572 | |
| chr6:26,103,452–26,105,109 | 147.7 kb | Distal (>10kb) Multiome | 1169 | |
| chr6:26,122,481–26,124,909 | 128.7 kb | Distal (>10kb) Multiome | 1216 | |
| chr6:26,125,788–26,126,592 | 125.4 kb | Distal (>10kb) Multiome | 670 | |
| chr6:26,156,184–26,158,744 | 93.5 kb | Distal (>10kb) Multiome | 1310 | |
| chr6:26,171,798–26,172,499 | 79.6 kb | Distal (>10kb) Multiome | 580 | |
| chr6:26,183,128–26,184,377 | 67.9 kb | Distal (>10kb) Multiome | 311 | |
| chr6:26,187,874–26,189,538 | 62.5 kb | Distal (>10kb) Multiome | 1053 | |
| chr6:26,196,695–26,197,676 | 54.3 kb | Distal (>10kb) Multiome | 842 | |
| chr6:26,198,203–26,200,197 | 52.2 kb | Distal (>10kb) Multiome | 939 | |
| chr6:26,203,791–26,205,119 | 47.1 kb | Distal (>10kb) Multiome | 1071 | |
| chr6:26,214,872–26,218,468 | 34.8 kb | Distal (>10kb) Multiome | 1096 | |
| chr6:26,223,716–26,224,480 | 27.6 kb | Distal (>10kb) Multiome | 507 | |
| chr6:26,224,856–26,226,566 | 26.4 kb | Distal (>10kb) Multiome | 451 | |
| chr6:26,239,944–26,240,920 | 11.3 kb | Distal (>10kb) Multiome | 375 | |
| chr6:26,243,607–26,244,004 | 7.6 kb | Proximal (<10kb) | 49 | |
| chr6:26,249,068–26,249,398 | 2.2 kb | Proximal (<10kb) | 50 | |
| chr6:26,249,682–26,251,138 | 1.3 kb | Proximal (<10kb) Multiome | 731 | |
| chr6:26,251,339–26,252,079 | 130 bp | At TSS Multiome | 445 | |
| chr6:26,270,815–26,273,967 | 21.3 kb | Distal (>10kb) Multiome | 742 | |
| chr6:26,285,011–26,286,121 | 34.0 kb | Distal (>10kb) Multiome | 1121 | |
| chr6:26,304,972–26,305,585 | 53.8 kb | Distal (>10kb) Multiome | 586 | |
| chr6:26,312,505–26,313,475 | 61.4 kb | Distal (>10kb) Multiome | 896 | |
| chr6:26,322,092–26,323,232 | 71.0 kb | Distal (>10kb) Multiome | 811 | |
| chr6:26,327,476–26,328,318 | 76.5 kb | Distal (>10kb) Multiome | 716 | |
| chr6:26,341,545–26,342,139 | 90.2 kb | Distal (>10kb) Multiome | 716 | |
| chr6:26,365,073–26,365,647 | 113.7 kb | Distal (>10kb) Multiome | 587 | |
| chr6:26,382,957–26,383,951 | 131.6 kb | Distal (>10kb) Multiome | 448 | |
| chr6:26,421,258–26,421,866 | 169.8 kb | Distal (>10kb) Multiome | 473 | |
| chr6:26,457,390–26,458,395 | 206.3 kb | Distal (>10kb) Multiome | 525 | |
| chr6:26,473,842–26,474,357 | 222.5 kb | Distal (>10kb) Multiome | 487 | |
| chr6:26,520,324–26,522,398 | 269.3 kb | Distal (>10kb) Multiome | 1082 | |
| chr6:26,532,765–26,533,409 | 281.5 kb | Distal (>10kb) Multiome | 830 | |
| chr6:26,537,180–26,538,912 | 286.7 kb | Distal (>10kb) Multiome | 1114 | |
| chr6:26,550,296–26,550,971 | 299.1 kb | Distal (>10kb) Multiome | 695 | |
| chr6:27,132,200–27,134,276 | 881.3 kb | Distal (>10kb) Multiome HiCAR | 975 | |
| chr6:27,139,091–27,140,128 | 887.7 kb | Distal (>10kb) Multiome HiCAR | 662 | |
| chr6:27,145,480–27,148,111 | 895.4 kb | Distal (>10kb) Multiome HiCAR | 951 | |
| chr6:27,806,645–27,808,975 | 1556.4 kb | Distal (>10kb) Multiome HiCAR | 963 | |
| chr6:27,809,816–27,810,576 | 1558.5 kb | Distal (>10kb) Multiome HiCAR | 914 | |
| chr6:27,813,688–27,816,146 | 1563.3 kb | Distal (>10kb) Multiome HiCAR | 564 | |
| chr6:27,865,093–27,868,152 | 1613.7 kb | Distal (>10kb) Multiome HiCAR | 744 | |
| chr6:27,870,957–27,872,527 | 1620.6 kb | Distal (>10kb) Multiome HiCAR | 426 | |
| chr6:27,872,808–27,873,995 | 1622.0 kb | Distal (>10kb) Multiome HiCAR | 372 |
Genomic view of the H2BC9 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.