H2AC6
H2A clustered histone 6 | H2AFL, HIST1H2AC

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 H2A 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]

Member of: DE-6 Developmental clusters: GC4
Biological processes 19 terms
DNA binding (GO:0003677)chromatin organization (GO:0006325)chromosome (GO:0005694)extracellular exosome (GO:0070062)extracellular exosome (GO:0070062)heterochromatin formation (GO:0031507)negative regulation of cell population proliferation (GO:0008285)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleosome (GO:0000786)nucleosome (GO:0000786)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)structural constituent of chromatin (GO:0030527)structural constituent of chromatin (GO:0030527)
Expression (TPM)
H2AC6 — as a Regulated Gene

TFs regulating H2AC6 0 TFs

Transcription factors with Perturb-seq knockdown data for H2AC6. 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 = H2AC6 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to H2AC6

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of H2AC6, 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
chr6:25,882,032–25,882,516 241.9 kb Distal (>10kb) Multiome 165
chr6:25,992,391–25,993,479 131.5 kb Distal (>10kb) Multiome 1012
chr6:26,020,104–26,022,401 103.8 kb Distal (>10kb) Multiome 920
chr6:26,025,866–26,027,859 97.8 kb Distal (>10kb) Multiome 1194
chr6:26,031,341–26,032,990 92.0 kb Distal (>10kb) Multiome 1083
chr6:26,033,113–26,034,309 90.5 kb Distal (>10kb) Multiome 800
chr6:26,054,926–26,057,287 68.8 kb Distal (>10kb) Multiome 1174
chr6:26,087,383–26,088,017 36.5 kb Distal (>10kb) Multiome 572
chr6:26,103,452–26,105,109 20.2 kb Distal (>10kb) Multiome 1169
chr6:26,122,481–26,124,909 1.2 kb Proximal (<10kb) Multiome 1216
chr6:26,125,788–26,126,592 2.0 kb Proximal (<10kb) Multiome 670
chr6:26,131,707–26,131,947 7.5 kb Proximal (<10kb) 37
chr6:26,156,184–26,158,744 33.9 kb Distal (>10kb) Multiome HiCAR 1310
chr6:26,171,798–26,172,499 47.8 kb Distal (>10kb) Multiome 580
chr6:26,183,128–26,184,377 59.6 kb Distal (>10kb) Multiome 311
chr6:26,187,874–26,189,538 64.9 kb Distal (>10kb) Multiome 1053
chr6:26,196,695–26,197,676 73.1 kb Distal (>10kb) Multiome HiCAR 842
chr6:26,198,203–26,200,197 75.2 kb Distal (>10kb) Multiome HiCAR 939
chr6:26,203,791–26,205,119 80.3 kb Distal (>10kb) Multiome 1071
chr6:26,214,872–26,218,468 92.7 kb Distal (>10kb) Multiome 1096
chr6:26,223,716–26,224,480 99.9 kb Distal (>10kb) Multiome 507
chr6:26,224,856–26,226,566 101.0 kb Distal (>10kb) Multiome 451
chr6:26,239,944–26,240,920 116.2 kb Distal (>10kb) Multiome 375
chr6:26,249,682–26,251,138 126.2 kb Distal (>10kb) Multiome 731
chr6:26,251,339–26,252,079 127.6 kb Distal (>10kb) Multiome 445
chr6:26,270,815–26,273,967 148.8 kb Distal (>10kb) Multiome 742
chr6:26,285,011–26,286,121 161.4 kb Distal (>10kb) Multiome 1121
chr6:26,304,972–26,305,585 181.2 kb Distal (>10kb) Multiome 586
chr6:26,312,505–26,313,475 188.8 kb Distal (>10kb) Multiome 896
chr6:26,322,092–26,323,232 198.5 kb Distal (>10kb) Multiome 811
chr6:26,327,476–26,328,318 204.0 kb Distal (>10kb) Multiome 716
chr6:26,341,545–26,342,139 217.6 kb Distal (>10kb) Multiome 716
chr6:26,365,073–26,365,647 241.1 kb Distal (>10kb) Multiome 587
chr6:26,382,957–26,383,951 259.0 kb Distal (>10kb) Multiome 448
chr6:26,421,258–26,421,866 297.2 kb Distal (>10kb) Multiome 473
chr6:27,132,200–27,134,276 1008.7 kb Distal (>10kb) Multiome HiCAR 975
chr6:27,139,091–27,140,128 1015.2 kb Distal (>10kb) Multiome HiCAR 662
chr6:27,809,816–27,810,576 1685.9 kb Distal (>10kb) Multiome HiCAR 914
chr6:27,813,688–27,816,146 1690.8 kb Distal (>10kb) Multiome HiCAR 564
chr6:27,836,792–27,839,128 1714.3 kb Distal (>10kb) Multiome HiCAR 1131
chr6:27,865,093–27,868,152 1741.1 kb Distal (>10kb) Multiome HiCAR 744

Genome Browser

Genomic view of the H2AC6 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.

chr6:25,872,032 – 27,878,152
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
Huangfu Lab · Publications · Resources · Contact