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LOC106799839 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7070721-7071520 [ Homo sapiens (human) ]

Gene ID: 106799839, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106799839
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7070721-7071520
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. A subregion, which is not conserved between human and mouse at the sequence level, can also function as an enhancer in human Jurkat T cells. The chromatin structure of that subregion represents a histone acetylation island in human T cells based on the diacetylation of histone H3 at lysines 9 and 14. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC106799839 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6961558..6962357)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6975032..6975831)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7070743..7071261)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:7052993-7053572 and GRCh37_chr12:7053573-7054152 Neighboring gene chromosome 12 open reading frame 57 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7054402-7055012 Neighboring gene RNA, U7 small nuclear 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7055013-7055621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4196 Neighboring gene protein tyrosine phosphatase non-receptor type 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7059817-7060752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7060753-7061686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7061687-7062621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7069919-7070720 Neighboring gene uncharacterized LOC105369634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7071521-7072322 Neighboring gene MIR200C and MIR141 host gene Neighboring gene microRNA 200c Neighboring gene microRNA 141

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. Ansari-Lari MA, et al. Genome Res, 1996 Apr. PMID 8723724
  2. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. Ansari-Lari MA, et al. Genome Res, 1997 Mar. PMID 9074930
  3. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Roh TY, et al. Genome Res, 2007 Jan. PMID 17135569, Free PMC Article
  4. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Roh TY, et al. Genes Dev, 2005 Mar 1. PMID 15706033, Free PMC Article
  5. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 5909
  • non-conserved AI 91
  • nonconserved acetylation island sequence 91 enhancer

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_046138.2 

    Range
    101..900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6961558..6962357
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6975032..6975831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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