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LOC123522806 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139525474-139526020 [ Homo sapiens (human) ]

Gene ID: 123522806, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123522806
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139525474-139526020
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. A subregion was also validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140145851..140146435)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140670944..140671528)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (139525709..139526003)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139494224-139494861 Neighboring gene purine rich element binding protein A Neighboring gene IgA inducing protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139526021-139526567 Neighboring gene uncharacterized LOC124901086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139533596-139534255 Neighboring gene uncharacterized LOC101929719 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:139549390-139549585 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16446 Neighboring gene cysteine rich transmembrane module containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:139618811-139619649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139620488-139621326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:139621327-139622163

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. 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
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

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 silent region 16445
  • Sharpr-MPRA regulatory region 8105

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_077835.3 

    Range
    101..685
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    140145851..140146435
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    140670944..140671528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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