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LOC112577471 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109820047-109820796 [ Homo sapiens (human) ]

Gene ID: 112577471, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577471
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109820047-109820796
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It 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 was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh). 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 LOC112577471 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109277425..109278174)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109310222..109310971)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (109820089..109820383)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1437 Neighboring gene seryl-tRNA synthetase 1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:109767996-109768680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109768681-109769365 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109772336-109773132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109773133-109773930 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:109779623-109780822 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:109781947-109782361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109782763-109783458 Neighboring gene Sharpr-MPRA regulatory region 12007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109785117-109785616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109791478-109792198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1144 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:109793618-109793808 Neighboring gene VISTA enhancer hs2216 Neighboring gene cadherin EGF LAG seven-pass G-type receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109802367-109802915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109803429-109803928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109806365-109807347 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:109807766-109807952 Neighboring gene VISTA enhancer hs2263 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109826136-109826861 Neighboring gene proline and serine rich coiled-coil 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109839316-109839887 Neighboring gene myosin binding protein H like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109842955-109843465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:109843466-109843975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:109849151-109849890

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 active region 1438
  • Sharpr-MPRA regulatory region 472

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_060035.2 

    Range
    101..850
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    109277425..109278174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    109310222..109310971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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