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LOC112935905 H3K27ac hESC enhancer GRCh37_chr3:169490847-169491350 [ Homo sapiens (human) ]

Gene ID: 112935905, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112935905
Gene description
H3K27ac hESC enhancer GRCh37_chr3:169490847-169491350
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 includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. 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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). 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 LOC112935905 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (169772936..169773562)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (172557161..172557787)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (169490724..169491350)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169486144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20783 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169487501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20784 Neighboring gene tRNA-Val (anticodon AAC) 1-1 Neighboring gene actin related protein T3 Neighboring gene myoneurin Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169512145 Neighboring gene leucine rich repeat containing 34 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169524016 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 3:169526272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20787 Neighboring gene leucine rich repeats and IQ motif containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20788 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:169564950-169565107 Neighboring gene leucine rich repeat containing 31

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 20785
  • Sharpr-MPRA regulatory region 7912

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_061421.3 

    Range
    101..727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    169772936..169773562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    172557161..172557787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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