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LOC127405289 H3K27ac hESC enhancer GRCh37_chr6:8435518-8436059 [ Homo sapiens (human) ]

Gene ID: 127405289, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127405289
Gene description
H3K27ac hESC enhancer GRCh37_chr6:8435518-8436059
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 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 histone modification. This locus also includes three accessible chromatin subregions that were validated as enhancers based on their 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. Another subregion containing a Neanderthal adaptively introgressed genetic variant was also validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 6:8435901 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC127405289 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (8435173..8435826)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (8304457..8305110)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (8435406..8436059)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374910 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:8180101-8180646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:8230067-8230588 Neighboring gene uncharacterized LOC105374911 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96039 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:8383593-8384467 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:8387849-8389048 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96052 Neighboring gene MPRA-validated peak5649 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96058 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96067 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96069 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96073 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96077 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23962 Neighboring gene uncharacterized LOC100506207 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96121 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96126 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96137 Neighboring gene solute carrier family 35 member B3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96153 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96161 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96186 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96299 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96383 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96450 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96469 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96472 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:8619731-8620403 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:8627414-8628613 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96605 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96748 Neighboring gene hepatocellular carcinoma up-regulated long non-coding RNA Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_96779 Neighboring gene uncharacterized LOC112267952

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. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23959
  • ATAC-STARR-seq lymphoblastoid active region 23960
  • ATAC-STARR-seq lymphoblastoid active region 23961
  • Neanderthal introgressed variant-containing enhancer experimental_96097

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_107260.2 

    Range
    101..754
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    8435173..8435826
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    8304457..8305110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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