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LOC127407314 H3K27ac hESC enhancer GRCh37_chr6:137540162-137540892 [ Homo sapiens (human) ]

Gene ID: 127407314, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127407314
Gene description
H3K27ac hESC enhancer GRCh37_chr6:137540162-137540892
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 region 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. This locus also includes three accessible chromatin subregions, two of which were validated as silencers and one as an enhancer based on their ability to repress or 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 LOC127407314 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 (137219025..137219855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (138407518..138408348)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (137540162..137540992)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:137322965-137323508 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90349 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90351 Neighboring gene interleukin 20 receptor subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17579 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137382319-137382457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25128 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137410449-137410629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25131 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90355 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25133 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90359 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90362 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137492881-137493639 Neighboring gene interleukin 22 receptor subunit alpha 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90370 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:137500946-137502145 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25139 Neighboring gene interferon gamma receptor 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137618853-137619479 Neighboring gene uncharacterized LOC105378017 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137636227-137636827 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:137672426-137672621 Neighboring gene FOXA motif-containing MPRA enhancer 183 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90385 Neighboring gene uncharacterized LOC102723633 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:137744471-137745316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25140

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. 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
  2. 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 25136
  • ATAC-STARR-seq lymphoblastoid silent region 17581
  • ATAC-STARR-seq lymphoblastoid silent region 17582

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_109285.2 

    Range
    101..931
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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
    137219025..137219855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    138407518..138408348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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