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LOC127397402 hESC enhancers GRCh37_chr3:48955152-48955902 and GRCh37_chr3:48955903-48956654 [ Homo sapiens (human) ]

Gene ID: 127397402, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397402
Gene description
hESC enhancers GRCh37_chr3:48955152-48955902 and GRCh37_chr3:48955903-48956654
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 two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in human embryonic stem cells, where both are marked by the H3K27ac histone modification and one is additionally marked by H3K4me1. 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, Jun 2023]
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Genomic context

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See LOC127397402 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (48917719..48919221)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48946725..48948227)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48955152..48956654)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14340 Neighboring gene PRKAR2A antisense RNA 1 Neighboring gene solute carrier family 25 member 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14341 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:48956655-48957405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48959089-48959589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48961592-48962092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48962093-48962593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19846 Neighboring gene ARIH2 opposite strand lncRNA Neighboring gene ariadne RBR E3 ubiquitin protein ligase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19847 Neighboring gene MPRA-validated peak4646 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:49000975-49001622 Neighboring gene uncharacterized LOC124909376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026394-49026957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026958-49027520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49028085-49028646 Neighboring gene uncharacterized LOC124906235 Neighboring gene prolyl 4-hydroxylase, transmembrane

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 19845
  • ATAC-STARR-seq lymphoblastoid silent region 14342
  • ATAC-STARR-seq lymphoblastoid silent region 14343
  • H3K27ac hESC enhancer GRCh37_chr3:48955903-48956654
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48955152-48955902

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_099371.2 

    Range
    101..1603
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    48917719..48919221
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    48946725..48948227
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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