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LOC127397481 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231316-50231832 [ Homo sapiens (human) ]

Gene ID: 127397481, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397481
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231316-50231832
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 primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 LOC127397481 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 (50193883..50194411)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50223215..50223743)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50231316..50231844)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak4650 silencer Neighboring gene RNA binding motif protein 5 Neighboring gene RBM5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50157731-50158609 Neighboring gene SEMA3F antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50158610-50159487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50160473-50160973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50162997-50163986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50170449-50170950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50172709-50173300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50177671-50178232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50178233-50178794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50188081-50188752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14381 Neighboring gene basic proline-rich protein-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14382 Neighboring gene Sharpr-MPRA regulatory region 10077 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:50207171-50207381 Neighboring gene semaphorin 3F Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50207797-50208770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50230799-50231315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50231833-50232348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50232401-50232932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14384 Neighboring gene G protein subunit alpha transducin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50246621-50247149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50250030-50250839 Neighboring gene solute carrier family 38 member 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257474-50257974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257975-50258475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50263389-50264198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14385 Neighboring gene microRNA 5787 Neighboring gene G protein subunit alpha i2

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 19889

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_099450.2 

    Range
    101..629
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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
    50193883..50194411
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50223215..50223743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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