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LOC127824354 H3K4me1 hESC enhancer GRCh37_chr12:57029126-57029638 [ Homo sapiens (human) ]

Gene ID: 127824354, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127824354
Gene description
H3K4me1 hESC enhancer GRCh37_chr12:57029126-57029638
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 H3K4me1 histone modification. 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 LOC127824354 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56635138..56635854)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56603135..56603851)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57028922..57029638)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, H/ACA box 105C Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56916039-56916782 Neighboring gene RNA binding motif single stranded interacting protein 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56959127-56959665 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56959666-56960203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6503 Neighboring gene RNA, U6 small nuclear 343, pseudogene Neighboring gene bromodomain adjacent to zinc finger domain 2A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57020987-57021488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6509 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:57030665-57031176 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57038866-57039576 Neighboring gene ATP synthase F1 subunit beta Neighboring gene small nucleolar RNA, C/D box 59B Neighboring gene small nucleolar RNA, C/D box 59A

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 6508

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_125871.2 

    Range
    101..817
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56635138..56635854
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56603135..56603851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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