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LOC127826040 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:31233439-31234198 [ Homo sapiens (human) ]

Gene ID: 127826040, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127826040
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:31233439-31234198
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive 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 LOC127826040 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (30659302..30660061)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (29881341..29882100)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (31233439..31234198)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene high mobility group box 1 Neighboring gene microfibril associated protein 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3331 Neighboring gene PTPN2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7542 Neighboring gene ubiquitin specific peptidase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5236 Neighboring gene tRNA-Asn (anticodon GTT) 2-4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7544 Neighboring gene MPRA-validated peak2063 silencer Neighboring gene uncharacterized LOC124903146 Neighboring gene arachidonate 5-lipoxygenase activating protein Neighboring gene ReSE screen-validated silencer GRCh37_chr13:31312711-31312902 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:31317812-31319011

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 7543

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_127551.1 

    Range
    101..860
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    30659302..30660061
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    29881341..29882100
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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