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LOC121740631 H3K4me1 hESC enhancer GRCh37_chr5:153920920-153921422 [ Homo sapiens (human) ]

Gene ID: 121740631, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121740631
Gene description
H3K4me1 hESC enhancer GRCh37_chr5:153920920-153921422
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (154541360..154541862)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (155075339..155075841)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (153921069..153921363)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr5:153855265-153855452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153855607-153856461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153859235-153859744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153863719-153864218 Neighboring gene heart and neural crest derivatives expressed 1 Neighboring gene VPS37A, ESCRT-I subunit pseudogene Neighboring gene myotubularin related protein 7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153898879-153899379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:153900569-153901172 Neighboring gene CIR1 pseudogene 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_83489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:153962321-153962904 Neighboring gene CIR1P1-LARP1 intergenic CAGE-defined high expression enhancer Neighboring gene microRNA 3141

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 8942

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_075693.2 

    Range
    101..603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    154541360..154541862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    155075339..155075841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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