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LOC127819993 H3K4me1 hESC enhancers GRCh37_chr11:548147-548965 and GRCh37_chr11:548966-549783 [ Homo sapiens (human) ]

Gene ID: 127819993, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127819993
Gene description
H3K4me1 hESC enhancers GRCh37_chr11:548147-548965 and GRCh37_chr11:548966-549783
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 active enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where both are marked by the H3K4me1 histone modification. A subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
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Genomic context

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See LOC127819993 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (548147..549783)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (595124..596768)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ribonuclease/angiogenin inhibitor 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21531 Neighboring gene leucine rich repeat containing 56 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:528505-529042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:533792-534649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:534650-535506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:535528-536235 Neighboring gene HRas proto-oncogene, GTPase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:540668-541490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:543860-544362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:544865-545366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:556675-557511 Neighboring gene lamin tail domain containing 2 Neighboring gene LMNTD2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:561773-562348 Neighboring gene Ras association domain family member 7

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr11:548147-548965
  • H3K4me1 hESC enhancer GRCh37_chr11:548966-549783
  • MPRA-validated peak1148 silencer

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_121460.2 

    Range
    101..1737
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    548147..549783
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187586.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    77787..79423
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    595124..596768
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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