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LOC121627916 H3K4me1 hESC enhancer GRCh37_chr20:62751601-62752100 [ Homo sapiens (human) ]

Gene ID: 121627916, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627916
Gene description
H3K4me1 hESC enhancer GRCh37_chr20:62751601-62752100
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 DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC121627916 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (64120248..64120747)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65942339..65942805)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62751769..62752063)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13209 Neighboring gene MPRA-validated peak4324 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62723260-62723993 Neighboring gene LKAAEAR motif containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62723994-62724726 Neighboring gene opioid related nociceptin receptor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62732783-62733284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62738466-62738966 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62740950-62741133 Neighboring gene neuropeptides B and W receptor 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:62754467-62755666 Neighboring gene B6.7 minisatellite repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62768655-62769156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62769157-62769656 Neighboring gene uncharacterized LOC105372727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62771493-62772406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62782269-62782948 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:62782949-62784148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62790052-62790772 Neighboring gene VISTA enhancer hs2609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62809687-62810387 Neighboring gene myelin transcription factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62819145-62820082 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62820083-62821020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62842693-62843192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62854891-62855746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62857693-62858192

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 6051

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_075107.2 

    Range
    101..600
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    64120248..64120747
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187624.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    25194..25693
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65942339..65942805
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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