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LOC121852977 H3K4me1 hESC enhancer GRCh37_chr19:11662408-11663379 [ Homo sapiens (human) ]

Gene ID: 121852977, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852977
Gene description
H3K4me1 hESC enhancer GRCh37_chr19:11662408-11663379
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 primed 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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (11551593..11552564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11679100..11680071)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11662749..11663043)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ECSIT signaling integrator Neighboring gene ribosomal protein S12 pseudogene 32 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11648637-11649582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14022 Neighboring gene calponin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14024 Neighboring gene Sharpr-MPRA regulatory region 7075 Neighboring gene elongation factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14025 Neighboring gene uncharacterized LOC124904638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11687946-11688558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11688559-11689170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10121 Neighboring gene acid phosphatase 5, tartrate resistant

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 1596

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_076085.2 

    Range
    101..1072
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    11551593..11552564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    11679100..11680071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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