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LOC121852975 H3K27ac hESC enhancer GRCh37_chr19:6065893-6066394 [ Homo sapiens (human) ]

Gene ID: 121852975, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852975
Gene description
H3K27ac hESC enhancer GRCh37_chr19:6065893-6066394
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 H3K27ac 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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [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 (6065882..6066383)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6053432..6053933)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (6065909..6066203)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13818 Neighboring gene RAN binding protein 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5939785-5939965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5944489-5945129 Neighboring gene calcyphosine Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5952179-5952738 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:5953075-5954274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5957025-5957534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5958162-5958810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5959460-5960108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5960757-5961406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13819 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5962704-5963351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5963485-5964036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5964037-5964587 Neighboring gene Sharpr-MPRA regulatory region 310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9942 Neighboring gene RANBP3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6015021-6015520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6018397-6018898 Neighboring gene regulatory factor X2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6074378-6075171 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6086791-6087292 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6087293-6087792 Neighboring gene ribosomal protein L32 pseudogene 37 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6092583-6093288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6109025-6109525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9944 Neighboring gene uncharacterized LOC105372255 Neighboring gene Sharpr-MPRA regulatory region 9390 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6134642-6135545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6135546-6136448 Neighboring gene acyl-CoA synthetase bubblegum family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9945

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 343

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_076082.2 

    Range
    101..602
    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
    6065882..6066383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6053432..6053933
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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