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LOC127890416 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10402483-10403475 [ Homo sapiens (human) ]

Gene ID: 127890416, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127890416
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10402483-10403475
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 was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. A genetic variant at this locus, rs2228615, may be associated with coronavirus disease 2019 (COVID-19) and hypertension. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
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Genomic context

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See LOC127890416 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10291807..10292799)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10417919..10418911)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10402483..10403475)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene lncRNA inflammatory and mucous response associated, antisense to ICAM1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13953 Neighboring gene intercellular adhesion molecule 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10397303-10398272 Neighboring gene ICAM4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10062 Neighboring gene intercellular adhesion molecule 4 (Landsteiner-Wiener blood group) Neighboring gene intercellular adhesion molecule 5 Neighboring gene CRISPRi-validated cis-regulatory element chr19.1775 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:10415538-10416737 Neighboring gene FDX2-ZGLP1 readthrough Neighboring gene zinc finger GATA like protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10064 Neighboring gene ferredoxin 2

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. Identifying shared genetic loci between coronavirus disease 2019 and cardiovascular diseases based on cross-trait meta-analysis. Guo H, et al. Front Microbiol, 2022. PMID 36187959, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article
  3. 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 10063

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_140352.1 

    Range
    101..1093
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    10291807..10292799
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    10417919..10418911
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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