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LOC127890412 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10340651-10341365 [ Homo sapiens (human) ]

Gene ID: 127890412, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127890412
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10340651-10341365
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 an enhancer that was validated 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. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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]
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Genomic context

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See LOC127890412 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 (10229956..10230689)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10356079..10356816)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10340632..10341365)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:10246117-10247316 Neighboring gene DNA methyltransferase 1 Neighboring gene origin of replication in DNMT1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10294611-10295111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10310838-10311338 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10330242-10330742 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10330743-10331243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13946 Neighboring gene sphingosine-1-phosphate receptor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13947 Neighboring gene Sharpr-MPRA regulatory region 3154 Neighboring gene microRNA 4322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10060 Neighboring gene H3K27ac hESC enhancers GRCh37_chr19:10362245-10362818 and GRCh37_chr19:10362819-10363392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13951 Neighboring gene mitochondrial ribosomal protein L4 Neighboring gene Sharpr-MPRA regulatory region 14536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13953 Neighboring gene lncRNA inflammatory and mucous response associated, antisense to ICAM1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13954 Neighboring gene intercellular adhesion molecule 1 Neighboring gene ICAM4 antisense RNA 1

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. 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
  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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 13945
  • ATAC-STARR-seq lymphoblastoid silent region 10058

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_140348.2 

    Range
    101..834
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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
    10229956..10230689
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    10356079..10356816
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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