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LOC127889952 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096431-2096958 [ Homo sapiens (human) ]

Gene ID: 127889952, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127889952
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096431-2096958
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 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]
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Genomic context

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See LOC127889952 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 (2096207..2096959)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2069262..2070014)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2096206..2096958)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985278 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:2028556-2029190 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2035637-2036137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2037698-2038472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9759 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2046519-2047019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2047523-2048180 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2048181-2048837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2049495-2050151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9761 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2053416-2053640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2058351-2059250 Neighboring gene MAPK interacting serine/threonine kinase 2 Neighboring gene CRISPRi-validated cis-regulatory element chr19.488 Neighboring gene CRISPRi-validated cis-regulatory element chr19.489 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2061953-2062851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2085331-2086056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2089069-2090031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13654 Neighboring gene MOB kinase activator 3A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2096959-2097484 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2104508-2104680 Neighboring gene IZUMO family member 4 Neighboring gene adaptor related protein complex 3 subunit delta 1 Neighboring gene MPRA-validated peak3230 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2141381-2141538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2144918-2145541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2145542-2146164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13657 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2150717-2150878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13658 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2151574-2152011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9771 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2165242-2165623 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:2168563-2169762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2171045-2171639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2171640-2172234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2173473-2173991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2180689-2181272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13665 Neighboring gene DOT1 like histone lysine methyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2195534-2196062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2196063-2196591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:2200246-2201219 Neighboring gene uncharacterized LOC124904611

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 silent region 9766

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_139914.2 

    Range
    101..853
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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
    2096207..2096959
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2069262..2070014
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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