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LOC127892003 OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143247-50143916 [ Homo sapiens (human) ]

Gene ID: 127892003, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127892003
Gene description
OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143247-50143916
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 associates with the OCT4 and NANOG transcription factors and 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 LOC127892003 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 (49639880..49640659)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52639915..52640694)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50143137..50143916)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50087865-50088490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10923 Neighboring gene proline rich and Gla domain 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50095111-50095610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10925 Neighboring gene proline rich 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50135833-50136332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50139452-50140018 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50143917-50144586 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50144587-50145256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10927 Neighboring gene RAS related Neighboring gene SR-related CTD associated factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50158945-50159720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50161341-50162044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10929 Neighboring gene interferon regulatory factor 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50175361-50175919 Neighboring gene BCL2 like 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:50180167-50180898 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50184019-50184183 Neighboring gene protein arginine methyltransferase 1 Neighboring gene microRNA 5088

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 10926

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_141834.2 

    Range
    101..880
    Download
    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
    49639880..49640659
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    52639915..52640694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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