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LOC127882761 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2029173-2029752 [ Homo sapiens (human) ]

Gene ID: 127882761, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127882761
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2029173-2029752
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. 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 LOC127882761 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (1979172..1979751)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (1999130..1999709)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2029173..2029752)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, H/ACA box 78 Neighboring gene small nucleolar RNA host gene 9 Neighboring gene ring finger protein 151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10249 Neighboring gene transducin beta like 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2028013-2028592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2028593-2029172 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:2029753-2030330 and GRCh37_chr16:2030331-2030910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10250 Neighboring gene NADPH oxidase organizer 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2032733-2032925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7014 Neighboring gene growth factor, augmenter of liver regeneration Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2038929-2039508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2041827-2042404 Neighboring gene synaptogyrin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2042985-2043562

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 7013

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_132728.1 

    Range
    101..680
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    1979172..1979751
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791799.1 Reference GRCh38.p14 PATCHES

    Range
    45320..45899
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    1999130..1999709
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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