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LOC112469010 H3K4me1 hESC enhancer GRCh37_chr16:57790901-57791540 [ Homo sapiens (human) ]

Gene ID: 112469010, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112469010
Gene description
H3K4me1 hESC enhancer GRCh37_chr16:57790901-57791540
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It 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 H3K4me1 histone modification. A subregion was also validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 25:Art, potential CNV or repetitive artifacts), with weaker activity in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). 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 LOC112469010 in Genome Data Viewer
Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (57756989..57757628)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (63552146..63552785)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (57791129..57791423)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene dynein regulatory complex subunit 7 Neighboring gene MTCH2 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57767533-57768510 Neighboring gene uncharacterized LOC107984852 Neighboring gene Sharpr-MPRA regulatory region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57777601-57778101 Neighboring gene katanin regulatory subunit B1 Neighboring gene kinesin family member C3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57808554-57809132 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57809711-57810289 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57817648-57818250 Neighboring gene microRNA 6772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57818251-57818852 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:57819145-57819804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57820464-57821122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57821123-57821781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57828526-57829344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:57829345-57830161 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57835346-57836022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57836700-57837376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:57850615-57851160 Neighboring gene uncharacterized LOC388282

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 7537
  • Sharpr-MPRA regulatory region 7405

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_056838.2 

    Range
    101..740
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    57756989..57757628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    63552146..63552785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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