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LOC127883238 H3K4me1 hESC enhancer GRCh37_chr16:14499557-14500058 [ Homo sapiens (human) ]

Gene ID: 127883238, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127883238
Gene description
H3K4me1 hESC enhancer GRCh37_chr16:14499557-14500058
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 primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. 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 LOC127883238 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 (14405700..14406201)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (14443325..14443826)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (14499557..14500058)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory regions 8431 and 11785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10494 Neighboring gene MIR193b-365a host gene Neighboring gene microRNA 365a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10495 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:14447139-14447668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14458211-14458712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14466520-14467096 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:14468174-14468349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14469696-14470196 Neighboring gene long intergenic non-protein coding RNA 2130 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:14487195-14487694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10498 Neighboring gene Sharpr-MPRA regulatory region 5329 Neighboring gene Sharpr-MPRA regulatory region 2182 Neighboring gene long intergenic non-protein coding RNA 3107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:14539490-14539990 Neighboring gene Sharpr-MPRA regulatory region 750 Neighboring gene poly(A)-specific ribonuclease Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:14579525-14580460 Neighboring gene uncharacterized LOC105371094

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 7233

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_133204.1 

    Range
    101..602
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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
    14405700..14406201
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    14443325..14443826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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