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LOC127828737 H3K4me1 hESC enhancer GRCh37_chr14:103380952-103381452 [ Homo sapiens (human) ]

Gene ID: 127828737, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127828737
Gene description
H3K4me1 hESC enhancer GRCh37_chr14:103380952-103381452
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 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 LOC127828737 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (102914615..102915115)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (97150862..97151362)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (103380952..103381452)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9084 Neighboring gene TNF receptor associated factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9085 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103276021-103276180 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103294403-103294902 Neighboring gene NANOG hESC enhancer GRCh37_chr14:103307110-103307650 Neighboring gene RNA, U6 small nuclear 1316, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:103352003-103353202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103357046-103357546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103357547-103358047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103366521-103367022 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103367023-103367522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103379429-103380018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103380019-103380608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6134 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103390587-103390785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6136 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:103411482-103412681 Neighboring gene CDC42 binding protein kinase beta Neighboring gene amnion associated transmembrane protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103452779-103453413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103453414-103454047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103464738-103465284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9093 Neighboring gene Sharpr-MPRA regulatory region 6354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103486267-103486822 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103489632-103489899 Neighboring gene Sharpr-MPRA regulatory region 14595 Neighboring gene ribosomal protein L13 pseudogene 6

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 6133

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_130233.1 

    Range
    101..601
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    102914615..102915115
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    97150862..97151362
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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