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LOC127397322 H3K4me1 hESC enhancer GRCh37_chr3:47007588-47008518 [ Homo sapiens (human) ]

Gene ID: 127397322, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397322
Gene description
H3K4me1 hESC enhancer GRCh37_chr3:47007588-47008518
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 in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC127397322 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46966098..46967028)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46982471..46983401)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47007588..47008518)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46966125-46966626 Neighboring gene BLVRB pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19800 Neighboring gene coiled-coil domain containing 12 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46972095-46972610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:46972611-46973126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46975255-46976022 Neighboring gene Sharpr-MPRA regulatory region 2536 Neighboring gene uncharacterized LOC124909375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981287-46981788 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46981789-46982288 Neighboring gene Sharpr-MPRA regulatory region 10220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47002103-47002604 Neighboring gene NANOG hESC enhancer GRCh37_chr3:47006121-47006678 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47008519-47009448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47016719-47017421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47017422-47018123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47018827-47019527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47021430-47022210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47022211-47022991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47026300-47027052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19806 Neighboring gene neurobeachin like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47039103-47039996 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47050749-47051546 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47051547-47052343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47054299-47054798 Neighboring gene neurotrophin receptor associated death domain, pseudogene

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, 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

  • ReSE screen-validated silencer GRCh37_chr3:47008050-47008221

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_099291.1 

    Range
    101..1031
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    46966098..46967028
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    46982471..46983401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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