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LOC127404990 H3K27ac hESC enhancer GRCh37_chr5:179160227-179160727 [ Homo sapiens (human) ]

Gene ID: 127404990, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127404990
Gene description
H3K27ac hESC enhancer GRCh37_chr5:179160227-179160727
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 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 LOC127404990 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (179733226..179733726)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (180288411..180288911)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (179160227..179160727)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179105237-179105852 Neighboring gene chibby family member 3 Neighboring gene calnexin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23757 Neighboring gene high mobility group box 3 pseudogene 22 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:179131736-179132236 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:179132237-179132737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16733 Neighboring gene mastermind like transcriptional coactivator 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:179176749-179177249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23759 Neighboring gene MPRA-validated peak5609 silencer Neighboring gene NADH:ubiquinone oxidoreductase subunit A12 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179220175-179220802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179222110-179222782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16737 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:179223416-179223627 Neighboring gene leukotriene C4 synthase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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 16734

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_106935.1 

    Range
    101..601
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    179733226..179733726
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107298.1 Reference GRCh38.p14 PATCHES

    Range
    498806..499306
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    180288411..180288911
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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