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LOC127397490 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50272904-50273514 [ Homo sapiens (human) ]

Gene ID: 127397490, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397490
Gene description
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50272904-50273514
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 includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 LOC127397490 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 (50235472..50236411)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50264810..50265749)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50272904..50273843)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50246621-50247149 Neighboring gene solute carrier family 38 member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50250030-50250839 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257474-50257974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50257975-50258475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50263389-50264198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19890 Neighboring gene microRNA 5787 Neighboring gene G protein subunit alpha i2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50272293-50272903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50275957-50276566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280231-50280841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280842-50281451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283071-50283786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283787-50284502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50297648-50298153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50298661-50299165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50301209-50301784 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:50301785-50302358 and GRCh37_chr3:50302359-50302934 Neighboring gene SEMA3B antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19897 Neighboring gene semaphorin 3B Neighboring gene microRNA 6872

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 14386

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_099459.2 

    Range
    101..1040
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    50235472..50236411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    50264810..50265749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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