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LOC127397125 H3K4me1 hESC enhancer GRCh37_chr3:39144473-39144972 [ Homo sapiens (human) ]

Gene ID: 127397125, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127397125
Gene description
H3K4me1 hESC enhancer GRCh37_chr3:39144473-39144972
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC127397125 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 (39102982..39103481)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (39115146..39115645)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39144473..39144972)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene sodium voltage-gated channel alpha subunit 11 Neighboring gene RNA, U6 small nuclear 1227, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39092668-39093540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14216 Neighboring gene WD repeat domain 48 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14217 Neighboring gene golgi reassembly stacking protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14218 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:39166834-39167009 Neighboring gene tetratricopeptide repeat domain 21A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:39177733-39178638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39187593-39188286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39188287-39188980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19693 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39193407-39194267 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39194268-39195127 Neighboring gene uncharacterized LOC101928263 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39195907-39196406 Neighboring gene microRNA 6822 Neighboring gene cysteine and serine rich nuclear protein 1

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 active region 19691

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_099094.1 

    Range
    101..600
    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
    39102982..39103481
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    39115146..39115645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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