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LOC127457609 H3K4me1 hESC enhancer GRCh37_chr7:128578271-128578854 [ Homo sapiens (human) ]

Gene ID: 127457609, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127457609
Gene description
H3K4me1 hESC enhancer GRCh37_chr7:128578271-128578854
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 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 LOC127457609 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (128937794..128938800)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130250720..130251726)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128577848..128578854)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:128531177-128531767 Neighboring gene uncharacterized LOC105375497 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:128532717-128533916 Neighboring gene kielin cysteine rich BMP regulator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128543906-128544411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128544412-128544916 Neighboring gene filamin C pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128569307-128569807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18620 Neighboring gene Sharpr-MPRA regulatory region 2205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26613 Neighboring gene interferon regulatory factor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26615 Neighboring gene transportin 3 Neighboring gene RNA, 7SL, cytoplasmic 306, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr7:128622104-128622662 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_97543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128669474-128669974 Neighboring gene ornithine decarboxylase 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. 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 18621

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_112383.2 

    Range
    101..1107
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    128937794..128938800
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    130250720..130251726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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