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LOC127272911 H3K4me1 hESC enhancer GRCh37_chr2:26785229-26785729 [ Homo sapiens (human) ]

Gene ID: 127272911, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127272911
Gene description
H3K4me1 hESC enhancer GRCh37_chr2:26785229-26785729
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 primed 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 LOC127272911 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (26562361..26562861)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (26601519..26602019)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (26785229..26785729)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15472 Neighboring gene dynein regulatory complex subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26680500-26681070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26681071-26681640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26683329-26684034 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:26685720-26686919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26703326-26703826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26704893-26705698 Neighboring gene otoferlin Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26712674-26712916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26728504-26729004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26734217-26735140 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26744163-26744328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26759696-26760624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26760625-26761553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26765926-26766660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26780985-26781778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26781779-26782571 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26788976-26789481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26799126-26799700 Neighboring gene ciliary microtubule inner protein 2C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26813715-26814459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26814460-26815203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26821036-26821536 Neighboring gene calcium and integrin binding family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26856058-26856598 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:26878417-26879132 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26888285-26888441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:26892685-26893186 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:26894826-26895015 Neighboring gene Sharpr-MPRA regulatory region 9124 Neighboring gene ribosomal protein L37 pseudogene 11

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 11275

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_094762.1 

    Range
    101..601
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    26562361..26562861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    26601519..26602019
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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