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LOC127273152 H3K27ac hESC enhancers GRCh37_chr2:42587530-42588274 and GRCh37_chr2:42588275-42589018 [ Homo sapiens (human) ]

Gene ID: 127273152, updated on 12-Sep-2024

Summary

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Gene symbol
LOC127273152
Gene description
H3K27ac hESC enhancers GRCh37_chr2:42587530-42588274 and GRCh37_chr2:42588275-42589018
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 two enhancers that were validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where they are marked by the H3K27ac histone modification. This locus also includes three accessible chromatin subregions, two of which were validated as enhancers and one as a silencer based on their ability to activate or 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, Jun 2023]
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Genomic context

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See LOC127273152 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 (42360390..42361878)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (42365804..42367296)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (42587530..42589018)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42328443-42329270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15642 Neighboring gene MPRA-validated peak3676 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15643 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42359847-42360820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42360821-42361792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42367980-42368777 Neighboring gene EML4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42396227-42396879 Neighboring gene HNF1 motif-containing MPRA enhancer 263/264 Neighboring gene EMAP like 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42567158-42568066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42568067-42568974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15648 Neighboring gene cytochrome c oxidase subunit 7A2 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:42597071-42597572 Neighboring gene potassium voltage-gated channel modifier subfamily G member 3 Neighboring gene small nucleolar RNA SNORD75 Neighboring gene voltage dependent anion channel 1 pseudogene 13

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 15646
  • ATAC-STARR-seq lymphoblastoid active region 15647
  • ATAC-STARR-seq lymphoblastoid silent region 11403
  • H3K27ac hESC enhancer GRCh37_chr2:42587530-42588274
  • H3K27ac hESC enhancer GRCh37_chr2:42588275-42589018

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_095003.2 

    Range
    101..1589
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    42360390..42361878
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    42365804..42367296
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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