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LOC108254669 H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197 [ Homo sapiens (human) ]

Gene ID: 108254669, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108254669
Gene description
H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 element is located in the intergenic region between the PTP4A2 (protein tyrosine phosphatase type IVA, member 2) and KHDRBS1 (KH RNA binding domain containing, signal transduction associated 1) genes. It was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive and primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. A subregion was also defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as a functional enhancer by reporter assays in HeLa cells. 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 LOC108254669 in Genome Data Viewer
Location:
1p35
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31955819..31956596)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31813776..31814553)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32421427..32422096)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SPOC domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 579 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32303933-32304116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 658 Neighboring gene uncharacterized LOC128031832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32389035-32389578 Neighboring gene protein tyrosine phosphatase 4A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32403472-32403643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32409768-32410302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32419864-32420642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32420643-32421419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 667 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:32473819-32474378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32479704-32480274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 583 Neighboring gene KH RNA binding domain containing, signal transduction associated 1 Neighboring gene VISTA enhancer hs645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:32526442-32527054 Neighboring gene Sharpr-MPRA regulatory region 15509 Neighboring gene Sharpr-MPRA regulatory region 7843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32532900-32533694 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32537939-32538544 Neighboring gene transmembrane protein 39B Neighboring gene microRNA 5585

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 664
  • PTP4A2-KHDRBS1 intergenic CAGE-defined high expression enhancer
  • PTP4A2-KHDRBS1 interval high CAGE FANTOM5 enhancer

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_051015.2 

    Range
    101..878
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31955819..31956596
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31813776..31814553
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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