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LOC109648317 enhancer 4 sub-fragment of super-enhancer upstream of RUNX1 [ Homo sapiens (human) ]

Gene ID: 109648317, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109648317
Gene description
enhancer 4 sub-fragment of super-enhancer upstream of RUNX1
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 region is located in the functional core of a larger super-enhancer that regulates expression of the RUNX1 (runt related transcription factor 1) gene, located greater than 180 kb downstream on chromosome 21. This region was shown to enhance expression of the RUNX1 P1 promoter in transfected DG75 lymphoma cells, with activation dependent on the EBNA2 transcription factor and the Notch pathway component RBP-J. Multiple Epstein-Barr virus (EBV) transcription factors target this region for positive or negative regulation of RUNX1 transcription in a cell type-specific manner. [provided by RefSeq, Jul 2018]
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Genomic context

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See LOC109648317 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (35233939..35236564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (33616722..33619347)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (36606236..36608861)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene RUNX family transcription factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18414 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18417 Neighboring gene RUNX1 intronic transcript 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36466332-36466488 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:36477528-36477706 Neighboring gene Sharpr-MPRA regulatory region 12281 Neighboring gene uncharacterized LOC124905015 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:36589399-36590598 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:36604354-36605553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36646465-36646966 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36743463-36743964 Neighboring gene uncharacterized LOC100506403 Neighboring gene Sharpr-MPRA regulatory region 14404 Neighboring gene Sharpr-MPRA regulatory region 5568 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36786783-36787398 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:36878653-36879242 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36880486-36881006 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:36897177-36898376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18420 Neighboring gene ribosomal protein L34 pseudogene 3 Neighboring gene NANOG hESC enhancer GRCh37_chr21:36965152-36965707 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:37006276-37007475 Neighboring gene microRNA 802

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. RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth. Gunnell A, et al. Nucleic Acids Res, 2016 Jun 2. PMID 26883634, Free PMC Article
  2. The DNA sequence of human chromosome 21. Hattori M, et al. Nature, 2000 May 18. PMID 10830953

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

  • RUNX1 super-enhancer element E4

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_052884.1 

    Range
    101..2726
    Download
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    35233939..35236564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    33616722..33619347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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