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LOC109851610 enhancer 2 sub-fragment of super enhancer upstream of RUNX3 [ Homo sapiens (human) ]

Gene ID: 109851610, updated on 17-Sep-2024

Summary

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Gene symbol
LOC109851610
Gene description
enhancer 2 sub-fragment of super enhancer upstream of RUNX3
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 represents a functional core fragment of a larger super enhancer that is thought to regulate expression of the runt related transcription factor 3 (RUNX3) gene P2 promoter, which is located approximately 93 kb downstream. Epstein-Barr virus (EBV) transcription factors can stimulate activity of this enhancer through the cellular trasnscriptional regulator protein Rbpj. 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC109851610 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (25022139..25023701)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (24857948..24859510)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (25348630..25350192)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RUNX family transcription factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25254973-25255707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25255708-25256441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25257881-25258470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 444 Neighboring gene microRNA 6731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25264973-25265472 Neighboring gene RUNX3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276177-25276700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25276701-25277226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 446 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:25281264-25282463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 421 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25310883-25311384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25316159-25316660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25345941-25346837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25347096-25347624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25347625-25348151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25351623-25352296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25353935-25354474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25354475-25355012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25355013-25355552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 441 Neighboring gene microRNA 4425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25372889-25373429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25373430-25373969 Neighboring gene long intergenic non-protein coding RNA 2793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:25378080-25378598 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:25381310-25381813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:25398512-25399127 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:25417097-25418296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 451 Neighboring gene MPRA-validated peak123 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 446 Neighboring gene IFITM3 pseudogene 7

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. 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

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 434

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_052963.1 

    Range
    101..1663
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    25022139..25023701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    24857948..24859510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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