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LOC109433679 enhancer downstream of BMP4 [ Homo sapiens (human) ]

Gene ID: 109433679, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109433679
Gene description
enhancer downstream of BMP4
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 an enhancer element located approximately 7.5 kb downstream of the translation start site of the bone morphogenetic protein 4 gene. This sequence contains a single nucleotide poolymorphism (rs4444235) that was found to be associated with colorectal cancer risk; the T allele is protective for cancer but has lower enhancer activity. A subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (53943726..53945475)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (48151954..48153703)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (54410749..54412193)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370504 Neighboring gene long intergenic non-protein coding RNA 2331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8407 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:54316803-54318002 Neighboring gene uncharacterized LOC107984676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8408 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:54409816-54410443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:54412534-54413066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:54413067-54413597 Neighboring gene BMP4 promoter region Neighboring gene uncharacterized LOC124903317 Neighboring gene microRNA 5580 Neighboring gene bone morphogenetic protein 4

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. Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci. Niittymäki I, et al. BMC Med Genet, 2011 Feb 14. PMID 21314996, Free PMC Article
  2. The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4. Lubbe SJ, et al. Oncogene, 2012 Aug 16. PMID 22158048
  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

  • NANOG-H3K27ac hESC enhancer GRCh37_chr14:54410444-54411070
  • rs4444235 enhancer element

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_052606.2 

    Range
    101..1850
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    53943726..53945475
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    48151954..48153703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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