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LOC112268486 Sharpr-MPRA regulatory region 1153 [ Homo sapiens (human) ]

Gene ID: 112268486, updated on 10-Dec-2024

Summary

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Gene symbol
LOC112268486
Gene description
Sharpr-MPRA regulatory region 1153
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). The same subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC112268486 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60094331..60094992)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (54300292..54300957)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (60561049..60561710)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:60124167-60124668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:60124669-60125168 Neighboring gene reticulon 1 Neighboring gene microRNA 5586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5807 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:60386022-60387221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8464 Neighboring gene leucine rich repeat containing 9 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:60459076-60459307 Neighboring gene PCNX4 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8466 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:60558835-60559468 Neighboring gene pecanex 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5808 Neighboring gene dehydrogenase/reductase 7 Neighboring gene short coiled-coil protein pseudogene 1 Neighboring gene proteasome subunit alpha 3 pseudogene 1

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac hESC enhancer GRCh37_chr14:60561126-60561710

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_056683.2 

    Range
    101..762
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    60094331..60094992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    54300292..54300957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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