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LOC121466721 Sharpr-MPRA regulatory region 12947 [ Homo sapiens (human) ]

Gene ID: 121466721, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121466721
Gene description
Sharpr-MPRA regulatory region 12947
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 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 naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (120401696..120402540)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (120388824..120389668)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (120840049..120840343)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene musashi RNA binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:120794238-120794738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:120796175-120796787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:120796788-120797399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:120798696-120799414 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:120799415-120800132 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:120803530-120803720 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:120814267-120814767 Neighboring gene ribosomal protein S27 pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7142 Neighboring gene MPRA-validated peak2004 silencer Neighboring gene MPRA-validated peak2005 silencer Neighboring gene MPRA-validated peak2007 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:120876089-120876610 Neighboring gene uncharacterized LOC124903126 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:120883528-120884727 Neighboring gene cytochrome c oxidase subunit 6A1 Neighboring gene TP53 regulated inhibitor of apoptosis 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-H3K4me1 hESC enhancer GRCh37_chr12:120839499-120840264

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_074654.2 

    Range
    101..945
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    120401696..120402540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    120388824..120389668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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