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LOC125387283 Sharpr-MPRA regulatory region 8498 [ Homo sapiens (human) ]

Gene ID: 125387283, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387283
Gene description
Sharpr-MPRA regulatory region 8498
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 a repressive element 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 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (47765660..47766599)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (49504766..49505705)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr20.2047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12980 Neighboring gene RNA, U6 small nuclear 563, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46152763-46153530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46158187-46158687 Neighboring gene nuclear receptor coactivator 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:46190110-46190292 Neighboring gene MPRA-validated peak4234 silencer Neighboring gene ribosomal protein S3A pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:46277615-46278332 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46276897-46277614 Neighboring gene nuclear receptor coactivator 3 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46293563-46294548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46294549-46295532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46303203-46304168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46307531-46308031 Neighboring gene sulfatase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46316712-46317262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46317263-46317814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46326206-46326710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339340-46339840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339841-46340341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381589-46382088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381087-46381588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386138-46386895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386896-46387654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46387655-46388411 Neighboring gene NANOG hESC enhancer GRCh37_chr20:46390145-46390683 Neighboring gene uncharacterized LOC124904922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18007 Neighboring gene uncharacterized LOC124904920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18008

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

General gene information

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Other Names

  • H3K27ac hESC enhancer GRCh37_chr20:46394404-46395176

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_080959.2 

    Range
    101..1040
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    47765660..47766599
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    49504766..49505705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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