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    LOC121853016 Sharpr-MPRA regulatory region 2062 [ Homo sapiens (human) ]

    Gene ID: 121853016, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC121853016
    Gene description
    Sharpr-MPRA regulatory region 2062
    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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jul 2021]
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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 (57586333..57586627)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59364211..59364505)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56161389..56161683)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56143743-56144243 Neighboring gene phosphoenolpyruvate carboxykinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56165049-56165804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13064 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:56172128-56172301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56193035-56193894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18167 Neighboring gene Z-DNA binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56229759-56230358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56230359-56230956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56236773-56237645 Neighboring gene prostate transmembrane protein, androgen induced 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56238905-56239419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56241925-56242541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56251833-56252416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56253071-56253587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56253588-56254103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56254668-56255192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56255193-56255716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56257022-56257522 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56267863-56268682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56271371-56271903 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:56272784-56273983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56279768-56280362 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:56283453-56284064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13067 Neighboring gene NF-kappaB interacting lncRNA

    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

    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)

    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_076124.1 

      Range
      101..395
      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
      57586333..57586627
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      59364211..59364505
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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