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LOC121853021 Sharpr-MPRA regulatory region 9823 [ Homo sapiens (human) ]

Gene ID: 121853021, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853021
Gene description
Sharpr-MPRA regulatory region 9823
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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121853021 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44113988..44114282)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42469598..42469892)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45533869..45534163)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372829 Neighboring gene RNA, U6 small nuclear 1150, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18561 Neighboring gene trafficking protein particle complex subunit 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45452244-45452456 Neighboring gene H2A.Z histone pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45487136-45487678 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45526826-45527342 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45530994-45531196 Neighboring gene PWP2 small subunit processome component Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:45553065-45553592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:45553593-45554120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45554121-45554648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13210 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45561103-45561261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45566085-45566744 Neighboring gene glutamine amidotransferase class 1 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18265 Neighboring gene long intergenic non-protein coding RNA 1678

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_076129.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    44113988..44114282
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42469598..42469892
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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