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LOC121853032 Sharpr-MPRA regulatory region 2423 [ Homo sapiens (human) ]

Gene ID: 121853032, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853032
Gene description
Sharpr-MPRA regulatory region 2423
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121853032 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 (43921548..43921842)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42277165..42277459)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45341429..45341723)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 3 Neighboring gene uncharacterized LOC124905034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45328253-45328754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45336568-45337118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45337119-45337668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45339493-45340392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45340393-45341290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45342191-45343088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45344887-45345786 Neighboring gene RNA, U6 small nuclear 859, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45345787-45346684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45351938-45352438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45354036-45354854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45358304-45359204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45359205-45360103 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45360643-45360814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45363715-45364558 Neighboring gene uncharacterized LOC105372826 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45376043-45376543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45401087-45401848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45401849-45402610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45402611-45403372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45405825-45406355 Neighboring gene uncharacterized LOC105372829 Neighboring gene RNA, U6 small nuclear 1150, pseudogene

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_076140.1 

    Range
    101..395
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    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
    43921548..43921842
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42277165..42277459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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