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LOC121852976 Sharpr-MPRA regulatory region 5032 [ Homo sapiens (human) ]

Gene ID: 121852976, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852976
Gene description
Sharpr-MPRA regulatory region 5032
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 unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121852976 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (6481978..6482272)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6471481..6471775)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (6481989..6482283)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 41 Neighboring gene solute carrier family 25 member 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6464149-6464690 Neighboring gene DENN domain containing 1C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6475606-6476345 Neighboring gene crumbs cell polarity complex component 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6479893-6480392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9956 Neighboring gene tubulin beta 4A class IVa Neighboring gene CRISPRi-validated cis-regulatory element chr19.1358 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6506805-6507716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6516143-6516683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532416-6532916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532917-6533417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13834 Neighboring gene TNF superfamily member 9

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_076083.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    6481978..6482272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6471481..6471775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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