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LOC121852972 Sharpr-MPRA regulatory region 8051 [ Homo sapiens (human) ]

Gene ID: 121852972, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852972
Gene description
Sharpr-MPRA regulatory region 8051
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 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3558131..3558425)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3536287..3536581)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3558129..3558423)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene fizzy and cell division cycle 20 related 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3518044-3518846 Neighboring gene uncharacterized LOC124904617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3520450-3521250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3539157-3540009 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 19:3540539 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 19:3542983 Neighboring gene tektin bundle interacting protein 1 Neighboring gene major facilitator superfamily domain containing 12 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 19:3550926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9850 Neighboring gene uncharacterized LOC124904618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3571588-3572156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3572157-3572724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9851 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9853 Neighboring gene high mobility group 20B Neighboring gene GIPC PDZ domain containing family member 3

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_076079.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3558131..3558425
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3536287..3536581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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