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LOC121627842 Sharpr-MPRA regulatory region 9324 [ Homo sapiens (human) ]

Gene ID: 121627842, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627842
Gene description
Sharpr-MPRA regulatory region 9324
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 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 (909269..909563)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (872006..872300)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (909269..909563)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:871223-871802 Neighboring gene mediator complex subunit 16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:885344-885844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:885845-886345 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13573 Neighboring gene MPRA-validated peak3217 silencer Neighboring gene RNA, U6 small nuclear 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:904059-904817 Neighboring gene R3H domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:918907-919847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:919848-920787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:926209-926969 Neighboring gene KISS1 receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932426-932957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932958-933488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:934552-935082 Neighboring gene AT-rich interaction domain 3A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:947299-947798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:952365-953066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:953067-953768 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:953750-953958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:955173-955874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:956577-957278 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:957654-957846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:962809-963327 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:965021-965198

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_075033.1 

    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
    909269..909563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    872006..872300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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