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LOC111811970 Sharpr-MPRA regulatory regions 411/7488 and 4104 [ Homo sapiens (human) ]

Gene ID: 111811970, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111811970
Gene description
Sharpr-MPRA regulatory regions 411/7488 and 4104
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. Two overlapping subregions were validated as functional enhancers by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). Both subregions also displayed weak activation by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (42034757..42035091)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (44854121..44854455)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (42538909..42539243)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14695 Neighboring gene Rab acceptor 1 Neighboring gene ATPase Na+/K+ transporting subunit alpha 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10682 Neighboring gene glutamate ionotropic receptor kainate type subunit 5 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:42536134-42536906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:42539441-42539940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14698 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10683 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10684 Neighboring gene zinc finger protein 574 Neighboring gene POU class 2 homeobox 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10686 Neighboring gene microRNA 4323 Neighboring gene long non-coding regulator of POU2F2

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 14696
  • Sharpr-MPRA regulatory region 4104
  • Sharpr-MPRA regulatory region 411
  • Sharpr-MPRA regulatory region 7488

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_056202.1 

    Range
    101..435
    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
    42034757..42035091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    44854121..44854455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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