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LOC112695081 Sharpr-MPRA regulatory region 4664 [ Homo sapiens (human) ]

Gene ID: 112695081, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695081
Gene description
Sharpr-MPRA regulatory region 4664
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. A subregion was validated as a functional enhancer 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 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched). 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:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30609322..30609670)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (31072893..31073239)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (31005309..31005603)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak4480 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30967053-30967554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30969210-30969891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30969892-30970572 Neighboring gene galactose-3-O-sulfotransferase 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:30982632-30983831 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30987725-30988440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:31002947-31003526 Neighboring gene pescadillo ribosomal biogenesis factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:31030490-31031194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13614 Neighboring gene transcobalamin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:31042177-31042759 Neighboring gene solute carrier family 35 member E4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18842 Neighboring gene ribosomal protein L13a pseudogene 26 Neighboring gene dual specificity phosphatase 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13616 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:31112835-31114034 Neighboring gene oxysterol binding protein 2 Neighboring gene microRNA 3200

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 18841

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_060862.2 

    Range
    101..449
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    30609322..30609670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    31072893..31073239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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