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LOC112272552 Sharpr-MPRA regulatory region 4438 [ Homo sapiens (human) ]

Gene ID: 112272552, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272552
Gene description
Sharpr-MPRA regulatory region 4438
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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, 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:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (68824912..68825206)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (63031768..63032062)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (69291629..69291923)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69247495-69247996 Neighboring gene HNF1 motif-containing MPRA enhancer 48 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5870 Neighboring gene Sharpr-MPRA regulatory region 7662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8617 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69256702-69257317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5872 Neighboring gene ZFP36 ring finger protein like 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69261405-69261949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69283011-69283750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69310317-69310829 Neighboring gene mago homolog 3, pseudogene Neighboring gene basic leucine zipper nuclear factor 2, pseudogene

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 8630

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_056690.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    68824912..68825206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    63031768..63032062
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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