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LOC112272551 Sharpr-MPRA regulatory region 7662 [ Homo sapiens (human) ]

Gene ID: 112272551, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272551
Gene description
Sharpr-MPRA regulatory region 7662
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 non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). It also displayed weak activation by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112272551 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (68786532..68786826)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (62993398..62993692)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (69253249..69253543)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69203012-69203538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69203539-69204063 Neighboring gene RNA, U6 small nuclear 921, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69229160-69229660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69229661-69230161 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36402 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 ATAC-STARR-seq lymphoblastoid active region 8615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69256702-69257317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5872 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 ZFP36 ring finger protein like 1 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 8623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8622 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 Sharpr-MPRA regulatory region 4438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69310317-69310829 Neighboring gene mago homolog 3, 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

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_056689.1 

    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
    68786532..68786826
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    62993398..62993692
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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