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LOC112577555 Sharpr-MPRA regulatory region 10666 [ Homo sapiens (human) ]

Gene ID: 112577555, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112577555
Gene description
Sharpr-MPRA regulatory region 10666
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). It also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer; flanking open chromatin of candidate enhancers). [provided by RefSeq, Jun 2018]
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Genomic context

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See LOC112577555 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (234643123..234643417)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234033558..234033852)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (234778869..234779163)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene interferon regulatory factor 2 binding protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1978 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234745399-234746096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2763 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:234752429-234752929 Neighboring gene long intergenic non-protein coding RNA 184 Neighboring gene uncharacterized LOC101927787 Neighboring gene uncharacterized LOC105373207 Neighboring gene uncharacterized LOC124904554 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:234792319-234793518

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_060472.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    234643123..234643417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    234033558..234033852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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