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LOC112163601 Sharpr-MPRA regulatory region 4642 [ Homo sapiens (human) ]

Gene ID: 112163601, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112163601
Gene description
Sharpr-MPRA regulatory region 4642
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112163601 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50933826..50934120)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50897100..50897394)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51327609..51327903)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene transmembrane serine protease 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51251231-51251732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51251733-51252232 Neighboring gene CRISPRi-validated cis-regulatory element chr12.1615 Neighboring gene MPRA-validated peak1732 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51319135-51319678 Neighboring gene thiol methyltransferase 1A Neighboring gene HIG1 hypoxia inducible domain family member 1C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51346409-51346909 Neighboring gene solute carrier family 11 member 2 Neighboring gene MPRA-validated peak1733 silencer Neighboring gene RNA, U7 small nuclear 39 pseudogene Neighboring gene RNA, U6 small nuclear 87, 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_056583.1 

    Range
    101..395
    Download
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    50933826..50934120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    50897100..50897394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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