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LOC112163636 Sharpr-MPRA regulatory region 2068 [ Homo sapiens (human) ]

Gene ID: 112163636, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163636
Gene description
Sharpr-MPRA regulatory region 2068
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 2:TssF, active promoter, flanking TSS/CpG islands). 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:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (92034973..92035300)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (92012466..92012793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (92428749..92429043)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2404 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:92296093-92297292 Neighboring gene uncharacterized LOC105369901 Neighboring gene MPRA-validated peak1883 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:92356292-92356496 Neighboring gene long intergenic non-protein coding RNA 1619 Neighboring gene NANOG hESC enhancer GRCh37_chr12:92415340-92415873 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:92471461-92472660 Neighboring gene Sharpr-MPRA regulatory region 10753 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:92501486-92502024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6723 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92538603-92539139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6725 Neighboring gene BTG1 divergent transcript Neighboring gene BTG anti-proliferation factor 1 Neighboring gene ribosomal protein L21 pseudogene 106

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 6718

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_056613.2 

    Range
    101..428
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    92034973..92035300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    92012466..92012793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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