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LOC112163533 Sharpr-MPRA regulatory region 1215 [ Homo sapiens (human) ]

Gene ID: 112163533, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163533
Gene description
Sharpr-MPRA regulatory region 1215
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW). [provided by RefSeq, Mar 2018]
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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 (122749922..122750216)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122745310..122745604)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123234469..123234763)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5019 Neighboring gene hydroxycarboxylic acid receptor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123214153-123214820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:123218665-123219164 Neighboring gene hydroxycarboxylic acid receptor 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:123235867-123236728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7236 Neighboring gene density regulated re-initiation and release factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5021 Neighboring gene Sharpr-MPRA regulatory region 13845 Neighboring gene coiled-coil domain containing 62 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:123274450-123275003 Neighboring gene MPRA-validated peak2023 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:123296784-123296959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7238

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_056558.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    122749922..122750216
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    122745310..122745604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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