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LOC112163544 Sharpr-MPRA regulatory region 3500 [ Homo sapiens (human) ]

Gene ID: 112163544, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112163544
Gene description
Sharpr-MPRA regulatory region 3500
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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112163544 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (13255755..13256049)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (13130042..13130336)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (13408689..13408983)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902882 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:13318180-13319379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13336996-13337496 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13337497-13337997 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:13351700-13352200 Neighboring gene epithelial membrane protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13409703-13410569 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:13417435-13418010 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:13418011-13418585 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:13492223-13493422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:13521335-13521834 Neighboring gene NANOG hESC enhancer GRCh37_chr12:13521894-13522420 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:13528282-13529481 Neighboring gene long intergenic non-protein coding RNA 1559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13591195-13591716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:13591717-13592238 Neighboring gene RNA, 5S ribosomal pseudogene 353

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_056568.1 

    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
    13255755..13256049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    13130042..13130336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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