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LOC112695101 Sharpr-MPRA regulatory region 5708 [ Homo sapiens (human) ]

Gene ID: 112695101, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695101
Gene description
Sharpr-MPRA regulatory region 5708
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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42940223..42940517)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (43421169..43421463)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (43336229..43336523)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43277300-43277874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43277875-43278449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43278450-43279023 Neighboring gene protein kinase C and casein kinase substrate in neurons 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43293568-43294344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43294345-43295119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43300517-43301037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43301932-43302607 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43311964-43312742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43321567-43322365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43330023-43330539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43330540-43331055 Neighboring gene uncharacterized LOC124905128 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43335396-43335896 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43337917-43338143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43342673-43343565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43343566-43344457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43348125-43348626 Neighboring gene Sharpr-MPRA regulatory region 1755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43359945-43360726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43360727-43361506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43366379-43367366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43381349-43381866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43381867-43382385 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43389036-43389156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19180 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43410757-43411460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43423546-43424046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43430053-43430554 Neighboring gene TTLL1 antisense RNA 1 Neighboring gene TTL family tubulin polyglutamylase complex subunit L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43474531-43475053 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43475054-43475575 Neighboring gene Sharpr-MPRA regulatory region 1995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13852 Neighboring gene ribosomal protein S25 pseudogene 10

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_060879.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    42940223..42940517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    43421169..43421463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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