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LOC112695097 Sharpr-MPRA regulatory region 14092 [ Homo sapiens (human) ]

Gene ID: 112695097, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112695097
Gene description
Sharpr-MPRA regulatory region 14092
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as an 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 non-DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin). [provided by RefSeq, Jan 2023]
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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 (41290645..41291387)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (41765598..41766340)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (41686649..41686943)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene L3MBTL histone methyl-lysine binding protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41632734-41633322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41633323-41633911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41633912-41634500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41634501-41635088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41636538-41637038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41637039-41637539 Neighboring gene chondroadherin like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41652381-41652924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41652925-41653468 Neighboring gene Ran GTPase activating protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41654013-41654555 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41660124-41660999 Neighboring gene microRNA 6889 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41667991-41668491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19112 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41685594-41686193 Neighboring gene Sharpr-MPRA regulatory region 10804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13783 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41697637-41698138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41704361-41704862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:41704863-41705362 Neighboring gene zinc finger CCCH-type containing 7B Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:41720150-41720650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41756000-41756522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41756523-41757045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:41760009-41760569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13785 Neighboring gene uncharacterized LOC100996598 Neighboring gene TEF transcription factor, PAR bZIP family member

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac hESC enhancer GRCh37_chr22:41686793-41687391

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_060875.2 

    Range
    101..843
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    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
    41290645..41291387
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    41765598..41766340
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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