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LOC112840910 Sharpr-MPRA regulatory region 15004 [ Homo sapiens (human) ]

Gene ID: 112840910, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112840910
Gene description
Sharpr-MPRA regulatory region 15004
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 human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. 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 DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activation in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (234862986..234863699)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (235352052..235352765)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (235772049..235772343)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:235596500-235597125 Neighboring gene Sharpr-MPRA regulatory region 2610 Neighboring gene long intergenic non-protein coding RNA 1173 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:235602982-235604181 Neighboring gene NANOG hESC enhancer GRCh37_chr2:235619073-235619654 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 10 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:235673486-235674685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235681449-235681948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235680947-235681448 Neighboring gene uncharacterized LOC101927896 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:235742667-235743866 Neighboring gene uncharacterized LOC105373937 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235810653-235811216 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235840873-235841418 Neighboring gene uncharacterized LOC105373938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235843604-235844104

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-H3K4me1 hESC enhancer GRCh37_chr2:235771630-235772202

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_060945.2 

    Range
    101..814
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    234862986..234863699
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    235352052..235352765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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