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LOC112540017 Sharpr-MPRA regulatory region 2175 [ Homo sapiens (human) ]

Gene ID: 112540017, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112540017
Gene description
Sharpr-MPRA regulatory region 2175
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, May 2018]
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Genomic context

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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26548485..26548779)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26742484..26742778)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (24128449..24128743)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13183 Neighboring gene long intergenic non-protein coding RNA 1543 Neighboring gene MPRA-validated peak3087 silencer Neighboring gene uncharacterized LOC124904274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13188 Neighboring gene potassium channel tetramerization domain containing 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:24060471-24061670 Neighboring gene uncharacterized LOC124904273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24126836-24127820 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:24128809-24129450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24129451-24130092 Neighboring gene Sharpr-MPRA regulatory region 221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24130735-24131376 Neighboring gene microRNA 8057 Neighboring gene cytokine induced apoptosis inhibitor 1 pseudogene

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_057368.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    26548485..26548779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    26742484..26742778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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