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LOC112543435 Sharpr-MPRA regulatory region 10096 [ Homo sapiens (human) ]

Gene ID: 112543435, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543435
Gene description
Sharpr-MPRA regulatory region 10096
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 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh). [provided by RefSeq, May 2018]
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Genomic context

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Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (8730411..8730705)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (8893385..8893679)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (8730409..8730703)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8690155-8691020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9274 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8708630-8709131 Neighboring gene TOMM20 pseudogene 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:8724358-8724941 Neighboring gene gastric cancer associated transcript 2 Neighboring gene microtubule crosslinking factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8766085-8766684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8766685-8767282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8771566-8772066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8772067-8772567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8790509-8791032 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:8800176-8801375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8818635-8819136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8829938-8830461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8830462-8830984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:8844937-8845437 Neighboring gene MPRA-validated peak3053 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8948615-8949387 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8977106-8977637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:8990234-8990766 Neighboring gene NANOG hESC enhancer GRCh37_chr18:8997551-8998052 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:9017064-9018263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:9022070-9022745 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:9037094-9037241 Neighboring gene ribosomal protein S4X pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9276 Neighboring gene uncharacterized LOC124904243

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_057386.1 

    Range
    101..395
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    8730411..8730705
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    8893385..8893679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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