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LOC112272606 Sharpr-MPRA regulatory region 569 [ Homo sapiens (human) ]

Gene ID: 112272606, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272606
Gene description
Sharpr-MPRA regulatory region 569
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, active chromatin). It also displayed weak activation by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Apr 2018]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (68206031..68206325)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66024780..66025074)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68498369..68498663)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S15a pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:68299513-68300103 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68301209-68302094 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:68302095-68302980 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68308948-68309655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68312077-68312615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68312616-68313153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68314382-68315165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68337310-68337830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68337831-68338350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68361989-68362489 Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene uncharacterized LOC105370871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68492859-68493630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68503536-68504076 Neighboring gene calmodulin like 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9642 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:68521930-68522109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9643 Neighboring gene CLN6 transmembrane ER protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68549209-68549856 Neighboring gene uncharacterized LOC124903593 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 40

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_056742.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    68206031..68206325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    66024780..66025074
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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