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LOC113146409 Sharpr-MPRA regulatory region 12057 [ Homo sapiens (human) ]

Gene ID: 113146409, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113146409
Gene description
Sharpr-MPRA regulatory region 12057
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 matched - State 5:Enh, candidate strong enhancer, open chromatin), with weak activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Sep 2018]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (126075323..126075617)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (127263937..127264231)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (126396469..126396763)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene nuclear receptor coactivator 7 Neighboring gene uncharacterized LOC124901397 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:126239365-126240564 Neighboring gene NCOA7-HINT3 intergenic CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25032 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25033 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:126307740-126308569 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:126306909-126307739 Neighboring gene RNA, 5S ribosomal pseudogene 216 Neighboring gene histidine triad nucleotide binding protein 3 Neighboring gene tRNA methyltransferase 11 homolog Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14B pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25036 Neighboring gene centromere protein W

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_061638.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    126075323..126075617
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    127263937..127264231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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