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LOC111946242 Sharpr-MPRA regulatory region 6566 [ Homo sapiens (human) ]

Gene ID: 111946242, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111946242
Gene description
Sharpr-MPRA regulatory region 6566
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Feb 2018]
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Genomic context

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Location:
10p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (5596026..5596320)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (5599855..5600149)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (5637989..5638283)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5595464-5595987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5595988-5596510 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:5599714-5600036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:5602693-5603194 Neighboring gene uncharacterized LOC105376381 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:5605907-5606133 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:5616073-5616688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5625367-5625895 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:5626502-5627701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:5629384-5630191 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_13345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:5638569-5639441 Neighboring gene lncRNA associated with SART3 regulation of splicing Neighboring gene long intergenic non-protein coding RNA 2678 Neighboring gene long intergenic non-protein coding RNA 2677

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_056331.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    5596026..5596320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    5599855..5600149
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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