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LOC122094857 Sharpr-MPRA regulatory region 8792 [ Homo sapiens (human) ]

Gene ID: 122094857, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094857
Gene description
Sharpr-MPRA regulatory region 8792
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element 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 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (85597826..85598120)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (85438641..85438935)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (86063509..86063803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:86046012-86046534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:86047581-86048102 Neighboring gene small nucleolar RNA SNORD81 Neighboring gene cellular communication network factor 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:86072656-86073855 Neighboring gene uncharacterized LOC112268231 Neighboring gene Sharpr-MPRA regulatory region 3870 Neighboring gene uncharacterized LOC107985057 Neighboring gene zinc finger HIT-type containing 6 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86157154-86157654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86157655-86158155 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:86173373-86174206

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_076371.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    85597826..85598120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    85438641..85438935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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