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LOC122056786 Sharpr-MPRA regulatory region 2075 [ Homo sapiens (human) ]

Gene ID: 122056786, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056786
Gene description
Sharpr-MPRA regulatory region 2075
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 DNase matched - State 2:TssF, active promoter, flanking TSS/CpG islands) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 2:TssF). [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 (22451096..22451390)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (22274801..22275095)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22777589..22777883)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22592955-22593474 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:22613139-22613638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22618619-22619118 Neighboring gene microRNA 4418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22623785-22624284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22651838-22652529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22702397-22702897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22716534-22717034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22717035-22717535 Neighboring gene uncharacterized LOC105376856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22743723-22744638 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769995-22770614 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:22769377-22769994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22778273-22778834 Neighboring gene zinc finger and BTB domain containing 40 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22791857-22792004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22880423-22881056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22881753-22882336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22882919-22883500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22883501-22884082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22890520-22891020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22898749-22899308 Neighboring gene EPH receptor A8 Neighboring gene Sharpr-MPRA regulatory region 15208 Neighboring gene microRNA 6127

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_076242.1 

    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
    22451096..22451390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    22274801..22275095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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