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LOC122056811 Sharpr-MPRA regulatory region 8493 [ Homo sapiens (human) ]

Gene ID: 122056811, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056811
Gene description
Sharpr-MPRA regulatory region 8493
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122056811 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27059058..27059352)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26897858..26898152)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27385549..27385843)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27320180-27320680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27324053-27324658 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:27325387-27326586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27328287-27328890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27330318-27330962 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27332251-27332894 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27332895-27333538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27333539-27334182 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:27334827-27335470 Neighboring gene TMF1 regulated nuclear protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27338587-27339240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27339241-27339895 Neighboring gene terminal nucleotidyltransferase 5B Neighboring gene uncharacterized LOC101928391 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27361397-27361898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27364454-27364954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27368765-27369317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27372795-27373295 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr1:27376127-27376944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27376945-27377760 Neighboring gene Sharpr-MPRA regulatory region 512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27428314-27429172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27429173-27430031 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:27431568-27432767 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27436564-27436768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27438447-27438948 Neighboring gene solute carrier family 9 member A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27440010-27440584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27440585-27441158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27443453-27444164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27444875-27445585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27445586-27446295 Neighboring gene Sharpr-MPRA regulatory region 8944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27464001-27464812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27482511-27483010 Neighboring gene uncharacterized LOC102723760

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_076267.1 

    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
    27059058..27059352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26897858..26898152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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