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LOC122056819 Sharpr-MPRA regulatory region 9119 [ Homo sapiens (human) ]

Gene ID: 122056819, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056819
Gene description
Sharpr-MPRA regulatory region 9119
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 23:Low, low signal proximal to active elements). [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 (30043482..30043776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (29886706..29887000)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (30516329..30516623)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984934 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:30108561-30108764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30162197-30162696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30179358-30179858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30179859-30180359 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:30182040-30183239 Neighboring gene MPRA-validated peak146 silencer Neighboring gene MPRA-validated peak147 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30257435-30257936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30272801-30273302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30283373-30284343 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:30296971-30297175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30297771-30298270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30317999-30318500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30318501-30319000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30328550-30329222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30329223-30329894 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:30331015-30331514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:30394348-30395242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30399701-30400346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30403757-30404338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30406301-30407056 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:30446776-30447975 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30454325-30454982 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:30481435-30481935 Neighboring gene long intergenic non-protein coding RNA 1648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30579535-30580036 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:30626667-30627480 Neighboring gene uncharacterized LOC105378617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30663183-30663713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:30667220-30667720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30702893-30703546 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6631 Neighboring gene uncharacterized LOC105378618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:30730647-30731414

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_076275.1 

    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
    30043482..30043776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    29886706..29887000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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