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LOC125371416 Sharpr-MPRA regulatory region 7610 [ Homo sapiens (human) ]

Gene ID: 125371416, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371416
Gene description
Sharpr-MPRA regulatory region 7610
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC125371416 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (48897100..48897573)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (49092367..49092840)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene cap binding complex dependent translation initiation factor Neighboring gene uncharacterized LOC105372106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13298 Neighboring gene uncharacterized LOC105372105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46359045-46359708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46362171-46363071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46363072-46363971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46364242-46365020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46365021-46365799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46370909-46371409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46384077-46384578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46388739-46389290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13301 Neighboring gene Sharpr-MPRA regulatory region 12870 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:46404101-46404331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46419523-46420032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46420541-46421048 Neighboring gene uncharacterized LOC124904355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46449409-46450340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46452405-46453366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46459221-46460106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13306 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:46468263-46469462 Neighboring gene NANOG hESC enhancer GRCh37_chr18:46474665-46475166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9439 Neighboring gene SMAD family member 7

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 13302
  • ATAC-STARR-seq lymphoblastoid active region 13303

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_080686.2 

    Range
    101..574
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    48897100..48897573
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_013171814.1 Reference GRCh38.p14 PATCHES

    Range
    386370..386843
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    49092367..49092840
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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