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LOC121175355 Sharpr-MPRA regulatory region 586 [ Homo sapiens (human) ]

Gene ID: 121175355, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121175355
Gene description
Sharpr-MPRA regulatory region 586
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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 LOC121175355 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101390948..101391325)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102712095..102712472)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (101034229..101034523)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100943223-100943888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100945388-100946089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100946090-100946792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100952259-100953086 Neighboring gene lncRNA p53 regulated and ESC associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18483 Neighboring gene E2F1 mRNA stabilizing lncRNA Neighboring gene intraflagellar transport 22 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101015900-101016438 Neighboring gene collagen type XXVI alpha 1 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101029559-101030174 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101041899-101042500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101044285-101044812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101054568-101055111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101063681-101064232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101064233-101064784 Neighboring gene NANOG hESC enhancer GRCh37_chr7:101065582-101066107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101079627-101080270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101080271-101080912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:101081787-101082746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101104635-101105147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101128605-101129258 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101129259-101129911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137182-101137752 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101137753-101138322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101146871-101147560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101147561-101148250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101150569-101151328 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:101185407-101186075 Neighboring gene Sharpr-MPRA regulatory region 7535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101207140-101208002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:101208003-101208864 Neighboring gene long intergenic non-protein coding RNA 1007 Neighboring gene uncharacterized LOC107986832

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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 26407

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_074287.2 

    Range
    101..478
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    101390948..101391325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102712095..102712472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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