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LOC121627856 Sharpr-MPRA regulatory region 7322 [ Homo sapiens (human) ]

Gene ID: 121627856, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627856
Gene description
Sharpr-MPRA regulatory region 7322
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. It 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (14366617..14366911)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14493291..14493585)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14477429..14477723)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:14328052-14328362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14332061-14332584 Neighboring gene RNA, 7SL, cytoplasmic 231, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14360564-14361081 Neighboring gene MPRA-validated peak3380 silencer Neighboring gene MPRA-validated peak3381 silencer Neighboring gene Sharpr-MPRA regulatory region 1520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14408885-14409384 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:14421820-14422074 Neighboring gene long intergenic non-protein coding RNA 1841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14429209-14429710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14429711-14430210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14444577-14445252 Neighboring gene MPRA-validated peak3382 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449292-14449792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14449793-14450293 Neighboring gene long intergenic non-protein coding RNA 1842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14459126-14460004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14460803-14461304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14461305-14461804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10244 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14507248-14508447 Neighboring gene adhesion G protein-coupled receptor E5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:14512346-14513545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14515967-14516596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14516597-14517226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10248 Neighboring gene DExD-box helicase 39A

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 silent region 10243

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_075047.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    14366617..14366911
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14493291..14493585
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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