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LOC121056751 Sharpr-MPRA regulatory region 724 [ Homo sapiens (human) ]

Gene ID: 121056751, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121056751
Gene description
Sharpr-MPRA regulatory region 724
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 non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands) and K562 erythroleukemia cells (group: K562 Activating 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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Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (184347376..184347897)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (187691213..187691734)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (185268529..185268823)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377582 Neighboring gene uncharacterized LOC124900825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15834 Neighboring gene MYL12B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185234973-185235474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185238635-185239134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15835 Neighboring gene long intergenic non-protein coding RNA 2363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22213 Neighboring gene long intergenic non-protein coding RNA 2362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22214 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:185304232-185305431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:185307527-185308285 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:185310291-185311024 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:185311025-185311758 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:185314606-185314781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22215 Neighboring gene interferon regulatory factor 2 Neighboring gene Sharpr-MPRA regulatory region 12125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22216 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:185339175-185340374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185351299-185351950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:185351951-185352602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15838

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 22211
  • ATAC-STARR-seq lymphoblastoid active region 22212

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_074143.2 

    Range
    101..622
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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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    184347376..184347897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    187691213..187691734
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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