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LOC123620107 Sharpr-MPRA regulatory region 3834 [ Homo sapiens (human) ]

Gene ID: 123620107, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620107
Gene description
Sharpr-MPRA regulatory region 3834
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac histone modification. Another subregion was validated as a repressive element 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 Repressive DNase matched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 20:ReprD). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (37553733..37554382)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37378777..37379425)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37521509..37521803)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37480625-37481226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37481227-37481828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37483099-37483883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37483884-37484668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24462 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:37487335-37487506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37504191-37504738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37513395-37514004 Neighboring gene uncharacterized LOC124901312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24472 Neighboring gene microRNA 4462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17142 Neighboring gene uncharacterized LOC124901313

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac hESC enhancer GRCh37_chr6:37521658-37522158

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_078091.2 

    Range
    101..750
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    37553733..37554382
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    37378777..37379425
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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