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LOC113839508 Sharpr-MPRA regulatory region 14561 [ Homo sapiens (human) ]

Gene ID: 113839508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839508
Gene description
Sharpr-MPRA regulatory region 14561
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127555646..127556364)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139762648..139763366)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130318349..130318643)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29042 Neighboring gene leucine rich repeat and sterile alpha motif containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226032-130226532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226533-130227033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251390-130251970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251971-130252551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130256483-130257002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130262849-130263350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130266531-130267404 Neighboring gene niban apoptosis regulator 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130285667-130286168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130286169-130286668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130287309-130287861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130293634-130294194 Neighboring gene uncharacterized LOC105376281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130314335-130314834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130323322-130324026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130324732-130325436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130325437-130326140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130328804-130329344 Neighboring gene FAM129B intron CAGE-defined low expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130331508-130332048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130332049-130332588 Neighboring gene Sharpr-MPRA regulatory region 10550 Neighboring gene uncharacterized LOC124902276 Neighboring gene uncharacterized LOC124902277

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-H3K4me1 hESC enhancer GRCh37_chr9:130317925-130318520

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_063125.2 

    Range
    101..819
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    127555646..127556364
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139762648..139763366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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