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LOC125146379 Sharpr-MPRA regulatory region 9802 [ Homo sapiens (human) ]

Gene ID: 125146379, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146379
Gene description
Sharpr-MPRA regulatory region 9802
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 H3K4me1 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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (3087168..3088185)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (3113647..3114664)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984896 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3124519-3124702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7112 Neighboring gene RNA, U1 small nuclear 22, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3139191-3139721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3140253-3140782 Neighboring gene zinc finger and SCAN domain containing 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3142715-3143302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7114 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3151352-3152052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3154929-3155612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3155613-3156296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7118 Neighboring gene uncharacterized LOC124903629

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

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr16:3137329-3138186

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_080308.2 

    Range
    101..1118
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    3087168..3088185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    3113647..3114664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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