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LOC121847993 Sharpr-MPRA regulatory region 2768 [ Homo sapiens (human) ]

Gene ID: 121847993, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121847993
Gene description
Sharpr-MPRA regulatory region 2768
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 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). The same subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81456984..81457747)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87517820..87518583)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (81490589..81490883)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene beta-carotene oxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7755 Neighboring gene gigaxonin Neighboring gene ReSE screen-validated silencer GRCh37_chr16:81420479-81420673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81430852-81431402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81431403-81431953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11179 Neighboring gene microRNA 4720 Neighboring gene Sharpr-MPRA regulatory region 12949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81466113-81467024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81467025-81467934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81477254-81477786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81479951-81480716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81480717-81481480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81482247-81483010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81489297-81489981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81491353-81492038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81497377-81497916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81503436-81503936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81527049-81527782 Neighboring gene c-Maf inducing protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81530785-81531426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11189 Neighboring gene peptidylprolyl isomerase A pseudogene 51 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81546458-81547288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81549519-81550168 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:81551802-81552499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:81553011-81553629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81565885-81566386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:81566387-81566886 Neighboring gene microRNA 7854

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_chr16:81490668-81491352

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_076013.2 

    Range
    101..864
    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
    81456984..81457747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87517820..87518583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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