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LOC122149315 Sharpr-MPRA regulatory region 12139 [ Homo sapiens (human) ]

Gene ID: 122149315, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122149315
Gene description
Sharpr-MPRA regulatory region 12139
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 a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122149315 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (179028730..179029668)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (178383798..178384736)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (178998509..178998803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Ral GEF with PH domain and SH3 binding motif 2 Neighboring gene angiopoietin like 1 Neighboring gene uncharacterized LOC102724754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:178908305-178908804 Neighboring gene MPRA-validated peak477 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:178915423-178916208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1582 Neighboring gene CRISPRi-validated cis-regulatory element chr1.10033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1584 Neighboring gene Sharpr-MPRA regulatory region 11809 Neighboring gene FAM20B glycosaminoglycan xylosylkinase Neighboring gene ribosomal protein S26 pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:179055021-179055521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179056771-179057672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179057673-179058574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179060592-179061092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179061093-179061593 Neighboring gene torsin family 3 member A

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_chr1:178997865-178998740

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_076507.2 

    Range
    101..1039
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    179028730..179029668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    178383798..178384736
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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