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LOC120908912 Sharpr-MPRA regulatory region 2676 [ Homo sapiens (human) ]

Gene ID: 120908912, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120908912
Gene description
Sharpr-MPRA regulatory region 2676
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (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). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (229031782..229032076)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (228410400..228410694)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (229167529..229167823)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene eukaryotic translation elongation factor 1 alpha 2 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:228947507-228947724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1924 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:228984653-228985467 Neighboring gene MPRA-validated peak749 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229001855-229002525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229003867-229004535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229035335-229035990 Neighboring gene Sharpr-MPRA regulatory region 14212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229054689-229055189 Neighboring gene uncharacterized LOC124904539 Neighboring gene uncharacterized LOC105373143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229092976-229093836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229115036-229115642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229125306-229126056 Neighboring gene Sharpr-MPRA regulatory region 10577 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229163271-229164008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229194589-229195089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229195717-229196216 Neighboring gene iron-sulfur cluster assembly 1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229223803-229224521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229227240-229228172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229228173-229229104 Neighboring gene long intergenic non-protein coding RNA 2815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229243991-229244514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229244515-229245036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229251653-229252154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229252155-229252654 Neighboring gene Sharpr-MPRA regulatory region 2560

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

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)

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_073945.1 

    Range
    101..395
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    229031782..229032076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    228410400..228410694
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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