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LOC120961779 Sharpr-MPRA regulatory region 7769 [ Homo sapiens (human) ]

Gene ID: 120961779, updated on 12-Sep-2024

Summary

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Gene symbol
LOC120961779
Gene description
Sharpr-MPRA regulatory region 7769
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 unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC120961779 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (111049852..111050146)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (111472900..111473198)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (111807429..111807723)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16374 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:111510337-111510838 Neighboring gene NANOG hESC enhancer GRCh37_chr2:111529706-111530207 Neighboring gene acyl-CoA oxidase like Neighboring gene ReSE screen-validated silencer GRCh37_chr2:111553982-111554181 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:111556532-111557731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111558229-111558834 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:111559681-111560360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:111570488-111570988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111594132-111595120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111616831-111617348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111623769-111624474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111624475-111625179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111626664-111627274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:111631628-111632251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111634418-111635282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111661014-111661514 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:111731587-111731774 Neighboring gene NANOG hESC enhancer GRCh37_chr2:111755936-111756510 Neighboring gene ribosomal protein L5 pseudogene 9 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:111789964-111791163 Neighboring gene uncharacterized LOC124907866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16380 Neighboring gene ACOXL antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11865 Neighboring gene Sharpr-MPRA regulatory region 8028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11866 Neighboring gene BCL2 like 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:111923374-111923874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16383

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_073996.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    111049852..111050146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    111472900..111473198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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