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LOC121853003 Sharpr-MPRA regulatory region 8915 [ Homo sapiens (human) ]

Gene ID: 121853003, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853003
Gene description
Sharpr-MPRA regulatory region 8915
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (32168546..32168840)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (33893184..33893478)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (30756349..30756643)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12774 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30641518-30641717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12776 Neighboring gene HCK proto-oncogene, Src family tyrosine kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30659475-30659975 Neighboring gene MPRA-validated peak4189 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30672211-30672710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30678826-30679621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30688747-30689248 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:30696834-30698033 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:30708941-30709834 Neighboring gene transmembrane 9 superfamily member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30737033-30737924 Neighboring gene Sharpr-MPRA regulatory region 10464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30747197-30748088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30752983-30753483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30762883-30763484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30763485-30764084 Neighboring gene ribosomal L24 domain containing 1 pseudogene 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30768259-30768439 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30769860-30770360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30776057-30776872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12777 Neighboring gene testis specific protein Y-linked 26, pseudogene

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_076111.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    32168546..32168840
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    33893184..33893478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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