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LOC121627902 Sharpr-MPRA regulatory region 5058 [ Homo sapiens (human) ]

Gene ID: 121627902, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627902
Gene description
Sharpr-MPRA regulatory region 5058
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 matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 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 (32534626..32534920)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (34259496..34259790)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (31122429..31122723)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nucleolar protein 4 like Neighboring gene uncharacterized LOC124904886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31084748-31085264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31093704-31094386 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31094387-31095068 Neighboring gene uncharacterized LOC101929698 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31098781-31099176 Neighboring gene VISTA enhancer hs2225 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12791 Neighboring gene uncharacterized LOC105372592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31124544-31125515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31126487-31127458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31128887-31129392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31129393-31129898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31149672-31150323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31151241-31151782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31158183-31158907 Neighboring gene Sharpr-MPRA regulatory region 4335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31164325-31165278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31168247-31168946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12795 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17718 Neighboring gene NOL4L divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31184984-31185484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31185485-31185985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31186003-31186504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31189553-31190054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31193059-31193558 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31193901-31194067

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_075093.1 

    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
    32534626..32534920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    34259496..34259790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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