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LOC121530604 Sharpr-MPRA regulatory region 4454 [ Homo sapiens (human) ]

Gene ID: 121530604, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121530604
Gene description
Sharpr-MPRA regulatory region 4454
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90141697..90141991)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87897751..87898045)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90684929..90685223)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 710 Neighboring gene ZNF710 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90627210-90627710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90627711-90628211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90630317-90631230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90634376-90634876 Neighboring gene NANOG hESC enhancer GRCh37_chr15:90638658-90639182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644126-90644981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644982-90645836 Neighboring gene isocitrate dehydrogenase (NADP(+)) 2 Neighboring gene IDH2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90664819-90665318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90686773-90687307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701094-90701611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701612-90702128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704142-90704734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704735-90705327 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90707039-90707194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90717667-90718167 Neighboring gene RNA, 7SL, cytoplasmic 346, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90721295-90722200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90727462-90728195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90744110-90745081 Neighboring gene semaphorin 4B Neighboring gene ribosomal protein S12 pseudogene 26

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_074802.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    90141697..90141991
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    87897751..87898045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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