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LOC121853024 Sharpr-MPRA regulatory region 6418 [ Homo sapiens (human) ]

Gene ID: 121853024, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121853024
Gene description
Sharpr-MPRA regulatory region 6418
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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (14879528..14879822)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (13234729..13235023)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (16251849..16252143)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61623 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18283 Neighboring gene adipocyte associated metabolic related lncRNA 1 Neighboring gene RBMX2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18286 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:16267450-16268649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18287 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16283327-16284086 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16284087-16284844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:16299057-16299650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:16299651-16300242 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61697 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61707 Neighboring gene nuclear receptor interacting protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16377340-16378275 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61740 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:16403577-16404776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18292 Neighboring gene long intergenic non-protein coding RNA 2920

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_076132.1 

    Range
    101..395
    Download
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    14879528..14879822
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    13234729..13235023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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