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LOC121627821 Sharpr-MPRA regulatory region 11006 [ Homo sapiens (human) ]

Gene ID: 121627821, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121627821
Gene description
Sharpr-MPRA regulatory region 11006
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 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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See LOC121627821 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (4182229..4182523)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (4342158..4342452)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (4182229..4182523)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene DLG associated protein 1 Neighboring gene DLGAP1 antisense RNA 3 Neighboring gene RNA, U6 small nuclear 831, pseudogene Neighboring gene DLGAP1 antisense RNA 4 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:4017491-4018172 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 66 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:4117736-4118323 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:4118324-4118910 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:4119078-4119849 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:4124501-4125480 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:4125481-4126460 Neighboring gene uncharacterized LOC124904239 Neighboring gene NANOG hESC enhancer GRCh37_chr18:4195745-4196246 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47861 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47879 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:4233399-4234316 Neighboring gene DLGAP1 antisense RNA 5 Neighboring gene Sharpr-MPRA regulatory region 437 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:4407683-4407856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9259 Neighboring gene elongin C pseudogene 27

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_075011.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    4182229..4182523
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    4342158..4342452
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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