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LOC121740709 Sharpr-MPRA regulatory region 2598 [ Homo sapiens (human) ]

Gene ID: 121740709, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121740709
Gene description
Sharpr-MPRA regulatory region 2598
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121740709 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (8461259..8461553)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (11281844..11282138, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (8318769..8319063)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:8256091-8256704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8269459-8270166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8270167-8270872 Neighboring gene long intergenic non-protein coding RNA 2949 Neighboring gene uncharacterized LOC107986913 Neighboring gene long intergenic non-protein coding RNA 2950 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:8324360-8325559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8328681-8329307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18897 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18898 Neighboring gene Sharpr-MPRA regulatory region 7090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26968 Neighboring gene uncharacterized LOC105379224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26969 Neighboring gene RNA, 7SL, cytoplasmic 178, 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_075771.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    8461259..8461553
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    4890564..4890858 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    11281844..11282138 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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