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LOC121366076 Sharpr-MPRA regulatory region 15191 [ Homo sapiens (human) ]

Gene ID: 121366076, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366076
Gene description
Sharpr-MPRA regulatory region 15191
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121366076 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (98361052..98361346)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (99241033..99241327)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (100120809..100121103)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100021241-100022130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100026897-100027398 Neighboring gene lysyl oxidase like 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100027399-100027898 Neighboring gene uncharacterized LOC124902489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100081209-100081774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3864 Neighboring gene NANOG hESC enhancer GRCh37_chr10:100113671-100114175 Neighboring gene uncharacterized LOC105378449 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:100127757-100128375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:100134557-100135058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:100135059-100135558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3865 Neighboring gene pyridine nucleotide-disulphide oxidoreductase domain 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3866 Neighboring gene microRNA 1287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3867 Neighboring gene MPRA-validated peak1064 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100182997-100183558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100183559-100184120 Neighboring gene HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 Neighboring gene microRNA 4685

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_074518.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    98361052..98361346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    99241033..99241327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
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