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LOC120893152 Sharpr-MPRA regulatory region 9477 [ Homo sapiens (human) ]

Gene ID: 120893152, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120893152
Gene description
Sharpr-MPRA regulatory region 9477
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 DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC120893152 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (109776907..109777201)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (109787047..109787341)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (110319529..110319823)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1158 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:110293035-110294234 Neighboring gene glutathione S-transferase mu 3 Neighboring gene uncharacterized LOC124904258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110303188-110303917 Neighboring gene EPS8 signaling adaptor L3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110312201-110313156 Neighboring gene Sharpr-MPRA regulatory region 10752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110329469-110330352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110330353-110331236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110350451-110351094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:110351095-110351737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1454 Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1160 Neighboring gene long intergenic non-protein coding RNA 1768 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:110407495-110408040 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:110420113-110420301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110422869-110423369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110423473-110424313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:110424314-110425153 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7635 Neighboring gene Sharpr-MPRA regulatory region 12342

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_073912.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    109776907..109777201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    109787047..109787341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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