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LOC113788256 Sharpr-MPRA regulatory region 6197 [ Homo sapiens (human) ]

Gene ID: 113788256, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113788256
Gene description
Sharpr-MPRA regulatory region 6197
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 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (128176903..128177197)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (129304566..129304860)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (129189149..129189443)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene Pvt1 oncogene Neighboring gene CRISPRi-validated MYC e4 enhancer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:129074055-129074702 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:129077402-129078601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27959 Neighboring gene microRNA 1207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:129118718-129119218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:129121159-129122087 Neighboring gene uncharacterized LOC124902020 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:129179416-129180615 Neighboring gene microRNA 1208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27960 Neighboring gene RN7SK pseudogene 226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27961 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:129325755-129326438 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:129327123-129327805 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:129356185-129356773 Neighboring gene NANOG hESC enhancer GRCh37_chr8:129374035-129374655 Neighboring gene long intergenic non-protein coding RNA 824 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:129566785-129567984 Neighboring gene NFE2L2 motif-containing MPRA enhancer 33

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_062549.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    128176903..128177197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    129304566..129304860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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