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LOC112694692 Sharpr-MPRA regulatory region 9877 [ Homo sapiens (human) ]

Gene ID: 112694692, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694692
Gene description
Sharpr-MPRA regulatory region 9877
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 matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 3:PromF, promoter flanking). [provided by RefSeq, Jul 2018]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (21096288..21096582)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (21155742..21156036)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (21076929..21077223)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein S11 pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 3083 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:20998081-20999280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:21000384-21001342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21033223-21033723 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:21070570-21071121 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:21081423-21082292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17616 Neighboring gene long intergenic non-protein coding RNA 237 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:21098327-21099526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17619 Neighboring gene RPL24 pseudogene 2 Neighboring gene RNA, 5S ribosomal pseudogene 477 Neighboring gene kizuna centrosomal protein

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_060722.1 

    Range
    101..395
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    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    21096288..21096582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    21155742..21156036
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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