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LOC112694754 Sharpr-MPRA regulatory region 1466 [ Homo sapiens (human) ]

Gene ID: 112694754, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112694754
Gene description
Sharpr-MPRA regulatory region 1466
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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
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Genomic context

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See LOC112694754 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46296375..46296669)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44681734..44682028)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47716289..47716583)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47614165-47614666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47614667-47615166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47621241-47621767 Neighboring gene small nucleolar RNA, C/D box 159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47638552-47639452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47640419-47640920 Neighboring gene lanosterol synthase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13414 Neighboring gene Sharpr-MPRA regulatory region 3947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13416 Neighboring gene MCM3AP antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18599 Neighboring gene minichromosome maintenance complex component 3 associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47709143-47709725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47709726-47710307 Neighboring gene Sharpr-MPRA regulatory region 4411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47715289-47715862 Neighboring gene chromosome 21 open reading frame 58 Neighboring gene ybeY metalloendoribonuclease Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47736113-47736948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47737784-47738618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47738619-47739453 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47741059-47741321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18600 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13420 Neighboring gene uncharacterized LOC128092249 Neighboring gene pericentrin

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_060781.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    46296375..46296669
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    44681734..44682028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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