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LOC112590814 Sharpr-MPRA regulatory region 6224 [ Homo sapiens (human) ]

Gene ID: 112590814, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112590814
Gene description
Sharpr-MPRA regulatory region 6224
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, Jun 2018]
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Genomic context

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See LOC112590814 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 (59730917..59731211)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (59609368..59609662)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (60196589..60196883)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 941 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:59764225-59765424 Neighboring gene FGGY divergent transcript Neighboring gene FGGY carbohydrate kinase domain containing Neighboring gene MPRA-validated peak254 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8792 Neighboring gene MPRA-validated peak255 silencer Neighboring gene uncharacterized LOC124904192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1110 Neighboring gene MPRA-validated peak256 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:60134970-60135524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:60139185-60139712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1111 Neighboring gene microRNA 4711 Neighboring gene uncharacterized LOC105378758 Neighboring gene uncharacterized LOC101926944

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_060604.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    59730917..59731211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    59609368..59609662
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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