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LOC112577574 Sharpr-MPRA regulatory region 8944 [ Homo sapiens (human) ]

Gene ID: 112577574, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577574
Gene description
Sharpr-MPRA regulatory region 8944
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 8:EnhW, candidate weak enhancer and open chromatin) 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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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27122658..27122952)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26963807..26964101)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27449149..27449443)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27332251-27332894 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27332895-27333538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27333539-27334182 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:27334827-27335470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27338587-27339240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27339241-27339895 Neighboring gene terminal nucleotidyltransferase 5B Neighboring gene uncharacterized LOC101928391 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27361397-27361898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27364454-27364954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27368765-27369317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27372795-27373295 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr1:27376127-27376944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27376945-27377760 Neighboring gene Sharpr-MPRA regulatory region 512 Neighboring gene Sharpr-MPRA regulatory region 8493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27428314-27429172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27429173-27430031 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:27431568-27432767 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27436564-27436768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27438447-27438948 Neighboring gene solute carrier family 9 member A1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27440010-27440584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27440585-27441158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27443453-27444164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27444875-27445585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27445586-27446295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27464001-27464812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27482511-27483010 Neighboring gene uncharacterized LOC102723760 Neighboring gene ribosomal protein L18a pseudogene 5

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_060490.1 

    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
    27122658..27122952
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26963807..26964101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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