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LOC112577526 Sharpr-MPRA regulatory region 10908 [ Homo sapiens (human) ]

Gene ID: 112577526, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577526
Gene description
Sharpr-MPRA regulatory region 10908
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-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:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (201019441..201019735)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (200276383..200276677)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (200988569..200988863)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200859988-200860816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200863922-200864432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200864433-200864944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200864945-200865455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200866179-200866766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:200866767-200867356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1682 Neighboring gene innate immunity activator Neighboring gene RNA, U6 small nuclear 704, pseudogene Neighboring gene maestro heat like repeat family member 3, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2304 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:200945792-200946991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2305 Neighboring gene kinesin family member 21B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200969230-200969730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200985675-200986222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:200991037-200991644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1684 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1685 Neighboring gene uncharacterized LOC101929305 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:200993410-200993567 Neighboring gene Sharpr-MPRA regulatory region 14143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201021057-201021557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201022145-201023102 Neighboring gene calcium voltage-gated channel subunit alpha1 S Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201028065-201028818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201031613-201032386 Neighboring gene uncharacterized LOC124904481

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_060445.1 

    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
    201019441..201019735
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    200276383..200276677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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