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LOC112163608 Sharpr-MPRA regulatory region 10893 [ Homo sapiens (human) ]

Gene ID: 112163608, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163608
Gene description
Sharpr-MPRA regulatory region 10893
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. A subregion was validated as an enhancer by Sharpr-MPRA (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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). Another subregion was validated as an enhancer by the ChIP-STARR-seq MPRA in naive human embryonic stem cells, where it is marked by the H3K27ac histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (53379269..53380099)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53345316..53346146)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (53773589..53773883)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6415 Neighboring gene aladin WD repeat nucleoporin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53717573-53718306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53721571-53722293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53722294-53723015 Neighboring gene Sp7 transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4509 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:53774734-53775492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6420 Neighboring gene Sp1 transcription factor Neighboring gene CRISPRi-validated cis-regulatory element chr12.1897 Neighboring gene anti-Mullerian hormone receptor type 2

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 6419
  • H3K27ac hESC enhancer GRCh37_chr12:53773053-53773553

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_056589.2 

    Range
    101..931
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    53379269..53380099
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791795.1 Reference GRCh38.p14 PATCHES

    Range
    103019..103849
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53345316..53346146
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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