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LOC121725017 Sharpr-MPRA regulatory region 246 [ Homo sapiens (human) ]

Gene ID: 121725017, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725017
Gene description
Sharpr-MPRA regulatory region 246
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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, May 2023]
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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 (41360977..41361729)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (41230387..41231139)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (41826649..41826943)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 861 Neighboring gene uncharacterized LOC124904159 Neighboring gene Sharpr-MPRA regulatory region 968 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 864 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41836248-41837147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41837148-41838046 Neighboring gene forkhead box O6 Neighboring gene FOXO6 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41852742-41853722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41860605-41861174 Neighboring gene Sharpr-MPRA regulatory region 9429 Neighboring gene Sharpr-MPRA regulatory region 3622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41889556-41890113 Neighboring gene uncharacterized LOC105378678 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:41893573-41893763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41899108-41899739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:41899838-41900622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:41916745-41917304 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:41928734-41929234

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

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 silent region 744

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_075487.2 

    Range
    101..853
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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
    41360977..41361729
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646194.1 Reference GRCh38.p14 PATCHES

    Range
    110650..111402
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    41230387..41231139
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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