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LOC123956151 Sharpr-MPRA regulatory region 1113 [ Homo sapiens (human) ]

Gene ID: 123956151, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956151
Gene description
Sharpr-MPRA regulatory region 1113
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (55568876..55569170)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (55729158..55729452)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (55636569..55636863)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA exonuclease 1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26014 Neighboring gene MPRA-validated peak6524 silencer Neighboring gene LanC like glutathione S-transferase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:55470127-55471114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55495178-55495682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55495683-55496185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55507999-55508825 Neighboring gene VOPP1 WW domain binding protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55535735-55536236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55540666-55541332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55545601-55546151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55556042-55556542 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:55560767-55561966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55579955-55580476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55580477-55580998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55584685-55585190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55592347-55592848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26033 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:55606949-55607581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26035 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:55622524-55623470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26041 Neighboring gene VOPP1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:55661073-55661572 Neighboring gene CDC42 pseudogene 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

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_078346.1 

    Range
    101..395
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    55568876..55569170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    55729158..55729452
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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