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LOC123956164 Sharpr-MPRA regulatory region 2459 [ Homo sapiens (human) ]

Gene ID: 123956164, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956164
Gene description
Sharpr-MPRA regulatory region 2459
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin) and 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:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (74581480..74581774)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (75783784..75784078)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73995809..73996103)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene GTF2I repeat domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73909445-73910043 Neighboring gene RNA, 5S ribosomal pseudogene 233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73919312-73919812 Neighboring gene Williams-Beuren syndrome chromosome region 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73995345-73995846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74001529-74002116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74002117-74002703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18282 Neighboring gene microRNA 10525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031162-74031727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031728-74032292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18286 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74075507-74076155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26175 Neighboring gene general transcription factor IIi Neighboring gene GTF2I antisense RNA 1

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_078358.1 

    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
    74581480..74581774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    75783784..75784078
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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