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LOC123956162 Sharpr-MPRA regulatory region 1083 [ Homo sapiens (human) ]

Gene ID: 123956162, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956162
Gene description
Sharpr-MPRA regulatory region 1083
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 non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956162 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (74294579..74294873)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (75496852..75497146)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73708909..73709203)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73667761-73668363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73668364-73668966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73668967-73669569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73676953-73677454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73677455-73677954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26153 Neighboring gene replication factor C subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73693216-73693846 Neighboring gene uncharacterized LOC107986742 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73696998-73697628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73704091-73704735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73704736-73705379 Neighboring gene NFE2L2 motif-containing MPRA enhancer 193 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73722243-73722881 Neighboring gene CAP-Gly domain containing linker protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73778293-73779164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73779165-73780034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73786483-73787481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73794630-73795130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73795131-73795631 Neighboring gene Sharpr-MPRA regulatory region 11240 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:73810181-73810370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73818996-73819860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73819861-73820723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18279 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73843950-73844923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73848492-73849112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73849734-73850353 Neighboring gene CAGE-defined high expression enhancer upstream of GTF2IRD1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26159 Neighboring gene GTF2I repeat domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892244-73892825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892826-73893408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26162 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

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_078356.1 

    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
    74294579..74294873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    75496852..75497146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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