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LOC123575671 Sharpr-MPRA regulatory region 4667 [ Homo sapiens (human) ]

Gene ID: 123575671, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575671
Gene description
Sharpr-MPRA regulatory region 4667
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575671 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (12034396..12034690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (11902550..11902844)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (12034629..12034923)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986570 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:11935862-11936084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24000 Neighboring gene uncharacterized LOC101928253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12010596-12011140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16921 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12036533-12037034 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:12037035-12037534 Neighboring gene HIVEP zinc finger 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12099563-12100062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24008 Neighboring gene Sharpr-MPRA regulatory region 8641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12164419-12164919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24013 Neighboring gene uncharacterized LOC124901260 Neighboring gene endothelin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12288202-12288702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:12288703-12289203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24015 Neighboring gene SUMO2 pseudogene 12

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_077930.1 

    Range
    101..395
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    12034396..12034690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    11902550..11902844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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