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LOC125177351 Sharpr-MPRA regulatory region 8667 [ Homo sapiens (human) ]

Gene ID: 125177351, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177351
Gene description
Sharpr-MPRA regulatory region 8667
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (74866211..74866505)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (80912929..80913223)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74763414-74763939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74763940-74764464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74767393-74767952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74771195-74771902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74781673-74782338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74782339-74783002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74786737-74787236 Neighboring gene fatty acid 2-hydroxylase Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:74793901-74795100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7703 Neighboring gene uncharacterized LOC105371343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11111 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74905369-74905917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74908123-74908848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:74909577-74910302 Neighboring gene WD repeat domain 59 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74997467-74997687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11112 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75020112-75020312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11116 Neighboring gene zinc and ring finger 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75095860-75097059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75108734-75109234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75109235-75109735 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75113000-75113201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75113937-75114482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75121619-75122275 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75127186-75127378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129219-75129949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129950-75130679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75136275-75136776 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11121

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

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_080419.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    74866211..74866505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    80912929..80913223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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