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LOC125371460 Sharpr-MPRA regulatory region 7356 [ Homo sapiens (human) ]

Gene ID: 125371460, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371460
Gene description
Sharpr-MPRA regulatory region 7356
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, May 2022]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5103178..5103472)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5088949..5089243)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4890817-4891318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4891319-4891818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4908546-4909452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4923227-4923955 Neighboring gene arrestin domain containing 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4930593-4931092 Neighboring gene ubiquitin like with PHD and ring finger domains 1 Neighboring gene microRNA 4747 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4983945-4984871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4988552-4989057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4989779-4990280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4989058-4989562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4990281-4990780 Neighboring gene Sharpr-MPRA regulatory region 13405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5004333-5004833 Neighboring gene lysine demethylase 4B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5026529-5027028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5036688-5037262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5042227-5042746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5042747-5043265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5046625-5047428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5048922-5049524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5052015-5052514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5083429-5084111 Neighboring gene Sharpr-MPRA regulatory region 3293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5092687-5093236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5093237-5093784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5096761-5097261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5095749-5096249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5096260-5096760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5109710-5110566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5111029-5111538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5114178-5115133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5115134-5116088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5121454-5121994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5125360-5125896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5125897-5126434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5126435-5126971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5126972-5127509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5128585-5129120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5129121-5129658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5129659-5130195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5130196-5130732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5130733-5131269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137253-5137754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137755-5138254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5151275-5152046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5153977-5154477 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5165571-5165790 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:5172675-5173874 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5173956-5174147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5191478-5192140 Neighboring gene PTPRS antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225323-5225942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225943-5226561 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5247733-5247924 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5268923-5269423 Neighboring gene ribosomal protein L32 pseudogene 34

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_080730.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    5103178..5103472
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    5088949..5089243
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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