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LOC124310657 Sharpr-MPRA regulatory region 6206 [ Homo sapiens (human) ]

Gene ID: 124310657, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310657
Gene description
Sharpr-MPRA regulatory region 6206
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129246410..129246704)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141449939..141450233)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132008689..132008983)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131937384-131938105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20367 Neighboring gene Sharpr-MPRA regulatory region 13939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131941425-131942348 Neighboring gene uncharacterized LOC105376289 Neighboring gene immediate early response 5 like Neighboring gene Sharpr-MPRA regulatory region 2152 Neighboring gene Sharpr-MPRA regulatory region 6917 Neighboring gene IER5L antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132010097-132010597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132015078-132015933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132020886-132021424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132039310-132040218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132040219-132041127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132046985-132047958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132047959-132048932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132049874-132050856 Neighboring gene long intergenic non-protein coding RNA 2975 Neighboring gene uncharacterized LOC107987133

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_078938.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    129246410..129246704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141449939..141450233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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