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LOC124310646 Sharpr-MPRA regulatory region 6068 [ Homo sapiens (human) ]

Gene ID: 124310646, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310646
Gene description
Sharpr-MPRA regulatory region 6068
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310646 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (126499250..126499544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (138704716..138705010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (129261529..129261823)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene multivesicular body subunit 12B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129177967-129178559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129183037-129183720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129183721-129184405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129185921-129186420 Neighboring gene uncharacterized LOC124902337 Neighboring gene VISTA enhancer hs186 Neighboring gene non-coding repressor of NFAT Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129214117-129214618 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:129236685-129237884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129238046-129238625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129238626-129239204 Neighboring gene Sharpr-MPRA regulatory region 3753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129270146-129270646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20288 Neighboring gene uncharacterized LOC105376276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129281950-129282456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129283760-129284260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129284261-129284761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129293424-129294057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129296024-129296550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129296551-129297075 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:129297602-129298126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129298952-129299452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129299453-129299953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129319165-129319741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129345084-129345584 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129350068-129350902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:129350903-129351737 Neighboring gene uncharacterized LOC124902272

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_078927.1 

    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
    126499250..126499544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    138704716..138705010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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