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LOC130056501 ATAC-STARR-seq lymphoblastoid active region 9062 [ Homo sapiens (human) ]

Gene ID: 130056501, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056501
Gene description
ATAC-STARR-seq lymphoblastoid active region 9062
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC130056501 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (101981060..101981109)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (96216675..96216724)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (102447397..102447446)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit B'gamma Neighboring gene uncharacterized LOC124903388 Neighboring gene Sharpr-MPRA regulatory region 9024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:102276373-102276955 Neighboring gene RNA, U6 small nuclear 790, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102299052-102299552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9055 Neighboring gene nucleophosmin 1 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9057 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102383507-102384162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102394426-102394926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102394927-102395427 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102411293-102411954 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102411955-102412614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102413937-102414598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9059 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:102427622-102427798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9061 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102430647-102431257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102431258-102431867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102436952-102437452 Neighboring gene dynein cytoplasmic 1 heavy chain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9064 Neighboring gene NANOG hESC enhancer GRCh37_chr14:102474230-102474777 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:102493659-102494858 Neighboring gene uncharacterized LOC107984661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102515797-102516781 Neighboring gene Sharpr-MPRA regulatory region 9666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102522673-102523378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102523379-102524082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102530418-102531305 Neighboring gene RNA, 7SL, cytoplasmic 472, pseudogene

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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_190922.1 

    Range
    101..150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    101981060..101981109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    96216675..96216724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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