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LOC130065063 ATAC-STARR-seq lymphoblastoid active region 15054 [ Homo sapiens (human) ]

Gene ID: 130065063, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065063
Gene description
ATAC-STARR-seq lymphoblastoid active region 15054
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 LOC130065063 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (52602181..52602260)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (55686629..55686708)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (53105434..53105513)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53072140-53072749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15051 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:53073969-53074577 Neighboring gene ribosomal protein L39 pseudogene 34 Neighboring gene zinc finger protein 701 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:53091538-53091757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53104606-53105112 Neighboring gene zinc finger protein 137, pseudogene Neighboring gene zinc finger protein 677-like Neighboring gene zinc finger protein 83 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53140536-53141054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:53141055-53141572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10996 Neighboring gene Sharpr-MPRA regulatory region 1800 Neighboring gene Zinc finger protein LOC122539214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:53167404-53167904 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:53171845-53172346 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:53172853-53174052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:53177263-53177762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:53179336-53179900 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:53179901-53180465 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:53192883-53193418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10997

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 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_199480.1 

    Range
    101..180
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    52602181..52602260
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    55686629..55686708
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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