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LOC130056741 ATAC-STARR-seq lymphoblastoid active region 9174 [ Homo sapiens (human) ]

Gene ID: 130056741, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056741
Gene description
ATAC-STARR-seq lymphoblastoid active region 9174
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 LOC130056741 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (34102203..34102292)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (31900409..31900498)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (34394404..34394493)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene apoptosis and caspase activation inhibitor Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34277417-34277940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34280047-34280546 Neighboring gene cholinergic receptor muscarinic 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34314668-34315168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:34315169-34315669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6276 Neighboring gene MPRA-validated peak2290 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:34393207-34394064 Neighboring gene ribosomal protein L32 pseudogene 2 Neighboring gene ER membrane protein complex subunit 7 Neighboring gene piggyBac transposable element derived 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:34446570-34447769 Neighboring gene katanin regulatory subunit B1 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6277 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:34506245-34506840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9175 Neighboring gene solute carrier family 12 member 6 Neighboring gene ER membrane protein complex subunit 4

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_191162.1 

    Range
    101..190
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    34102203..34102292
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    31900409..31900498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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