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LOC130057592 ATAC-STARR-seq lymphoblastoid active region 9839 [ Homo sapiens (human) ]

Gene ID: 130057592, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057592
Gene description
ATAC-STARR-seq lymphoblastoid active region 9839
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 LOC130057592 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 (75196109..75196168)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (73066152..73066211)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (75488450..75488509)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9836 Neighboring gene uncharacterized LOC124903530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9837 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:75432358-75433049 Neighboring gene MPRA-validated peak2388 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75448835-75449336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75449337-75449836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75450542-75451042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75451043-75451543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75469758-75470317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75480455-75480956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75480957-75481456 Neighboring gene ribosomal protein L36a pseudogene 45 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75484212-75484914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75487637-75488181 Neighboring gene uncharacterized LOC107984772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75493826-75494548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6665 Neighboring gene chromosome 15 open reading frame 39 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9846 Neighboring gene taste receptor cell gene 1, 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_192013.1 

    Range
    101..160
    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
    75196109..75196168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    73066152..73066211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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