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LOC130057507 ATAC-STARR-seq lymphoblastoid active region 9738 [ Homo sapiens (human) ]

Gene ID: 130057507, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057507
Gene description
ATAC-STARR-seq lymphoblastoid active region 9738
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 LOC130057507 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 (73995129..73995298)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71812474..71812643)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74287470..74287639)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene LOXL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74219309-74220142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74220143-74220976 Neighboring gene Sharpr-MPRA regulatory region 13651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74229856-74230455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74232882-74233777 Neighboring gene lysyl oxidase like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74244872-74245555 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74249081-74250280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9732 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74280304-74281503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9737 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6644 Neighboring gene stomatin like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74289929-74290431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9739 Neighboring gene PML nuclear body scaffold Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74311530-74311700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74329432-74330313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74333577-74334149 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74338704-74338895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74357879-74358380 Neighboring gene dynamin 1 pseudogene 33 Neighboring gene RNA, 7SL, cytoplasmic 429, pseudogene Neighboring gene golgin A6 family member A

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_191928.1 

    Range
    101..270
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    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
    73995129..73995298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    71812474..71812643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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