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LOC130009458 ATAC-STARR-seq lymphoblastoid active region 7514 [ Homo sapiens (human) ]

Gene ID: 130009458, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009458
Gene description
ATAC-STARR-seq lymphoblastoid active region 7514
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 LOC130009458 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (28429887..28430286)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (27652130..27652529)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (29004024..29004423)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene poly(A) specific ribonuclease subunit PAN3 Neighboring gene uncharacterized LOC124903140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28863191-28863692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28863693-28864192 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:28870451-28870609 Neighboring gene uncharacterized LOC124903141 Neighboring gene Sharpr-MPRA regulatory region 10890 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:28896366-28897565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28902230-28902730 Neighboring gene fms related receptor tyrosine kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7513 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:29004443-29005102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:29010702-29011644 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:29012644-29013428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:29014214-29014998 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32819 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:29041404-29041635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5213 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:29078159-29078659 Neighboring gene Sharpr-MPRA regulatory region 5274 Neighboring gene Sharpr-MPRA regulatory region 7947 Neighboring gene uncharacterized LOC124903142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7516 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:29148510-29149709 Neighboring gene uncharacterized LOC105370135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:29157670-29158170

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_189061.1 

    Range
    101..500
    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    28429887..28430286
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    27652130..27652529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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