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LOC130009935 ATAC-STARR-seq lymphoblastoid active region 7850 [ Homo sapiens (human) ]

Gene ID: 130009935, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009935
Gene description
ATAC-STARR-seq lymphoblastoid active region 7850
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 LOC130009935 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 (79194238..79194327)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (78422484..78422573)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (79768373..79768462)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7849 Neighboring gene NIPA2 pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:79693371-79693913 Neighboring gene BCAS2 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7852 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:79772046-79772677 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7855 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:79853422-79854140 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:79857373-79858352 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:79862351-79862939 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:79881601-79882102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:79904806-79905306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:79905307-79905807 Neighboring gene RNA binding motif protein 26 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7857 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:79980055-79981046 Neighboring gene RNA, 5S ribosomal pseudogene 33 Neighboring gene RBM26 antisense RNA 1 Neighboring gene uncharacterized LOC105370274

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_189439.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    79194238..79194327
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    78422484..78422573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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