U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    LOC130004596 ATAC-STARR-seq lymphoblastoid active region 3927 [ Homo sapiens (human) ]

    Gene ID: 130004596, updated on 12-Sep-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC130004596
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 3927
    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]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC130004596 in Genome Data Viewer
    Location:
    chromosome: 10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102394381..102394670)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (103279329..103279618)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (104154138..104154427)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3926 Neighboring gene paired like homeodomain 3 Neighboring gene golgi brefeldin A resistant guanine nucleotide exchange factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029238-104029738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104029739-104030239 Neighboring gene Sharpr-MPRA regulatory region 13217 Neighboring gene Sharpr-MPRA regulatory region 15234 Neighboring gene uncharacterized LOC107984263 Neighboring gene MPRA-validated peak1080 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:104147078-104147638 Neighboring gene NANOG hESC enhancer GRCh37_chr10:104151284-104151791 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:104151792-104152298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3929 Neighboring gene Sharpr-MPRA regulatory region 13585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104160632-104161328 Neighboring gene Sharpr-MPRA regulatory region 3575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104169870-104170552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:104170553-104171234 Neighboring gene nuclear factor kappa B subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3934 Neighboring gene pleckstrin and Sec7 domain containing Neighboring gene F-box and leucine rich repeat protein 15

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_184041.1 

      Range
      101..390
      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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      102394381..102394670
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      103279329..103279618
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases