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

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

Summary

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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]
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Genomic context

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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

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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_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

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