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LOC130063542 ATAC-STARR-seq lymphoblastoid active region 13997 [ Homo sapiens (human) ]

Gene ID: 130063542, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063542
Gene description
ATAC-STARR-seq lymphoblastoid active region 13997
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 LOC130063542 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (10873643..10873762)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11000655..11000774)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10984319..10984438)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10945386-10946023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10946661-10947297 Neighboring gene transmembrane p24 trafficking protein 1 Neighboring gene chromosome 19 open reading frame 38 Neighboring gene HIKESHI pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10973529-10974377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13996 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10984976-10985476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10985477-10985977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13999 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10989664-10990506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10991348-10992190 Neighboring gene coactivator associated arginine methyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10992191-10993032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10993033-10993874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10993875-10994715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11004683-11005484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11009921-11010538 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11015702-11015889 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11031708-11031887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11037946-11038648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11038649-11039349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10096 Neighboring gene Yip1 domain family member 2 Neighboring gene translocase of inner mitochondrial membrane 29

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_197959.1 

    Range
    101..220
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    10873643..10873762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    11000655..11000774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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