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LOC130058576 ATAC-STARR-seq lymphoblastoid active region 10513 [ Homo sapiens (human) ]

Gene ID: 130058576, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058576
Gene description
ATAC-STARR-seq lymphoblastoid active region 10513
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 LOC130058576 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (17530307..17530426)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (17537358..17537477)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (17624164..17624283)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene xylosyltransferase 1 Neighboring gene uncharacterized LOC107987234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:17564811-17565312 Neighboring gene uncharacterized LOC105371106 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:17591055-17591654 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:17665142-17666341 Neighboring gene NANOG hESC enhancer GRCh37_chr16:17672718-17673219 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:17700860-17702059 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:17839175-17839850 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:17840527-17841202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:17838498-17839174 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:17851169-17851784 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:17851785-17852400 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:17870498-17870998 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:17930405-17931604 Neighboring gene uncharacterized LOC107984893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:18065894-18066422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:18066423-18066951 Neighboring gene ribosomal protein L7 pseudogene 47 Neighboring gene uncharacterized LOC105371108

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_192997.1 

    Range
    101..220
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    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    17530307..17530426
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    17537358..17537477
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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