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LOC130061558 ATAC-STARR-seq lymphoblastoid active region 12676 [ Homo sapiens (human) ]

Gene ID: 130061558, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061558
Gene description
ATAC-STARR-seq lymphoblastoid active region 12676
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 LOC130061558 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72424763..72424842)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (73297830..73297909)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70420904..70420983)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12668 Neighboring gene long intergenic non-protein coding RNA 2003 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70374994-70375570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8914 Neighboring gene Sharpr-MPRA regulatory region 1101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70382797-70383298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70383299-70383798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12669 Neighboring gene Sharpr-MPRA regulatory region 2052 Neighboring gene long intergenic non-protein coding RNA 673 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:70417088-70418287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70426388-70426888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70464235-70464912 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70472481-70473394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12679 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:70511237-70511737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12680 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70513037-70513545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70552918-70553418 Neighboring gene Sharpr-MPRA regulatory region 2461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12681 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70598976-70599943 Neighboring gene long intergenic non-protein coding RNA 511 Neighboring gene uncharacterized LOC107985005 Neighboring gene ribosomal protein L32 pseudogene 33

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_196707.1 

    Range
    101..180
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    72424763..72424842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    73297830..73297909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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