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LOC130060169 ATAC-STARR-seq lymphoblastoid active region 11639 [ Homo sapiens (human) ]

Gene ID: 130060169, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130060169
Gene description
ATAC-STARR-seq lymphoblastoid active region 11639
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 LOC130060169 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7627730..7627809)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7531931..7532010)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene FMR1 autosomal homolog 2 Neighboring gene uncharacterized LOC124904134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8133 Neighboring gene MPRA-validated peak2713 silencer Neighboring gene tRNA-undetermined (NNN) 6-1 Neighboring gene sex hormone binding globulin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11640 Neighboring gene spermidine/spermine N1-acetyltransferase family member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:7551198-7551407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7552896-7553396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7553397-7553897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7554172-7554814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7558514-7559332 Neighboring gene ATPase Na+/K+ transporting subunit beta 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7571230-7572027 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7580287-7580898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7580899-7581510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7581511-7582121 Neighboring gene tumor protein p53 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11641 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:7589699-7590898 Neighboring gene WD repeat containing antisense to TP53

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

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_194590.1 

    Range
    101..180
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    7627730..7627809
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    7531931..7532010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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