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LOC130000079 ATAC-STARR-seq lymphoblastoid active region 27145 [ Homo sapiens (human) ]

Gene ID: 130000079, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000079
Gene description
ATAC-STARR-seq lymphoblastoid active region 27145
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 LOC130000079 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (27374476..27374525)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (27651293..27651342)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (27231993..27232042)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27093978-27094478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27094479-27094979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:27099673-27100624 Neighboring gene stathmin 4 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:27132319-27132821 Neighboring gene tripartite motif containing 35 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27183969-27184798 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:27184956-27185152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27139 Neighboring gene protein tyrosine kinase 2 beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19048 Neighboring gene Sharpr-MPRA regulatory region 9089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27141 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:27219644-27220174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27153 Neighboring gene Sharpr-MPRA regulatory region 13363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27287852-27288568 Neighboring gene microRNA 6842 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:27316840-27317083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27319910-27320838 Neighboring gene cholinergic receptor nicotinic alpha 2 subunit

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_179525.1 

    Range
    101..150
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    27374476..27374525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    27651293..27651342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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