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LOC130000635 ATAC-STARR-seq lymphoblastoid active region 27549 [ Homo sapiens (human) ]

Gene ID: 130000635, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000635
Gene description
ATAC-STARR-seq lymphoblastoid active region 27549
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 LOC130000635 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 (79765464..79765703)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (80196800..80197039)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (80677699..80677938)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901965 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:80635352-80636551 Neighboring gene uncharacterized LOC107986893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19311 Neighboring gene uncharacterized LOC101927040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:80695841-80696641 Neighboring gene long intergenic non-protein coding RNA 1607 Neighboring gene U7 small nuclear RNA Neighboring gene hes related family bHLH transcription factor with YRPW motif 1 Neighboring gene RNA, U7 small nuclear 85 pseudogene Neighboring gene Sharpr-MPRA regulatory region 4298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19315 Neighboring gene uncharacterized LOC124901966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19316 Neighboring gene TPD52-MRPS28 readthrough Neighboring gene mitochondrial ribosomal protein S28

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_180081.1 

    Range
    101..340
    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
    79765464..79765703
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    80196800..80197039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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