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LOC130001557 ATAC-STARR-seq lymphoblastoid active region 28213 [ Homo sapiens (human) ]

Gene ID: 130001557, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001557
Gene description
ATAC-STARR-seq lymphoblastoid active region 28213
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 LOC130001557 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (7976751..7976860)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (7983273..7983382)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (7976751..7976860)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:7799542-7800088 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:7879626-7880126 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:7880127-7880627 Neighboring gene uncharacterized LOC105375971 Neighboring gene distal membrane arm assembly component 1 Neighboring gene VISTA enhancer hs304 Neighboring gene Sharpr-MPRA regulatory region 3353 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:8485393-8486592 Neighboring gene NANOG hESC enhancer GRCh37_chr9:8514616-8515117 Neighboring gene protein tyrosine phosphatase receptor type D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:8600067-8600567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:8643271-8644250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:8644251-8645230 Neighboring gene ribosomal protein L18a pseudogene 11 Neighboring gene RNA, U7 small nuclear 185 pseudogene

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_181003.1 

    Range
    101..210
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    7976751..7976860
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    7983273..7983382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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