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LOC130002882 ATAC-STARR-seq lymphoblastoid active region 29223 [ Homo sapiens (human) ]

Gene ID: 130002882, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002882
Gene description
ATAC-STARR-seq lymphoblastoid active region 29223
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 LOC130002882 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 (132873444..132873553)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145085257..145085366)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135748831..135748940)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135545227-135546094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29221 Neighboring gene general transcription factor IIIC subunit 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135597764-135598270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135599285-135599790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608498-135608998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135608999-135609499 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:135620695-135621194 Neighboring gene adenylate kinase 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29222 Neighboring gene Sharpr-MPRA regulatory region 7884 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:135683689-135684190 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135711155-135711317 Neighboring gene U6 spliceosomal RNA Neighboring gene ReSE screen-validated silencer GRCh37_chr9:135729901-135730092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135731149-135731650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135731651-135732150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135732573-135733346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135738096-135738827 Neighboring gene sperm acrosome associated 9 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:135778941-135779625 Neighboring gene TSC complex subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20438 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20439 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135819875-135820608

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_182328.1 

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

    Range
    132873444..132873553
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145085257..145085366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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