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LOC130002738 ATAC-STARR-seq lymphoblastoid active region 29104 [ Homo sapiens (human) ]

Gene ID: 130002738, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002738
Gene description
ATAC-STARR-seq lymphoblastoid active region 29104
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 LOC130002738 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129139584..129139673)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141343038..141343127)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20359 Neighboring gene dolichyldiphosphatase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131864095-131864840 Neighboring gene carnitine O-acetyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:131873890-131874430 Neighboring gene protein phosphatase 2 phosphatase activator Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131889125-131890047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131893809-131894363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131895457-131895957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131900767-131901394 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131902025-131902652 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131902653-131903282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131905799-131906426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131907685-131908314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131910837-131911337 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131929576-131930565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131937384-131938105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20367 Neighboring gene Sharpr-MPRA regulatory region 13939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131941425-131942348 Neighboring gene uncharacterized LOC105376289 Neighboring gene immediate early response 5 like Neighboring gene Sharpr-MPRA regulatory region 2152

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_182184.1 

    Range
    101..190
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    129139584..129139673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141343038..141343127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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