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LOC130068482 ATAC-STARR-seq lymphoblastoid active region 29799 [ Homo sapiens (human) ]

Gene ID: 130068482, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130068482
Gene description
ATAC-STARR-seq lymphoblastoid active region 29799
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 LOC130068482 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (97398441..97398530)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (95837882..95837971)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene diaphanous related formin 2 Neighboring gene uncharacterized LOC124905287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96454836-96455540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96455541-96456245 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:96506917-96507740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96544328-96544889 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96544890-96545450 Neighboring gene NANOG hESC enhancer GRCh37_chrX:96596543-96597044 Neighboring gene RNA, 7SL, cytoplasmic 74, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:96737386-96738055 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:96759203-96760072 Neighboring gene DIAPH2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29800 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96838258-96838906 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96838907-96839554 Neighboring gene NANOG hESC enhancer GRCh37_chrX:96852041-96852542 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:96871608-96872807 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96894224-96894852 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:96894853-96895479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:97058194-97058694 Neighboring gene endogenous retrovirus group FC1 Env polyprotein

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_202897.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    97398441..97398530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    95837882..95837971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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