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LOC129930592 ATAC-STARR-seq lymphoblastoid active region 1067 [ Homo sapiens (human) ]

Gene ID: 129930592, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930592
Gene description
ATAC-STARR-seq lymphoblastoid active region 1067
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 LOC129930592 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (54804882..54805091)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (54685100..54685309)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (55270555..55270764)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:55229956-55230579 Neighboring gene prolyl-tRNA synthetase 2, mitochondrial Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55246797-55247339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55247340-55247881 Neighboring gene uncharacterized LOC124904182 Neighboring gene tetratricopeptide repeat domain 22 Neighboring gene Sharpr-MPRA regulatory region 10932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55261394-55261933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55261934-55262472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:55266799-55267564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55277747-55278246 Neighboring gene ciliary microtubule associated protein 2 Neighboring gene uncharacterized LOC124904183 Neighboring gene MPRA-validated peak246 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55316729-55317230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55317231-55317730 Neighboring gene 24-dehydrocholesterol reductase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:55348920-55349489 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:55352395-55352896

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_163642.1 

    Range
    101..310
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    54804882..54805091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    54685100..54685309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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