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LOC129932078 ATAC-STARR-seq lymphoblastoid active region 2213 [ Homo sapiens (human) ]

Gene ID: 129932078, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932078
Gene description
ATAC-STARR-seq lymphoblastoid active region 2213
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 LOC129932078 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 (183281833..183281892)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (182641136..182641195)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183250968..183251027)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:183154769-183155968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2212 Neighboring gene laminin subunit gamma 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183197656-183197861 Neighboring gene Sharpr-MPRA regulatory region 7016 Neighboring gene Sharpr-MPRA regulatory region 596 Neighboring gene nicotinamide nucleotide adenylyltransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:183247773-183248584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:183248585-183249395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1629 Neighboring gene RPS3A pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183271685-183272658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183272659-183273632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183300194-183300759 Neighboring gene Sharpr-MPRA regulatory region 8277 Neighboring gene uncharacterized LOC105371646 Neighboring gene MPRA-validated peak501 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1630 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:183440685-183441316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1631 Neighboring gene SMG7 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2214 Neighboring gene SMG7 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1632

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_165118.1 

    Range
    101..160
    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
    183281833..183281892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    182641136..182641195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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