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LOC129932211 ATAC-STARR-seq lymphoblastoid active region 2309 [ Homo sapiens (human) ]

Gene ID: 129932211, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932211
Gene description
ATAC-STARR-seq lymphoblastoid active region 2309
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 LOC129932211 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 (201153711..201153860)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (200410687..200410836)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (201122839..201122988)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel subunit alpha1 S Neighboring gene uncharacterized LOC124904481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201070239-201070740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201070741-201071240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201072987-201073503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201084381-201084901 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201095506-201096496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201096497-201097487 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:201103675-201103881 Neighboring gene achaete-scute family bHLH transcription factor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1687 Neighboring gene transmembrane protein 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2310 Neighboring gene immunoglobulin like and fibronectin type III domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201194684-201195676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201252475-201253004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201271917-201272422 Neighboring gene plakophilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201290713-201291214

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_165248.1 

    Range
    101..250
    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
    201153711..201153860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    200410687..200410836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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