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LOC129932823 ATAC-STARR-seq lymphoblastoid active region 2772 [ Homo sapiens (human) ]

Gene ID: 129932823, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932823
Gene description
ATAC-STARR-seq lymphoblastoid active region 2772
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 LOC129932823 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 (234882598..234882667)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234273353..234273422)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235018345..235018414)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:234915140-234915338 Neighboring gene uncharacterized LOC124904557 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234915801-234916406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234916407-234917010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234920999-234921744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234941970-234942552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234942553-234943136 Neighboring gene uncharacterized LOC107985365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:234951823-234952324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:234952325-234952824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2771 Neighboring gene Sharpr-MPRA regulatory region 4610 Neighboring gene RNY4 pseudogene 16 Neighboring gene Sharpr-MPRA regulatory region 12865 Neighboring gene GATA motif-containing MPRA enhancer 94/95 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:235017825-235017961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235034177-235035114 Neighboring gene RNA, 7SL, cytoplasmic 668, pseudogene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:235048721-235049466 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:235049467-235050211 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235053443-235054122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235056123-235056622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235067947-235068447 Neighboring gene long intergenic non-protein coding RNA 2971 Neighboring gene lncRNA negative regulator of antiviral signaling

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_165848.1 

    Range
    101..170
    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
    234882598..234882667
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    234273353..234273422
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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