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LOC129932591 ATAC-STARR-seq lymphoblastoid active region 2611 [ Homo sapiens (human) ]

Gene ID: 129932591, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932591
Gene description
ATAC-STARR-seq lymphoblastoid active region 2611
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 LOC129932591 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 (224377967..224378056)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (223566831..223566920)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (224565669..224565758)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear VCP like Neighboring gene RNA, U6 small nuclear 1008, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2608 Neighboring gene Sharpr-MPRA regulatory region 12366 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224523487-224523975 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:224527150-224527870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224528593-224529312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224544931-224545431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2610 Neighboring gene cornichon family member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224616083-224616672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224616673-224617262 Neighboring gene WD repeat domain 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1853 Neighboring gene microRNA 4742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2612 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224661692-224661861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224667779-224668305 Neighboring gene cornichon family AMPA receptor auxiliary protein 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:224685507-224686036 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224686037-224686568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:224687944-224688444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:224688445-224688945 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224696756-224697667 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224703315-224703519 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224759465-224759964 Neighboring gene aldehyde reductase family 1 member B1 pseudogene 1

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_165616.1 

    Range
    101..190
    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
    224377967..224378056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    223566831..223566920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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