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LOC129995380 ATAC-STARR-seq lymphoblastoid active region 23718 [ Homo sapiens (human) ]

Gene ID: 129995380, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995380
Gene description
ATAC-STARR-seq lymphoblastoid active region 23718
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 LOC129995380 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177431650..177431869)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177974901..177975120)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176858651..176858870)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176828971-176829828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176830685-176831542 Neighboring gene profilin 3 Neighboring gene coagulation factor XII Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176853351-176853890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23719 Neighboring gene G protein-coupled receptor kinase 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176867639-176868335 Neighboring gene PRR7 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176874472-176875100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876138-176876638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876639-176877139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16688 Neighboring gene proline rich 7, synaptic Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176881361-176882061 Neighboring gene Sharpr-MPRA regulatory region 1974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176884168-176884868 Neighboring gene drebrin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176894101-176894646 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895193-176895738 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895739-176896284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176897377-176897922 Neighboring gene hESC enhancers GRCh37_chr5:176899493-176899996 and GRCh37_chr5:176899997-176900498

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 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_174826.1 

    Range
    101..320
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    177431650..177431869
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177974901..177975120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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