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LOC129997626 ATAC-STARR-seq lymphoblastoid active region 25404 [ Homo sapiens (human) ]

Gene ID: 129997626, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997626
Gene description
ATAC-STARR-seq lymphoblastoid active region 25404
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 LOC129997626 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (160789281..160789800)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (162146010..162146529)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (161210313..161210832)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901454 Neighboring gene lipoprotein(a) Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:161025992-161027191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:161106525-161107079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17762 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:161158745-161159944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25403 Neighboring gene plasminogen Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17764 Neighboring gene plasminogen-like protein B Neighboring gene NANOG hESC enhancer GRCh37_chr6:161200290-161200791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25406 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91154 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:161262159-161263358 Neighboring gene uncharacterized LOC112267969 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:161298543-161299475 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:161303800-161304432 Neighboring gene MPRA-validated peak6293 silencer Neighboring gene MPRA-validated peak6294 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:161309865-161310670 Neighboring gene MPRA-validated peak6295 silencer Neighboring gene uncharacterized LOC105378093 Neighboring gene uncharacterized LOC102724087

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_177072.1 

    Range
    101..620
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    160789281..160789800
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    162146010..162146529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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