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LOC129997187 ATAC-STARR-seq lymphoblastoid active region 25081 [ Homo sapiens (human) ]

Gene ID: 129997187, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997187
Gene description
ATAC-STARR-seq lymphoblastoid active region 25081
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 LOC129997187 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 (133967026..133967075)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (135155046..135155095)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (134288164..134288213)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene TCF21 antisense RNA inducing promoter demethylation Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17554 Neighboring gene long intergenic non-protein coding RNA 1312 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:134175312-134176050 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:134209799-134210712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:134211964-134212728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:134213614-134214222 Neighboring gene transcription factor 21 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17555 Neighboring gene umcharacterized LOC128092253 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90026 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90028 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90037 Neighboring gene epithelial splicing regulatory protein 1 pseudogene Neighboring gene TATA-box binding protein like 1 Neighboring gene solute carrier family 2 member 12 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:134381498-134382162 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:134382163-134382827 Neighboring gene uncharacterized LOC124901404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17556 Neighboring gene high mobility group AT-hook 1 pseudogene 7

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_176633.1 

    Range
    101..150
    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
    133967026..133967075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    135155046..135155095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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