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LOC129997353 ATAC-STARR-seq lymphoblastoid active region 25205 [ Homo sapiens (human) ]

Gene ID: 129997353, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997353
Gene description
ATAC-STARR-seq lymphoblastoid active region 25205
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 LOC129997353 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 (143843372..143843581)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (145036052..145036261)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (144164509..144164718)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378035 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143832494-143833156 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143833157-143833817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25203 Neighboring gene PHACTR2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17630 Neighboring gene phosphatase and actin regulator 2 Neighboring gene MPRA-validated peak6177 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:143958702-143959245 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:143998446-143999294 Neighboring gene MPRA-validated peak6179 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144059920-144060420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144065167-144065836 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144067178-144067848 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144067849-144068518 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144068519-144069188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25206 Neighboring gene MPRA-validated peak6180 silencer Neighboring gene MPRA-validated peak6181 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25207 Neighboring gene zinc finger C2HC-type containing 1B Neighboring gene LTV1 ribosome biogenesis factor Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144279682-144280240 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:144285771-144286284 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144293958-144294542 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144294543-144295127 Neighboring gene PLAG1 like zinc finger 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144328825-144329007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17632 Neighboring gene hydatidiform mole associated and imprinted

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_176799.1 

    Range
    101..310
    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
    143843372..143843581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    145036052..145036261
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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