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LOC129996846 ATAC-STARR-seq lymphoblastoid silent region 17403 [ Homo sapiens (human) ]

Gene ID: 129996846, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996846
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17403
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC129996846 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 (93454071..93454120)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (94666039..94666088)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (94163789..94163838)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr6:93833219-93833931 Neighboring gene COP9 signalosome subunit 5 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:93881681-93882492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:93908284-93908784 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_97174 Neighboring gene EPH receptor A7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17402 Neighboring gene uncharacterized LOC105377899 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:94346522-94347093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:94347094-94347664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:94373923-94374424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:94374425-94374924 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:94495986-94496512 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:94496513-94497037 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:94497038-94497563 Neighboring gene uncharacterized LOC124901496 Neighboring gene tumor suppressor TSG1

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_176292.1 

    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
    93454071..93454120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    94666039..94666088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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