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LOC129995649 ATAC-STARR-seq lymphoblastoid silent region 16856 [ Homo sapiens (human) ]

Gene ID: 129995649, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129995649
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16856
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 LOC129995649 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 (3751767..3752006)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (3620705..3620944)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (3752001..3752240)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100507336 Neighboring gene TOMM5 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3724209-3724747 Neighboring gene Sharpr-MPRA regulatory region 15708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3737712-3738338 Neighboring gene PX domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16857 Neighboring gene NANOG hESC enhancer GRCh37_chr6:3756018-3756884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3757047-3758012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:3761087-3761600 Neighboring gene Sharpr-MPRA regulatory region 8997 Neighboring gene uncharacterized LOC124901244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3810000-3810500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:3810501-3811001 Neighboring gene uncharacterized LOC107986557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16858 Neighboring gene family with sequence similarity 50 member B

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_175095.1 

    Range
    101..340
    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
    3751767..3752006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    3620705..3620944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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