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LOC129996654 ATAC-STARR-seq lymphoblastoid silent region 17294 [ Homo sapiens (human) ]

Gene ID: 129996654, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996654
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17294
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 LOC129996654 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 (53794871..53795110)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (53634819..53635058)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (53659669..53659908)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24700 Neighboring gene Sharpr-MPRA regulatory region 11274 Neighboring gene kelch like family member 31 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:53587553-53587738 Neighboring gene uncharacterized LOC124901334 Neighboring gene NANOG hESC enhancer GRCh37_chr6:53595032-53595549 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53599001-53600200 Neighboring gene uncharacterized LOC124901333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17293 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:53659875-53660587 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17295 Neighboring gene Sharpr-MPRA regulatory region 10889 Neighboring gene leucine rich repeat containing 1 Neighboring gene Sharpr-MPRA regulatory region 6720 Neighboring gene uncharacterized LOC101927189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:53810369-53810988 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:53810989-53811607 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:53826656-53827156 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:53841998-53842202 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:53848425-53849624 Neighboring gene MLIP intronic transcript 1

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_176100.1 

    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
    53794871..53795110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    53634819..53635058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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