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LOC129996744 ATAC-STARR-seq lymphoblastoid silent region 17345 [ Homo sapiens (human) ]

Gene ID: 129996744, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996744
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17345
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 LOC129996744 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 (79076973..79077472)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (80254688..80255187)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (79786690..79787189)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene interleukin 1 receptor associated kinase 1 binding protein 1 Neighboring gene tRNA-Phe (anticodon GAA) 8-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:79680931-79681480 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:79681481-79682028 Neighboring gene pleckstrin homology domain interacting protein Neighboring gene uncharacterized LOC124901346 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:79756655-79757261 Neighboring gene nucleoporin 155kDa pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79844665-79845165 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:79861851-79862574 Neighboring gene uncharacterized LOC124901347 Neighboring gene MPRA-validated peak5913 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79915779-79916280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79916281-79916780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:79939419-79939919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79942937-79943727 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:79943728-79944517 Neighboring gene high mobility group nucleosomal binding domain 3 Neighboring gene HMGN3 antisense RNA 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_176190.1 

    Range
    101..600
    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
    79076973..79077472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    80254688..80255187
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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