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LOC129997333 ATAC-STARR-seq lymphoblastoid silent region 17620 [ Homo sapiens (human) ]

Gene ID: 129997333, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129997333
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17620
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 LOC129997333 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (142945776..142946405)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (144138171..144138800)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14737 Neighboring gene adhesion G protein-coupled receptor G6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142695388-142695989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:142695947-142697146 Neighboring gene Sharpr-MPRA regulatory regions 3748 and 6738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:142872203-142872704 Neighboring gene uncharacterized LOC153910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:142898477-142899003 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:142968516-142969102 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:142969103-142969689 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:142970487-142971223 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:142992915-142994114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25178 Neighboring gene MPRA-validated peak6174 silencer Neighboring gene Sharpr-MPRA regulatory region 15083 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25179 Neighboring gene HIVEP zinc finger 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25181 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:143167126-143167819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25184 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:143206090-143207289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25185 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:143233161-143234017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17616 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25189 Neighboring gene HIVEP2 divergent transcript Neighboring gene long intergenic non-protein coding RNA 1277 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:143323875-143325074 Neighboring gene MPRA-validated peak6176 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25190

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

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_176779.1 

    Range
    101..730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    142945776..142946405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    144138171..144138800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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