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LOC129995831 ATAC-STARR-seq lymphoblastoid silent region 16939 [ Homo sapiens (human) ]

Gene ID: 129995831, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995831
Gene description
ATAC-STARR-seq lymphoblastoid silent region 16939
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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (13813745..13814414)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13687346..13688015)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RAN binding protein 9 Neighboring gene U7 small nuclear RNA Neighboring gene Sharpr-MPRA regulatory region 12249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16937 Neighboring gene uncharacterized LOC124901264 Neighboring gene Sharpr-MPRA regulatory region 2979 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:13755870-13756079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24039 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13769328-13769828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13787884-13788716 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:13789385-13789553 Neighboring gene uncharacterized LOC107986571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16940 Neighboring gene mitochondrial calcium uniporter regulator 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13872467-13873049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16941 Neighboring gene CRISPRi-validated cis-regulatory element chr6.697 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13924078-13924578 Neighboring gene NANOG hESC enhancer GRCh37_chr6:13944174-13944689 Neighboring gene ring finger protein 182 Neighboring gene mitochondrial ribosomal protein L35 pseudogene 1 Neighboring gene CRISPRi-validated cis-regulatory element chr6.702 Neighboring gene CRISPRi-validated cis-regulatory element chr6.703 Neighboring gene CRISPRi-validated cis-regulatory element chr6.704 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14001334-14002533 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:14035147-14036346 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14069795-14069896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24042 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14088959-14089460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24043 Neighboring gene CRISPRi-FlowFISH-validated CD83 regulatory element GRCh37_chr6:14095567-14096067 Neighboring gene uncharacterized LOC105374939

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_175277.1 

    Range
    101..770
    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
    13813745..13814414
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13687346..13688015
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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