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LOC129932678 ATAC-STARR-seq lymphoblastoid silent region 1893 [ Homo sapiens (human) ]

Gene ID: 129932678, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932678
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1893
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 LOC129932678 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (226870419..226871018)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (226058306..226058905)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (227058120..227058719)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1892 Neighboring gene ribosomal protein S27 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2672 Neighboring gene uncharacterized LOC124904530 Neighboring gene Sharpr-MPRA regulatory region 12356 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:227038591-227039325 Neighboring gene uncharacterized LOC105373119 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:227051075-227051623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1894 Neighboring gene MPRA-validated peak736 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2673 Neighboring gene presenilin 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227083595-227083826 Neighboring gene uncharacterized LOC107985354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:227126665-227127356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227138969-227139468 Neighboring gene coenzyme Q8A Neighboring gene MPRA-validated peak738 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227161529-227162142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227166346-227167094 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227172247-227172425

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_165703.1 

    Range
    101..700
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    226870419..226871018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    226058306..226058905
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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