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LOC129929208 ATAC-STARR-seq lymphoblastoid silent region 130 [ Homo sapiens (human) ]

Gene ID: 129929208, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929208
Gene description
ATAC-STARR-seq lymphoblastoid silent region 130
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 LOC129929208 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 (3901173..3901352)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3413077..3413256)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3817737..3817916)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 67 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 127 Neighboring gene Sharpr-MPRA regulatory region 4254 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3787529-3787731 Neighboring gene DNA fragmentation factor subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 128 Neighboring gene chromosome 1 open reading frame 174 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3815928-3816498 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3816499-3817067 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3817068-3817637 Neighboring gene long intergenic non-protein coding RNA 1134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 131 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3827787-3828672 Neighboring gene long intergenic non-protein coding RNA 1346 Neighboring gene long intergenic non-protein coding RNA 1345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4015013-4015738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4017862-4018398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:4018399-4018934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4037314-4037814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4037815-4038315 Neighboring gene long intergenic non-protein coding RNA 2780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:4071131-4071631

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_162265.1 

    Range
    101..280
    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
    3901173..3901352
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    3413077..3413256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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