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LOC129934047 ATAC-STARR-seq lymphoblastoid silent region 11613 [ Homo sapiens (human) ]

Gene ID: 129934047, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934047
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11613
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 LOC129934047 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (70553887..70553956)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (70564642..70564711)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (70781019..70781088)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene tRNA-undetermined (NNN) 9-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70683068-70683568 Neighboring gene uncharacterized LOC107985895 Neighboring gene transforming growth factor alpha Neighboring gene TGFA intronic transcript 1 Neighboring gene Sharpr-MPRA regulatory region 10182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70741406-70741908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70751144-70751760 Neighboring gene uncharacterized LOC124907824 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:70796083-70797282 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:70823358-70824557 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:70847073-70847578 Neighboring gene uncharacterized LOC105374794 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:70904853-70906052 Neighboring gene adducin 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:70937501-70938030 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:70939798-70940354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70940355-70940910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70940911-70941466 Neighboring gene Sharpr-MPRA regulatory region 8528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70963227-70963968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70971761-70972262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70994467-70995032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70995033-70995598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70996008-70996572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16008 Neighboring gene folliculogenesis specific bHLH transcription factor

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_167071.1 

    Range
    101..170
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    70553887..70553956
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    70564642..70564711
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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