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LOC129936408 ATAC-STARR-seq lymphoblastoid silent region 14162 [ Homo sapiens (human) ]

Gene ID: 129936408, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936408
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14162
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 LOC129936408 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (31533078..31533207)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (31535544..31535673)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (31574570..31574699)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2436 Neighboring gene H3 histone pseudogene 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:31398204-31399403 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:31418321-31419520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19628 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:31453982-31455181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14159 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:31490161-31490339 Neighboring gene Sharpr-MPRA regulatory region 4459 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69494 Neighboring gene THRAP3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31568343-31568843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31576589-31577090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:31577091-31577590 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69549 Neighboring gene STT3 oligosaccharyltransferase complex catalytic subunit B Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69593 Neighboring gene NANOG hESC enhancer GRCh37_chr3:31720020-31720521 Neighboring gene uncharacterized LOC124909360 Neighboring gene OSBPL10 antisense RNA 1 Neighboring gene oxysterol binding protein like 10

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_169419.1 

    Range
    101..230
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    31533078..31533207
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    31535544..31535673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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