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LOC129935789 ATAC-STARR-seq lymphoblastoid silent region 12413 [ Homo sapiens (human) ]

Gene ID: 129935789, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935789
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12413
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 LOC129935789 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 (230828197..230828726)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231311334..231311863)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231692912..231693441)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene calcium binding protein 39 Neighboring gene BANF1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17248 Neighboring gene RNA, U6 small nuclear 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231654665-231655164 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:231657991-231659190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17249 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:231708391-231709016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231726605-231727215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231728341-231728999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231729658-231730316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231730317-231730973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734265-231734922 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734923-231735580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231742513-231743287 Neighboring gene integral membrane protein 2C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231757691-231758270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231758271-231758850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12419 Neighboring gene GPR55 cis regulatory suppressor of immune response RNA

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_168800.1 

    Range
    101..630
    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
    230828197..230828726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231311334..231311863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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