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LOC129935501 ATAC-STARR-seq lymphoblastoid silent region 12280 [ Homo sapiens (human) ]

Gene ID: 129935501, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935501
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12280
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 LOC129935501 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 (207531101..207531270)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (208005097..208005266)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (208395825..208395994)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17035 Neighboring gene uncharacterized LOC105373851 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:208259108-208260307 Neighboring gene NANOG hESC enhancer GRCh37_chr2:208265954-208266524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17038 Neighboring gene uncharacterized LOC124907970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12278 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208396403-208396904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:208396905-208397404 Neighboring gene cAMP responsive element binding protein 1 Neighboring gene methyltransferase 21A, HSPA lysine Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208490584-208491288 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208491289-208491991 Neighboring gene ribosomal protein S29 pseudogene 9

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_168514.1 

    Range
    101..270
    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
    207531101..207531270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    208005097..208005266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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