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LOC129935658 ATAC-STARR-seq lymphoblastoid silent region 12359 [ Homo sapiens (human) ]

Gene ID: 129935658, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935658
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12359
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 LOC129935658 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 (219543341..219544050)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (220028040..220028749)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220408063..220408772)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ASIC4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17153 Neighboring gene GDP-mannose pyrophosphorylase A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17154 Neighboring gene GATA motif-containing MPRA enhancer 279/280 Neighboring gene Sharpr-MPRA regulatory region 4906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220377201-220377842 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:220379127-220379302 Neighboring gene acid sensing ion channel subunit family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220387632-220388132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220388133-220388633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220396965-220397562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220402386-220402940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220402941-220403496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12360 Neighboring gene chondroitin polymerizing factor Neighboring gene transmembrane protein 198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220417356-220417856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220417857-220418357 Neighboring gene microRNA 3132 Neighboring gene obscurin like cytoskeletal adaptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:220422411-220422601 Neighboring gene Sharpr-MPRA regulatory region 8831 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220425347-220426210 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220429659-220430520 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220430521-220431382 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220431383-220432244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220434367-220435204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220435205-220436042 Neighboring gene Sharpr-MPRA regulatory region 8639 Neighboring gene inhibin subunit alpha

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_168670.1 

    Range
    101..810
    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
    219543341..219544050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    220028040..220028749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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