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LOC129934328 ATAC-STARR-seq lymphoblastoid silent region 11757 [ Homo sapiens (human) ]

Gene ID: 129934328, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934328
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11757
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 LOC129934328 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 (96208244..96208503)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (96714852..96715111)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (96873982..96874241)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:96798301-96798801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:96800355-96800854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16190 Neighboring gene astacin like metalloendopeptidase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:96810561-96811062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:96813301-96814190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:96818462-96819055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16199 Neighboring gene dual specificity phosphatase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16200 Neighboring gene Sharpr-MPRA regulatory region 4518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:96824357-96824894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16206 Neighboring gene StAR related lipid transfer domain containing 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:96874259-96874849 Neighboring gene STARD7 antisense RNA 1 Neighboring gene small nucleolar RNA, H/ACA box 112 Neighboring gene Sharpr-MPRA regulatory region 4718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16210 Neighboring gene VISTA enhancer hs1919 Neighboring gene transmembrane protein 127 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11761

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_167346.1 

    Range
    101..360
    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
    96208244..96208503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    96714852..96715111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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