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LOC129933085 ATAC-STARR-seq lymphoblastoid silent region 11152 [ Homo sapiens (human) ]

Gene ID: 129933085, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933085
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11152
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 LOC129933085 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 (10044084..10044133)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (10072860..10072894)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (10184211..10184260)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene KLF11-I enhancer Neighboring gene uncharacterized LOC112268412 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:10170473-10170643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10173619-10174119 Neighboring gene KLF11 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11153 Neighboring gene KLF11 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10185594-10186333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10188595-10189095 Neighboring gene KLF transcription factor 11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10197717-10198660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:10198661-10199603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10200462-10201324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10201325-10202185 Neighboring gene cystin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10203342-10203940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10203941-10204538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10204790-10205668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10205669-10206546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:10211417-10211918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15296 Neighboring gene uncharacterized LOC124900536

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_166110.1 

    Range
    101..150
    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
    10044084..10044133
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    10072860..10072894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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