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LOC129935857 ATAC-STARR-seq lymphoblastoid silent region 12456 [ Homo sapiens (human) ]

Gene ID: 129935857, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935857
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12456
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 LOC129935857 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 (232276213..232276262)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (232762929..232762978)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (233140923..233140972)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232791796-232792450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12454 Neighboring gene natriuretic peptide C Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:232854631-232855252 Neighboring gene DIS3 like 3'-5' exoribonuclease 2 Neighboring gene MPRA-validated peak4085 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:232986245-232986439 Neighboring gene Sharpr-MPRA regulatory region 7061 Neighboring gene microRNA 562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233096173-233096674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12457 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233141549-233142064 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233156819-233157542 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233157543-233158264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233194285-233195258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233197669-233198468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233198469-233199268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233201669-233202468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233207551-233208060 Neighboring gene NRBF2 pseudogene 6 Neighboring gene endothelin converting enzyme like 1 pseudogene 3

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 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_168868.1 

    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
    232276213..232276262
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    232762929..232762978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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