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LOC129996590 ATAC-STARR-seq lymphoblastoid silent region 17271 [ Homo sapiens (human) ]

Gene ID: 129996590, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996590
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17271
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 LOC129996590 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (46492012..46492071)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (46329655..46329714)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (46459749..46459808)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene regulator of calcineurin 2 Neighboring gene uncharacterized LOC101926915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:46373192-46373692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46426210-46426710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46426711-46427211 Neighboring gene ribosomal protein L36 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:46455408-46456020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17270 Neighboring gene RCAN2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46542802-46543302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46543303-46543803 Neighboring gene cytochrome P450 family 39 subfamily A member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17273 Neighboring gene solute carrier family 25 member 27 Neighboring gene TDRD6 and SLC25A27 antisense RNA 1

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_176036.1 

    Range
    101..160
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    46492012..46492071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    46329655..46329714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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