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LOC129998987 ATAC-STARR-seq lymphoblastoid silent region 18466 [ Homo sapiens (human) ]

Gene ID: 129998987, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998987
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18466
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 LOC129998987 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100875355..100875584)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102115459..102115688)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100472976..100473205)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene solute carrier family 12 member 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100434739-100435658 Neighboring gene SLC12A9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456152-100456652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456653-100457153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100457811-100458310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100458529-100459030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26390 Neighboring gene microRNA 6875 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100471610-100472274 Neighboring gene thyroid hormone receptor interactor 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100472275-100472939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100478564-100479401 Neighboring gene serrate, RNA effector molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100483425-100484158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18467 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr7:100487829-100488562 and GRCh37_chr7:100488563-100489295 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100489576-100490315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100490316-100491054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100493326-100493946 Neighboring gene UFM1 specific peptidase 1 Neighboring gene acetylcholinesterase (Yt blood group)

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_178432.1 

    Range
    101..330
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    100875355..100875584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102115459..102115688
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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