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LOC129929201 ATAC-STARR-seq lymphoblastoid silent region 123 [ Homo sapiens (human) ]

Gene ID: 129929201, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929201
Gene description
ATAC-STARR-seq lymphoblastoid silent region 123
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 LOC129929201 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3747065..3747554)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3258666..3259155)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3663629..3664118)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TP73 antisense RNA 3 Neighboring gene tumor protein p73 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 63 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 64 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3596796-3596963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3597253-3597988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3600129-3600889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3605575-3606096 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3606097-3606618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3623899-3624726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3624727-3625555 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3631158-3631397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3634425-3634984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3634985-3635544 Neighboring gene TP73 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3636665-3637223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3637224-3637783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3637784-3638342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 65 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3650019-3650807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3661686-3662521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3662522-3663358 Neighboring gene Gfo/Idh/MocA-like oxidoreductase domain containing 3, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3678785-3679286 Neighboring gene coiled-coil domain containing 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3679287-3679786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3687696-3688374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3689661-3690176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3690177-3690692 Neighboring gene MPRA functional variant 1:3691528:A:G red blood cell enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3691725-3692240 Neighboring gene small integral membrane protein 1 (Vel 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_162258.1 

    Range
    101..590
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    3747065..3747554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    3258666..3259155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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