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LOC129929640 ATAC-STARR-seq lymphoblastoid silent region 400 [ Homo sapiens (human) ]

Gene ID: 129929640, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929640
Gene description
ATAC-STARR-seq lymphoblastoid silent region 400
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 LOC129929640 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 (22143187..22143516)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21966953..21967283)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (22469680..22470009)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene cell division cycle 42 Neighboring gene MPHOSPH6 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 348 Neighboring gene Sharpr-MPRA regulatory region 8542 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22446773-22447390 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22448010-22448627 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22457824-22458584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22458585-22459343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22459683-22460408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22462663-22463176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22465050-22466004 Neighboring gene Wnt family member 4 Neighboring gene uncharacterized LOC105376845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 399 Neighboring gene uncharacterized LOC105376850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 351 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22498925-22499424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22555405-22556038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22558878-22559426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22559427-22559973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22562845-22563345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22574593-22575302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22575303-22576012 Neighboring gene uncharacterized LOC107985377 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22580206-22581110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22581111-22582013

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_162697.1 

    Range
    101..430
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    22143187..22143516
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    21966953..21967283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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