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LOC129929863 ATAC-STARR-seq lymphoblastoid silent region 506 [ Homo sapiens (human) ]

Gene ID: 129929863, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929863
Gene description
ATAC-STARR-seq lymphoblastoid silent region 506
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 LOC129929863 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 (27235262..27235311)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27076482..27076531)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27561753..27561802)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SNRPE pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 505 Neighboring gene WDTC1 divergent transcript Neighboring gene WD and tetratricopeptide repeats 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27613415-27614057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27615731-27616716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27625813-27626326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 541 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27627354-27627866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27627867-27628380 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27633747-27634272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27634273-27634798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27634799-27635323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27648068-27648614 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27648615-27649162 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27649163-27649709 Neighboring gene actin gamma 1 pseudogene 20 Neighboring gene transmembrane protein 222 Neighboring gene RNA, U6 small nuclear 48, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27669148-27669765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27673548-27674088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27674089-27674627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 509 Neighboring gene synaptotagmin like 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_162916.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    27235262..27235311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    27076482..27076531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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