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LOC129932245 ATAC-STARR-seq lymphoblastoid silent region 1701 [ Homo sapiens (human) ]

Gene ID: 129932245, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932245
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1701
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 LOC129932245 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 (202342064..202342163)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201604176..201604275)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202311192..202311291)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929388 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202204747-202205439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2333 Neighboring gene leucine rich repeat containing G protein-coupled receptor 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202210709-202211209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202233148-202233648 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202287549-202287709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202305669-202306193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202306194-202306717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202310134-202310759 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202317574-202318114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202328014-202328965 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:202330368-202331110 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:202331111-202331852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202333448-202334185 Neighboring gene ubiquitin conjugating enzyme E2 T Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene MPRA-validated peak653 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202347411-202347912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202347913-202348412 Neighboring gene NANOG hESC enhancer GRCh37_chr1:202348949-202349479 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202368272-202368533 Neighboring gene CYCS pseudogene 4 Neighboring gene RNA, U6 small nuclear 89, pseudogene

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_165281.1 

    Range
    101..200
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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
    202342064..202342163
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201604176..201604275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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