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LOC129929247 ATAC-STARR-seq lymphoblastoid silent region 161 [ Homo sapiens (human) ]

Gene ID: 129929247, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929247
Gene description
ATAC-STARR-seq lymphoblastoid silent region 161
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 LOC129929247 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 (6497780..6497869)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (6023424..6023513)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (6557840..6557929)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6499737-6500250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 155 Neighboring gene microRNA 4252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6501479-6501980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6501981-6502480 Neighboring gene espin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6503341-6503883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6506945-6507603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6507628-6508502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6509377-6510250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6512972-6513929 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6518900-6519106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6526054-6527002 Neighboring gene TNF receptor superfamily member 25 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6534424-6534945 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6534946-6535466 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:6536823-6538022 Neighboring gene pleckstrin homology and RhoGEF domain containing G5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 160 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:6555381-6556136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6562565-6563294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6566857-6567357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6571620-6572434 Neighboring gene MPRA-validated peak31 silencer Neighboring gene Sharpr-MPRA regulatory region 8211 Neighboring gene Sharpr-MPRA regulatory region 5048 Neighboring gene nucleolar protein 9 Neighboring gene RNA, U6 small nuclear 731, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6612384-6612884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 162 Neighboring gene uncharacterized LOC107984912 Neighboring gene taste 1 receptor member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6639438-6640137

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_162304.1 

    Range
    101..190
    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
    6497780..6497869
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    6023424..6023513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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