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LOC129997544 ATAC-STARR-seq lymphoblastoid silent region 17725 [ Homo sapiens (human) ]

Gene ID: 129997544, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997544
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17725
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 LOC129997544 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (157381968..157382017)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (158623962..158624011)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (157803000..157803049)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene chromosome 18 open reading frame 21 pseudogene Neighboring gene uncharacterized LOC124901446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157800546-157801158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17723 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:157801770-157802381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25331 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr6:157818864-157819364 and GRCh37_chr6:157819365-157819865 Neighboring gene zinc finger DHHC-type palmitoyltransferase 14 Neighboring gene MPRA-validated peak6255 silencer Neighboring gene MPRA-validated peak6257 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:157867979-157868480 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:157868882-157869106 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157876133-157877024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157885378-157885878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157885879-157886379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157887214-157888001 Neighboring gene MPRA-validated peak6259 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157938365-157938888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157938889-157939410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157951781-157952686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157952687-157953591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954158-157954658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954659-157955159 Neighboring gene MPRA-validated peak6260 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157973253-157974075 Neighboring gene microRNA 3692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157977751-157978536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157982847-157983820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157993864-157994596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014729-158015228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014227-158014728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037061-158037562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037563-158038062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158066653-158067153 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:158069048-158070247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158090399-158091006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158091007-158091612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158109923-158110424 Neighboring gene uncharacterized LOC107986663 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158127150-158127715 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158131630-158132829 Neighboring gene uncharacterized LOC124901555

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_176990.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    157381968..157382017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    158623962..158624011
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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