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LOC129997640 ATAC-STARR-seq lymphoblastoid silent region 17771 [ Homo sapiens (human) ]

Gene ID: 129997640, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997640
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17771
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 LOC129997640 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 (163415297..163415346)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (164780463..164780512)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (163836329..163836378)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378100 Neighboring gene Sharpr-MPRA regulatory region 14773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25418 Neighboring gene basic proline-rich protein-like Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:163835002-163835654 and GRCh37_chr6:163835655-163836308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17772 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:163844209-163844453 Neighboring gene colon adenocarcinoma hypermethylated Neighboring gene QKI, KH domain containing RNA binding Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25419 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:163956589-163956770 Neighboring gene NANOG hESC enhancer GRCh37_chr6:163964125-163964810 Neighboring gene Sharpr-MPRA regulatory region 9625 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:164008464-164009663 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:164013504-164014052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:164032378-164032878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:164032879-164033379 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:164039878-164041077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25420 Neighboring gene uncharacterized LOC102724152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25423 Neighboring gene uncharacterized LOC124901498

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_177086.1 

    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
    163415297..163415346
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    164780463..164780512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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