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LOC129997104 ATAC-STARR-seq lymphoblastoid silent region 17518 [ Homo sapiens (human) ]

Gene ID: 129997104, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997104
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17518
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 LOC129997104 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 (125747787..125747966)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (126936302..126936481)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (126068933..126069112)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125711176-125711724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125765831-125766344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:125766345-125766856 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:125849225-125850424 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:125854657-125855265 Neighboring gene NANOG hESC enhancer GRCh37_chr6:125870255-125870862 Neighboring gene HEY2 antisense RNA 1 Neighboring gene MPRA-validated peak6111 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:125991600-125992310 Neighboring gene long intergenic non-protein coding RNA 2523 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:126023017-126023671 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:126028243-126028789 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:126028790-126029335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25029 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:126066495-126067162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17519 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:126091955-126092877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17520 Neighboring gene tRNA-Glu (anticodon CTC) 1-7 Neighboring gene hes related family bHLH transcription factor with YRPW motif 2

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_176550.1 

    Range
    101..280
    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
    125747787..125747966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    126936302..126936481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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