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LOC129996634 ATAC-STARR-seq lymphoblastoid silent region 17284 [ Homo sapiens (human) ]

Gene ID: 129996634, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996634
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17284
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 LOC129996634 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 (52574866..52574915)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (52413616..52413665)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (52439664..52439713)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17283 Neighboring gene progestin and adipoQ receptor family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24676 Neighboring gene VISTA enhancer hs2064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24678 Neighboring gene Sharpr-MPRA regulatory region 10279 Neighboring gene uncharacterized LOC124901331 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:52285109-52285700 Neighboring gene EF-hand domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:52362612-52362813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24679 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:52368564-52369763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24680 Neighboring gene translocation associated membrane protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:52389524-52390029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:52390030-52390534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24685 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_92132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:52438134-52438662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17285 Neighboring gene TRAM2 antisense RNA 1 (head to head) Neighboring gene FOXA motif-containing MPRA enhancer 62 Neighboring gene uncharacterized LOC124901330

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_176080.1 

    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
    52574866..52574915
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    52413616..52413665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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