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LOC129997941 ATAC-STARR-seq lymphoblastoid silent region 17949 [ Homo sapiens (human) ]

Gene ID: 129997941, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129997941
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17949
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 LOC129997941 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (6504094..6504263)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (6623333..6623502)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (6543725..6543894)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene KDEL endoplasmic reticulum protein retention receptor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25625 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17945 Neighboring gene ribosomal protein L31 pseudogene 34 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17950 Neighboring gene uncharacterized LOC101927325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25629 Neighboring gene Grid2 interacting protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6576361-6577340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17953 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6617713-6618328 Neighboring gene uncharacterized LOC124901582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6628794-6629632 Neighboring gene zinc finger DHHC-type palmitoyltransferase 4

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_177382.1 

    Range
    101..270
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    6504094..6504263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    6623333..6623502
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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