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LOC129998395 ATAC-STARR-seq lymphoblastoid silent region 18162 [ Homo sapiens (human) ]

Gene ID: 129998395, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998395
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18162
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 LOC129998395 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 (45000148..45000677)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (45160711..45161252)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (45039747..45040276)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45025394-45026140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45026141-45026888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45030540-45031094 Neighboring gene uncharacterized LOC102723334 Neighboring gene small nucleolar RNA host gene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25966 Neighboring gene small nucleolar RNA, H/ACA box 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18161 Neighboring gene CCM2 scaffold protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45112087-45112746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45112747-45113406 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99227 Neighboring gene NAC alpha domain containing Neighboring gene ReSE screen-validated silencer GRCh37_chr7:45143162-45143329 Neighboring gene transforming growth factor beta regulator 4 Neighboring gene small nucleolar RNA, H/ACA box 5A

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_177841.1 

    Range
    101..630
    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
    45000148..45000677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    45160711..45161252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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