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LOC129933216 ATAC-STARR-seq lymphoblastoid silent region 11210 [ Homo sapiens (human) ]

Gene ID: 129933216, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933216
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11210
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 LOC129933216 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (20517383..20517482)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (20550707..20550806)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (20717143..20717242)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11207 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:20649962-20650523 Neighboring gene ras homolog family member B Neighboring gene uncharacterized LOC107985856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20687149-20687946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15392 Neighboring gene uncharacterized LOC102724948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20732136-20733133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20734131-20735128 Neighboring gene NDUFAF2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20741509-20742494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20742495-20743479 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11211 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20760853-20761375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20763577-20764533 Neighboring gene HCLS1 binding protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20771337-20771837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:20774924-20775424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15393 Neighboring gene VISTA enhancer hs2384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780177-20780738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20780739-20781299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784034-20784599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20784600-20785164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:20785731-20786294 Neighboring gene HS1BP3 intronic transcript 1

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_166241.1 

    Range
    101..200
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    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    20517383..20517482
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    20550707..20550806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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