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LOC130005614 ATAC-STARR-seq lymphoblastoid silent region 3279 [ Homo sapiens (human) ]

Gene ID: 130005614, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005614
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3279
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 LOC130005614 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (44727925..44728094)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (44884818..44884987)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (44749475..44749644)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44656670-44657458 Neighboring gene ribosomal protein L34 pseudogene 22 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44675065-44675680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44676298-44676913 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:44685723-44686240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44692285-44693064 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44693065-44693844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44693845-44694623 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:44710524-44711057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44713680-44714180 Neighboring gene long intergenic non-protein coding RNA 2704 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:44729901-44731100 Neighboring gene Sharpr-MPRA regulatory region 8672 Neighboring gene TSPAN18 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44747040-44747900 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44747901-44748762 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:44750014-44750516 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:44750517-44751017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44763637-44764332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44764333-44765028 Neighboring gene tetraspanin 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44770929-44771430 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44774444-44775252 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44775253-44776059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44787811-44788311 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44795688-44796462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44798427-44798928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44798929-44799428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21411 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44806959-44807560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44807561-44808160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44816852-44817768 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:44819455-44820133 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21423 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44844210-44845075 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44845076-44845940 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44845941-44846806 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21436 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21441 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44869391-44869986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44870581-44871176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44871177-44871770 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44878622-44879400 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44883049-44883676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4663 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44883677-44884304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44907116-44907616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44907617-44908117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44914725-44915296 Neighboring gene uncharacterized LOC124902664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44932558-44933414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44944349-44944850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:44952242-44952850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44957874-44958474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44960045-44960758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44964865-44965513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:44966723-44967326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3281 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3282 Neighboring gene tumor protein p53 inducible protein 11

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_185059.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    44727925..44728094
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    44884818..44884987
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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