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LOC130006418 ATAC-STARR-seq lymphoblastoid silent region 3759 [ Homo sapiens (human) ]

Gene ID: 130006418, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006418
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3759
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 LOC130006418 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 (75241680..75241929)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (75171287..75171536)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (74952725..74952974)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902717 Neighboring gene zinc finger DHHC-type containing 20 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3760 Neighboring gene trophoblast glycoprotein like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74972903-74973402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:74973761-74974692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74976727-74977228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74977229-74977728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74983603-74984104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74988922-74989422 Neighboring gene arrestin beta 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:74991005-74991880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75002568-75003068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75014529-75015343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75019873-75020374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75024683-75025599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75033894-75034520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75035773-75036398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75037071-75037602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75037603-75038135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5264 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75041995-75042528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75042529-75043062 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75043063-75043596 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75044132-75044665 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75045734-75046268 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75046269-75046802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75051565-75052428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75052429-75053292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75057563-75058076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:75058077-75058590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5266 Neighboring gene microRNA 326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75062958-75063913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75092225-75092873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5267 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:75111125-75111988 Neighboring gene small nucleolar RNA, C/D box 15A Neighboring gene ribosomal protein S3

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_185863.1 

    Range
    101..350
    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
    75241680..75241929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    75171287..75171536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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