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LOC130056416 ATAC-STARR-seq lymphoblastoid silent region 6060 [ Homo sapiens (human) ]

Gene ID: 130056416, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056416
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6060
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 LOC130056416 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99272044..99272123)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (93503614..93503693)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99738381..99738460)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99600505-99601228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99608696-99609604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99640571-99641086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99658267-99658828 Neighboring gene uncharacterized LOC124903412 Neighboring gene BCL11 transcription factor B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99677677-99678177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99695676-99696574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99703507-99704031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99713148-99714044 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99723824-99724098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99734631-99735236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99735237-99735841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9002 Neighboring gene uncharacterized LOC105370660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99750257-99750979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99784572-99785298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99787223-99787850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99786594-99787222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99788913-99789673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99798343-99799050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99799051-99799757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99814550-99815224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99815225-99815898 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99827260-99827481 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99849405-99850263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99860795-99861575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99874757-99875323 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:99878378-99879044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99879711-99880376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99890523-99891386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99891387-99892249 Neighboring gene SET domain containing 3, actin N3(tau)-histidine methyltransferase Neighboring gene RNA, U6 small nuclear 91, pseudogene

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_190837.1 

    Range
    101..180
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    99272044..99272123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    93503614..93503693
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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