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LOC130058884 ATAC-STARR-seq lymphoblastoid silent region 7406 [ Homo sapiens (human) ]

Gene ID: 130058884, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058884
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7406
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 LOC130058884 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30958373..30958462)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (31345833..31345922)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30969694..30969783)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancers GRCh37_chr16:30932963-30933931 and GRCh37_chr16:30933932-30934899 Neighboring gene FBXL19 antisense RNA 1 Neighboring gene F-box and leucine rich repeat protein 19 Neighboring gene Sharpr-MPRA regulatory region 7559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7401 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30953885-30954827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30960708-30961226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30961745-30962262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30964322-30964887 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30968383-30969146 Neighboring gene ORAI calcium release-activated calcium modulator 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7405 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30974870-30975017 Neighboring gene SET domain containing 1A, histone lysine methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30995997-30996509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30999355-30999854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31001361-31002004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31002005-31002648 Neighboring gene hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7407 Neighboring gene syntaxin 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31011808-31012308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:31012309-31012809

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_193305.1 

    Range
    101..190
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    30958373..30958462
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    31345833..31345922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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