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LOC130067866 ATAC-STARR-seq lymphoblastoid silent region 13988 [ Homo sapiens (human) ]

Gene ID: 130067866, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067866
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13988
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 LOC130067866 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50529860..50530709)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (51040421..51041270)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50968289..50969138)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13983 Neighboring gene lipase maturation factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13984 Neighboring gene non-SMC condensin II complex subunit H2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50955745-50956678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50965237-50965808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19324 Neighboring gene synthesis of cytochrome C oxidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13989 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50969361-50969866 Neighboring gene thymidine phosphorylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13994 Neighboring gene ciliary microtubule associated protein 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19326 Neighboring gene ODF3B-KLHDC7B intergenic CAGE-defined mid-level expression enhancer Neighboring gene uncharacterized LOC102724608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19329 Neighboring gene Sharpr-MPRA regulatory region 5393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19330 Neighboring gene KLHDC7B divergent transcript Neighboring gene Sharpr-MPRA regulatory region 13947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13996 Neighboring gene kelch domain containing 7B

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_202281.1 

    Range
    101..950
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50529860..50530709
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    51040421..51041270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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