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LOC129930966 ATAC-STARR-seq lymphoblastoid silent region 1087 [ Homo sapiens (human) ]

Gene ID: 129930966, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930966
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1087
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 LOC129930966 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (93846533..93846912)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (93692268..93692647)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (94312089..94312468)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:94057721-94058221 Neighboring gene BCAR3 adaptor protein, NSP family member Neighboring gene BCAR3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:94075253-94075816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94079051-94079704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94079705-94080357 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94081011-94081663 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94082971-94083623 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94101848-94102406 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:94102407-94102965 Neighboring gene Sharpr-MPRA regulatory region 755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94104972-94105607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1333 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94109607-94110328 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:94127441-94128640 Neighboring gene Sharpr-MPRA regulatory region 8830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1084 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:94158555-94159754 Neighboring gene uncharacterized LOC102723480 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:94166702-94167901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1085 Neighboring gene Sharpr-MPRA regulatory region 5000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1341 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:94203124-94204323 Neighboring gene Sharpr-MPRA regulatory region 10321 Neighboring gene MPRA-validated peak324 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94261424-94262012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:94279629-94280169 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:94298677-94299315 Neighboring gene MPRA-validated peak325 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1086 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:94312484-94313274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1343 Neighboring gene tRNA-Arg (anticodon TCT) 1-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:94344769-94345584 Neighboring gene microRNA 760 Neighboring gene deoxynucleotidyltransferase terminal interacting protein 2

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_164014.1 

    Range
    101..480
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    93846533..93846912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    93692268..93692647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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