U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936247 ATAC-STARR-seq lymphoblastoid silent region 14092 [ Homo sapiens (human) ]

Gene ID: 129936247, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129936247
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14092
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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129936247 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14216464..14216543)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14218328..14218407)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14257964..14258043)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14192355-14192855 Neighboring gene XPC antisense RNA 1 Neighboring gene XPC complex subunit, DNA damage recognition and repair factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19501 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14251094-14251594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14251595-14252095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14091 Neighboring gene uncharacterized LOC105376958 Neighboring gene CRISPRi-validated cis-regulatory element chr3.770 Neighboring gene CRISPRi-validated cis-regulatory element chr3.771 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:14293769-14294968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14308196-14308835 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14313268-14314040 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:14314041-14314814 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14314815-14315586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14317906-14318677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14323255-14323756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14324521-14325022 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:14332587-14333288 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14333289-14333989 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14334913-14335413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14339415-14339967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14348760-14349494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19503 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14364440-14365033 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64938 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14370566-14370759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14373654-14374183 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14394065-14394622 Neighboring gene long intergenic non-protein coding RNA 1267

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_169258.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    14216464..14216543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    14218328..14218407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases