U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936077 ATAC-STARR-seq lymphoblastoid silent region 14020 [ Homo sapiens (human) ]

Gene ID: 129936077, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129936077
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14020
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 LOC129936077 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 (4978379..4979148)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4972161..4972930)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5020064..5020833)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene inositol 1,4,5-trisphosphate receptor type 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19354 Neighboring gene Sharpr-MPRA regulatory region 7157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19355 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:4824730-4825689 Neighboring gene eosinophil granule ontogeny transcript Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:4855759-4856958 Neighboring gene uncharacterized LOC124906209 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4859780-4860166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:4866229-4866729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14019 Neighboring gene small nucleolar RNA U13 Neighboring gene BHLHE40 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:4947837-4948542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:4958477-4959105 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4987703-4987867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5021511-5022105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024435-5024994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024995-5025554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5027373-5028270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5028271-5029168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5030786-5031286 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5036716-5037915 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5043965-5044466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5054312-5055114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5055115-5055916 Neighboring gene basic helix-loop-helix family member e40 Neighboring gene CRISPRi-validated cis-regulatory element chr3.91 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5064405-5065604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5073333-5073834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19375 Neighboring gene ring finger protein 10 pseudogene 1

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_169088.1 

    Range
    101..870
    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
    4978379..4979148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    4972161..4972930
    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