U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130000206 ATAC-STARR-seq lymphoblastoid silent region 19110 [ Homo sapiens (human) ]

Gene ID: 130000206, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130000206
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19110
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 LOC130000206 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (37797408..37797497)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38073803..38073892)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (37654926..37655015)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901934 Neighboring gene Sharpr-MPRA regulatory region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27231 Neighboring gene pyridoxal phosphate binding protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:37638448-37639647 Neighboring gene uncharacterized LOC105379381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37645266-37645774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37652831-37653396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37653397-37653962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27233 Neighboring gene adhesion G protein-coupled receptor A2 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37667034-37667256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37671601-37672366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37672367-37673132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37673133-37673898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37679325-37679898 Neighboring gene VISTA enhancer hs1665 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:37685664-37686632 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:37696873-37697010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37699228-37699928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27235 Neighboring gene BRF2 general transcription factor IIIB subunit Neighboring gene RAB11 family interacting protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37737517-37738231 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37738232-37738945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27237 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37747172-37748110 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:37748111-37749049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19111 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:37754638-37755270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19112

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_179652.1 

    Range
    101..190
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    37797408..37797497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    38073803..38073892
    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