U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC130001328 ATAC-STARR-seq lymphoblastoid silent region 19621 [ Homo sapiens (human) ]

Gene ID: 130001328, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC130001328
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19621
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 LOC130001328 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 (143407996..143408195)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144555782..144555982)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144490166..144490365)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase I mitochondrial Neighboring gene RNA, U6 small nuclear 220, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144450004-144450559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144451300-144452207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144452208-144453114 Neighboring gene RHPN1 antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28070 Neighboring gene rhophilin Rho GTPase binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144482673-144483320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483321-144483968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144483969-144484616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144484617-144485263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144487803-144488782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19620 Neighboring gene MAFA antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144504663-144505250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144517937-144518722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144518723-144519506 Neighboring gene Sharpr-MPRA regulatory region 10662 Neighboring gene MAF bZIP transcription factor A Neighboring gene zinc finger CCCH-type containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144544126-144544839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144544840-144545552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144547684-144548592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144550408-144551314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144552747-144553448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144561253-144561753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144569950-144570487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144570488-144571024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144583622-144584122 Neighboring gene small nucleolar RNA, C/D box 149

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_180774.1 

    Range
    101..300
    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
    143407996..143408195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    144555782..144555982
    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