U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129935840 ATAC-STARR-seq lymphoblastoid silent region 12435 [ Homo sapiens (human) ]

Gene ID: 129935840, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129935840
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12435
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 LOC129935840 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (231662005..231662204)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (232146549..232146748)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232526716..232526915)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232477143-232477789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232477790-232478435 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:232478436-232479082 and GRCh37_chr2:232479083-232479728 Neighboring gene Sharpr-MPRA regulatory region 726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17300 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:232510968-232511721 Neighboring gene RNA, 7SL, cytoplasmic 499, pseudogene Neighboring gene RN7SL499P-PTMA intergenic region enhancers Neighboring gene Sharpr-MPRA regulatory region 275 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232544680-232545472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12439 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232546266-232547057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232550745-232551470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232552197-232552921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232561163-232561664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232561665-232562164 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232571367-232572005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232572645-232573282 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232573283-232573921 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232573922-232574559 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232575199-232575835 Neighboring gene uncharacterized LOC124906134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232576909-232577409 Neighboring gene microRNA 1244-1 Neighboring gene prothymosin alpha

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_168851.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    231662005..231662204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    232146549..232146748
    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