U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129929621 ATAC-STARR-seq lymphoblastoid silent region 385 [ Homo sapiens (human) ]

Gene ID: 129929621, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129929621
Gene description
ATAC-STARR-seq lymphoblastoid silent region 385
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 LOC129929621 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (21659356..21659515)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21483251..21483410)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (21985849..21986008)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21835859-21836429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21836430-21836999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:21860784-21861513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21863949-21864466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21864467-21864985 Neighboring gene alkaline phosphatase, biomineralization associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21895010-21895594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21900641-21901315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21901316-21901990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21904065-21904588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21917321-21917860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21917861-21918399 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21928741-21928970 Neighboring gene long intergenic non-protein coding RNA 2596 Neighboring gene Sharpr-MPRA regulatory region 12165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21937517-21938264 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:21939576-21939868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21945135-21945976 Neighboring gene RAP1 GTPase activating protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21958265-21959233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21961087-21961835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21960338-21961086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21966135-21966964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21977615-21978365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21992551-21993051 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 387 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:21996570-21997769 Neighboring gene ubiquitin specific peptidase 48 Neighboring gene uncharacterized LOC124904736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 336 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:22099067-22099566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 337 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22108688-22109459 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:22109460-22110230 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22112153-22112327 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:22137244-22137394 Neighboring gene Sharpr-MPRA regulatory region 6146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:22148116-22148982 Neighboring gene low density lipoprotein receptor class A domain containing 2 Neighboring gene heparan sulfate proteoglycan 2

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_162678.1 

    Range
    101..260
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    21659356..21659515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    21483251..21483410
    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