U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936897 ATAC-STARR-seq lymphoblastoid active region 19965 [ Homo sapiens (human) ]

Gene ID: 129936897, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129936897
Gene description
ATAC-STARR-seq lymphoblastoid active region 19965
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC129936897 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 (53188483..53188562)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53221387..53221466)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (53222499..53222578)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53106949-53107566 Neighboring gene Sharpr-MPRA regulatory region 3047 Neighboring gene RFT1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19952 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53136831-53137332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53148350-53149549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53182771-53183578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53190496-53190996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14459 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53201730-53202410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53202411-53203091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53208863-53209718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19963 Neighboring gene protein kinase C delta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19967 Neighboring gene Sharpr-MPRA regulatory region 8375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53236717-53237216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14463 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53261945-53263144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53270389-53271197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53274891-53275886 Neighboring gene transketolase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14464 Neighboring gene Sharpr-MPRA regulatory region 10976 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:53303617-53304816 Neighboring gene uncharacterized LOC107986087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53305434-53306319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53307415-53307967 Neighboring gene small nucleolar RNA U13

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_169908.1 

    Range
    101..180
    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
    53188483..53188562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    53221387..53221466
    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