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STIN2-VNTR serotonin transporter intronic VNTR enhancer [ Homo sapiens (human) ]

Gene ID: 110806307, updated on 10-Oct-2023

Summary

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Gene symbol
STIN2-VNTR
Gene description
serotonin transporter intronic VNTR enhancer
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
protein_bind
regulatory: enhancer, transcriptional_cis_regulatory_region
repeat_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VNTR2; STin2.9; 5HTTVNTR; STin2.10; STin2.12; 5HTT-VNTR2
Summary
This genomic sequence represents the STin2 enhancer element in an intron of the solute carrier family 6 member 4 (SLC6A4) gene on chromosome 17. It also represents a polymorphic region consisting of a variable number of tandem repeats (VNTR), where each repeat unit is 16-17 bp in length. Three major alleles have been identified in human populations, STin2.9, STin2.10 and STin2.12, carrying 9, 10 and 12 copies of the repeat unit, respectively. Enhancer activity levels vary based on the allele, with each repeat unit making varying contributions to activity. This region can bind to transcription factors including CTCF and YB-1, and it may also co-operate with the 5-HTTLPR regulatory element, which is another VNTR polymorphic region located in the SLC6A4 promoter. Polymorphisms in this STin2 region may be associated with a variety of mood, behavioral and stress-related psychopathologies, possibly in a population-dependent fashion, in combination with other polymorphisms (such as the 5-HTTLPR), and/or related to epigenetic processes. [provided by RefSeq, Aug 2017]
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Genomic context

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Location:
17q11.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (30221317..30221615)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (31165885..31166150)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (28548335..28548633)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:28443345-28444544 Neighboring gene microRNA 3184 Neighboring gene microRNA 423 Neighboring gene nuclear speckle splicing regulatory protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28468415-28468916 Neighboring gene uncharacterized LOC124903970 Neighboring gene solute carrier family 6 member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28549461-28549976 Neighboring gene MPRA-validated peak2787 silencer Neighboring gene solute carrier family 6 member 4 gene promoter Neighboring gene uncharacterized LOC105371720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28565347-28566247 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:28575475-28576674 Neighboring gene bleomycin hydrolase Neighboring gene RNA, U6 small nuclear 1267, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Investigation of the relationship between ischemic stroke and endothelial nitric oxide synthase gene polymorphisms [G894T, intron 4 VNTR and T786C]. Anlıaçık SÖ, et al. Turk J Med Sci, 2019 Apr 18. PMID 30997974, Free PMC Article
  2. Association analysis of SLC6A4 and HTR2A genes with obsessive-compulsive disorder: Influence of the STin2 polymorphism. Gomes CKF, et al. Compr Psychiatry, 2018 Apr. PMID 29331882
  3. The Risk of Congenital Heart Anomalies Following Prenatal Exposure to Serotonin Reuptake Inhibitors-Is Pharmacogenetics the Key? Daud AN, et al. Int J Mol Sci, 2016 Aug 13. PMID 27529241, Free PMC Article
  4. Development of Ego-Resiliency: Relations to Observed Parenting and Polymorphisms in the Serotonin Transporter Gene During Early Childhood. Taylor ZE, et al. Soc Dev, 2014 Aug 1. PMID 25346579, Free PMC Article
  5. Genetics of temporal lobe epilepsy: a review. Salzmann A, et al. Epilepsy Res Treat, 2012. PMID 22957248, Free PMC Article

See all (122) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Our findings indicate that the eNOS G894T and T786C [rs2070744] polymorphisms are not associated with the risk of ischemic stroke, whereas the intron 4 [27-bpTR] VNTR may be a risk factor in the Anatolian population.
    Title: Investigation of the relationship between ischemic stroke and endothelial nitric oxide synthase gene polymorphisms [G894T, intron 4 VNTR and T786C].
  2. A STin 2 polymorphism was found to be associated with obsessive compulsive disorder.
    Title: Association analysis of SLC6A4 and HTR2A genes with obsessive-compulsive disorder: Influence of the STin2 polymorphism.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • 5-HTT polymorphic intron 2 enhancer
  • SLC6A4 intronic VNTR enhancer
  • serotonin transporter gene variable number tandem repeat in intron 2

NCBI Reference Sequences (RefSeq)

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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_055510.1 

    Range
    101..399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    30221317..30221615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    31165885..31166150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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