rs12126638

Homo sapiens
T>C
USH2A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0168 (5044/29944,GnomAD)
C=0167 (4865/29116,TOPMED)
C=0133 (667/5008,1000G)
C=0203 (784/3854,ALSPAC)
C=0215 (796/3708,TWINSUK)
chr1:216002354 (GRCh38.p7) (1q41)
ND
GWASdb2
2   publication(s)
See rs on genome
4 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.216002354T>C
GRCh37.p13 chr 1NC_000001.10:g.216175696T>C
USH2A RefSeqGeneNG_009497.1:g.426043A>G

Gene: USH2A, Usher syndrome 2A (autosomal recessive, mild)(minus strand)

Molecule type Change Amino acid[Codon] SO Term
USH2A transcript variant 2NM_206933.2:c.N/AIntron Variant
USH2A transcript variant 1NM_007123.5:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.860C=0.140
1000GenomesAmericanSub694T=0.860C=0.140
1000GenomesEast AsianSub1008T=0.941C=0.059
1000GenomesEuropeSub1006T=0.793C=0.207
1000GenomesGlobalStudy-wide5008T=0.867C=0.133
1000GenomesSouth AsianSub978T=0.880C=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.797C=0.203
The Genome Aggregation DatabaseAfricanSub8730T=0.863C=0.137
The Genome Aggregation DatabaseAmericanSub836T=0.880C=0.120
The Genome Aggregation DatabaseEast AsianSub1606T=0.938C=0.062
The Genome Aggregation DatabaseEuropeSub18470T=0.805C=0.194
The Genome Aggregation DatabaseGlobalStudy-wide29944T=0.831C=0.168
The Genome Aggregation DatabaseOtherSub302T=0.820C=0.180
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.832C=0.167
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.785C=0.215
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet
22719919Glutamate and synaptic plasticity systems and smoking behavior: results from a genetic association study.dos Santos VAPLoS One

P-Value

SNP ID p-value Traits Study
rs121266389.56E-05nicotine smoking19268276

eQTL of rs12126638 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs12126638 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr1216220947216221144E07045251
chr1216223179216223369E07047483
chr1216220947216221144E08145251
chr1216220947216221144E08245251