rs16894341

Homo sapiens
T>C
CDH12 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0081 (2437/29958,GnomAD)
C=0098 (2859/29118,TOPMED)
C=0110 (552/5008,1000G)
C=0036 (138/3854,ALSPAC)
C=0037 (138/3708,TWINSUK)
chr5:22344141 (GRCh38.p7) (5p14.3)
ND
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.22344141T>C
GRCh37.p13 chr 5NC_000005.9:g.22344250T>C

Gene: CDH12, cadherin 12(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH12 transcript variant 1NM_004061.4:c.N/AIntron Variant
CDH12 transcript variant 2NM_001317227.1:c.N/AGenic Upstream Transcript Variant
CDH12 transcript variant 3NM_001317228.1:c.N/AGenic Upstream Transcript Variant
CDH12 transcript variant X1XM_017008920.1:c.N/AIntron Variant
CDH12 transcript variant X3XM_017008921.1:c.N/AIntron Variant
CDH12 transcript variant X2XM_011513927.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.813C=0.187
1000GenomesAmericanSub694T=0.960C=0.040
1000GenomesEast AsianSub1008T=0.878C=0.122
1000GenomesEuropeSub1006T=0.964C=0.036
1000GenomesGlobalStudy-wide5008T=0.890C=0.110
1000GenomesSouth AsianSub978T=0.880C=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.964C=0.036
The Genome Aggregation DatabaseAfricanSub8716T=0.828C=0.172
The Genome Aggregation DatabaseAmericanSub836T=0.960C=0.040
The Genome Aggregation DatabaseEast AsianSub1614T=0.894C=0.106
The Genome Aggregation DatabaseEuropeSub18490T=0.961C=0.038
The Genome Aggregation DatabaseGlobalStudy-wide29958T=0.918C=0.081
The Genome Aggregation DatabaseOtherSub302T=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.901C=0.098
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.963C=0.037
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs168943410.000127nicotine smoking19268276

eQTL of rs16894341 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 rs16894341 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 )
chr52230626222306429E069-37821
chr52230626222306429E074-37821