rs17688077

Homo sapiens
C>T
CDH13 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0109 (3282/29986,GnomAD)
T=0084 (2464/29118,TOPMED)
T=0064 (320/5008,1000G)
T=0161 (621/3854,ALSPAC)
T=0155 (576/3708,TWINSUK)
chr16:83622659 (GRCh38.p7) (16q23.3)
ND
GWASdb2
1   publication(s)
See rs on genome
30 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.83622659C>T
GRCh37.p13 chr 16NC_000016.9:g.83656264C>T

Gene: CDH13, cadherin 13(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH13 transcript variant 2NM_001220488.1:c.N/AIntron Variant
CDH13 transcript variant 3NM_001220489.1:c.N/AIntron Variant
CDH13 transcript variant 4NM_001220490.1:c.N/AIntron Variant
CDH13 transcript variant 1NM_001257.4:c.N/AIntron Variant
CDH13 transcript variant 5NM_001220491.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant 6NM_001220492.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant X1XM_011522804.2:c.N/AIntron Variant
CDH13 transcript variant X2XM_017022848.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant X3XM_017022849.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.978T=0.022
1000GenomesAmericanSub694C=0.950T=0.050
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=0.861T=0.139
1000GenomesGlobalStudy-wide5008C=0.936T=0.064
1000GenomesSouth AsianSub978C=0.880T=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.839T=0.161
The Genome Aggregation DatabaseAfricanSub8732C=0.957T=0.043
The Genome Aggregation DatabaseAmericanSub838C=0.940T=0.060
The Genome Aggregation DatabaseEast AsianSub1622C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18492C=0.848T=0.151
The Genome Aggregation DatabaseGlobalStudy-wide29986C=0.890T=0.109
The Genome Aggregation DatabaseOtherSub302C=0.860T=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.915T=0.084
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.845T=0.155
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
rs176880770.000231nicotine smoking19268276

eQTL of rs17688077 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 rs17688077 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 )
chr168368644183686521E06830177
chr168368308983683249E07026825
chr168368327683683350E07027012
chr168368370483683776E07027440
chr168365779883657850E0811534
chr168365802583658116E0811761
chr168365820883658334E0811944
chr168365841383658559E0812149
chr168365868583658735E0812421
chr168365880083658921E0812536
chr168366146583661515E0815201
chr168366161083661909E0815346
chr168366240883662458E0816144
chr168366255483662752E0816290
chr168366280183662863E0816537
chr168366305783663330E0816793
chr168366336783663449E0817103
chr168366349783663771E0817233
chr168366463983664908E0818375
chr168366493083664980E0818666
chr168366547983665638E0819215
chr168366568083665730E0819416
chr168368102883681078E08124764
chr168365802583658116E0821761
chr168365820883658334E0821944
chr168365841383658559E0822149
chr168366146583661515E0825201
chr168366161083661909E0825346
chr168368595883686008E08229694
chr168368602683686076E08229762