rs7716554

Homo sapiens
G>A
CDH6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0265 (7942/29904,GnomAD)
G==0248 (7233/29118,TOPMED)
G==0251 (1257/5008,1000G)
G==0258 (996/3854,ALSPAC)
G==0248 (919/3708,TWINSUK)
chr5:31200829 (GRCh38.p7) (5p13.3)
AD
GWASdb2
1   publication(s)
See rs on genome
32 Enhancers around
79 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.31200829G>A
GRCh37.p13 chr 5NC_000005.9:g.31200936G>A

Gene: CDH6, cadherin 6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH6 transcript variant 1NM_004932.3:c.N/AIntron Variant
CDH6 transcript variant X1XM_011513921.2:c.N/AIntron Variant
CDH6 transcript variant X3XM_017008911.1:c.N/AIntron Variant
CDH6 transcript variant X2XM_017008910.1:c.N/AGenic Upstream Transcript Variant
CDH6 transcript variant X4XR_001741972.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.262A=0.738
1000GenomesAmericanSub694G=0.300A=0.700
1000GenomesEast AsianSub1008G=0.272A=0.728
1000GenomesEuropeSub1006G=0.257A=0.743
1000GenomesGlobalStudy-wide5008G=0.251A=0.749
1000GenomesSouth AsianSub978G=0.170A=0.830
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.258A=0.742
The Genome Aggregation DatabaseAfricanSub8696G=0.259A=0.741
The Genome Aggregation DatabaseAmericanSub836G=0.300A=0.700
The Genome Aggregation DatabaseEast AsianSub1612G=0.272A=0.728
The Genome Aggregation DatabaseEuropeSub18458G=0.268A=0.731
The Genome Aggregation DatabaseGlobalStudy-wide29904G=0.265A=0.734
The Genome Aggregation DatabaseOtherSub302G=0.130A=0.870
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.248A=0.751
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.248A=0.752
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs77165540.000827alcohol dependence21314694

eQTL of rs7716554 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 rs7716554 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 )
chr53119312431193174E068-7762
chr53115795931158100E069-42836
chr53119293631192986E069-7950
chr53121360931213679E06912673
chr53121453531214594E06913599
chr53121360931213679E07012673
chr53119293631192986E073-7950
chr53119312431193174E073-7762
chr53116165831162443E074-38493
chr53119293631192986E074-7950
chr53121453531214594E07413599
chr53124220431242293E07441268
chr53115260631152859E081-48077
chr53115292031153413E081-47523
chr53115349031153585E081-47351
chr53115368731153898E081-47038
chr53115392131154100E081-46836
chr53115497931155403E081-45533
chr53120063431200684E081-252
chr53121453531214594E08113599
chr53122706831227169E08126132
chr53122989831230045E08128962
chr53123009031230163E08129154
chr53123119131231266E08130255
chr53123701631237070E08136080
chr53115368731153898E082-47038
chr53115392131154100E082-46836
chr53119293631192986E082-7950
chr53121453531214594E08213599
chr53122942031229733E08228484
chr53122989831230045E08228962
chr53123009031230163E08229154







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr53119340631193580E067-7356
chr53119364331194440E067-6496
chr53119444331194591E067-6345
chr53119460531194721E067-6215
chr53119475031194803E067-6133
chr53119497131195133E067-5803
chr53119522831195324E067-5612
chr53119533131195504E067-5432
chr53121382331214242E06712887
chr53119340631193580E068-7356
chr53119364331194440E068-6496
chr53119444331194591E068-6345
chr53119460531194721E068-6215
chr53119475031194803E068-6133
chr53119497131195133E068-5803
chr53119522831195324E068-5612
chr53119533131195504E068-5432
chr53119564931195880E068-5056
chr53119600531196077E068-4859
chr53121382331214242E06812887
chr53119340631193580E069-7356
chr53119364331194440E069-6496
chr53119444331194591E069-6345
chr53119460531194721E069-6215
chr53119475031194803E069-6133
chr53119497131195133E069-5803
chr53119522831195324E069-5612
chr53119533131195504E069-5432
chr53119564931195880E069-5056
chr53121382331214242E06912887
chr53119340631193580E070-7356
chr53119364331194440E070-6496
chr53119444331194591E070-6345
chr53119460531194721E070-6215
chr53119475031194803E070-6133
chr53119497131195133E070-5803
chr53119522831195324E070-5612
chr53121382331214242E07012887
chr53119340631193580E071-7356
chr53119364331194440E071-6496
chr53119444331194591E071-6345
chr53119460531194721E071-6215
chr53119475031194803E071-6133
chr53119497131195133E071-5803
chr53119522831195324E071-5612
chr53119533131195504E071-5432
chr53121382331214242E07112887
chr53119340631193580E072-7356
chr53119364331194440E072-6496
chr53119444331194591E072-6345
chr53119600531196077E072-4859
chr53119340631193580E073-7356
chr53119364331194440E073-6496
chr53119444331194591E073-6345
chr53119497131195133E073-5803
chr53119522831195324E073-5612
chr53119533131195504E073-5432
chr53119564931195880E073-5056
chr53121382331214242E07312887
chr53119340631193580E074-7356
chr53119364331194440E074-6496
chr53119444331194591E074-6345
chr53119460531194721E074-6215
chr53119475031194803E074-6133
chr53119497131195133E074-5803
chr53119522831195324E074-5612
chr53119533131195504E074-5432
chr53121382331214242E07412887
chr53119340631193580E081-7356
chr53119444331194591E081-6345
chr53119460531194721E081-6215
chr53119475031194803E081-6133
chr53119340631193580E082-7356
chr53119364331194440E082-6496
chr53119444331194591E082-6345
chr53119460531194721E082-6215
chr53119475031194803E082-6133
chr53119564931195880E082-5056
chr53119600531196077E082-4859