SNP Detail Info-rs117557854

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CNTN5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0017 (514/29966,GnomAD)
A=0010 (303/29118,TOPMED)
A=0007 (34/5008,1000G)
A=0023 (88/3854,ALSPAC)
A=0021 (79/3708,TWINSUK)

Position: chr11:100268439 (GRCh38.p7) (11q22.1)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 15 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.100268439G>A
GRCh37.p13 chr 11	NC_000011.9:g.100139171G>A

Molecule type	Change	Amino acid[Codon]	SO Term
CNTN5 transcript variant 2	NM_001243270.1:c.	N/A	Intron Variant
CNTN5 transcript variant 4	NM_001243271.1:c.	N/A	Intron Variant
CNTN5 transcript variant 1	NM_014361.3:c.	N/A	Intron Variant
CNTN5 transcript variant 3	NM_175566.2:c.	N/A	Intron Variant
CNTN5 transcript variant X2	XM_011542871.1:c.	N/A	Intron Variant
CNTN5 transcript variant X1	XM_017017926.1:c.	N/A	Intron Variant
CNTN5 transcript variant X3	XM_011542873.1:c.	N/A	Genic Downstream Transcript Variant
CNTN5 transcript variant X4	XM_017017927.1:c.	N/A	Genic Downstream Transcript Variant
CNTN5 transcript variant X5	XM_017017928.1:c.	N/A	Genic Downstream Transcript Variant
CNTN5 transcript variant X7	XM_017017929.1:c.	N/A	Genic Downstream Transcript Variant
CNTN5 transcript variant X6	XR_001747909.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.985	A=0.015
1000Genomes	Global	Study-wide	5008	G=0.993	A=0.007
1000Genomes	South Asian	Sub	978	G=0.990	A=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.977	A=0.023
The Genome Aggregation Database	African	Sub	8728	G=0.996	A=0.004
The Genome Aggregation Database	American	Sub	838	G=0.990	A=0.010
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18478	G=0.974	A=0.025
The Genome Aggregation Database	Global	Study-wide	29966	G=0.982	A=0.017
The Genome Aggregation Database	Other	Sub	302	G=0.980	A=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.989	A=0.010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.979	A=0.021

PMID	Title	Author	Journal
26365420	The genetics of alcohol dependence: Twin and SNP-based heritability, and genome-wide association study based on AUDIT scores.	Mbarek H	Am J Med Genet B Neuropsychiatr Genet

SNP ID	p-value	Traits	Study
rs117557854	2E-06	alcohol dependence	26365420

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

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr11	100145907	100145957	E070	6736
chr11	100146080	100146210	E070	6909
chr11	100146328	100146388	E070	7157
chr11	100146574	100146624	E070	7403
chr11	100165238	100165288	E070	26067
chr11	100165390	100165516	E070	26219
chr11	100165568	100165769	E070	26397
chr11	100165849	100166012	E070	26678
chr11	100167203	100167295	E070	28032
chr11	100177149	100177260	E070	37978
chr11	100177396	100177446	E070	38225
chr11	100091662	100091831	E074	-47340
chr11	100184816	100184948	E081	45645
chr11	100186660	100187281	E081	47489
chr11	100146574	100146624	E082	7403

rs117557854