SNP Detail Info-rs481440

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ZYG11A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0361 (10811/29944,GnomAD)
C==0345 (10060/29118,TOPMED)
C==0438 (2194/5008,1000G)
C==0372 (1435/3854,ALSPAC)
C==0345 (1280/3708,TWINSUK)

Position: chr1:52879304 (GRCh38.p7) (1p32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 18 Enhancers around

Promoter: 28 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.52879304C>T
GRCh37.p13 chr 1	NC_000001.10:g.53344976C>T

Molecule type	Change	Amino acid[Codon]	SO Term
ZYG11A transcript variant 1	NM_001004339.2:c.	N/A	Intron Variant
ZYG11A transcript variant 2	NM_001307931.1:c.	N/A	Intron Variant
ZYG11A transcript variant X1	XM_011541480.2:c.	N/A	Intron Variant
ZYG11A transcript variant X2	XM_011541481.2:c.	N/A	Intron Variant
ZYG11A transcript variant X3	XM_011541482.2:c.	N/A	Intron Variant
ZYG11A transcript variant X4	XM_011541483.2:c.	N/A	Intron Variant
ZYG11A transcript variant X5	XM_011541484.1:c.	N/A	Intron Variant
ZYG11A transcript variant X6	XM_011541485.1:c.	N/A	Intron Variant
ZYG11A transcript variant X7	XM_011541486.1:c.	N/A	Intron Variant
ZYG11A transcript variant X8	XM_011541487.2:c.	N/A	Genic Downstream Transcript Variant
ZYG11A transcript variant X9	XM_011541488.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.204	T=0.796
1000Genomes	American	Sub	694	C=0.580	T=0.420
1000Genomes	East Asian	Sub	1008	C=0.750	T=0.250
1000Genomes	Europe	Sub	1006	C=0.362	T=0.638
1000Genomes	Global	Study-wide	5008	C=0.438	T=0.562
1000Genomes	South Asian	Sub	978	C=0.410	T=0.590
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.372	T=0.628
The Genome Aggregation Database	African	Sub	8704	C=0.256	T=0.744
The Genome Aggregation Database	American	Sub	838	C=0.590	T=0.410
The Genome Aggregation Database	East Asian	Sub	1614	C=0.746	T=0.254
The Genome Aggregation Database	Europe	Sub	18486	C=0.365	T=0.634
The Genome Aggregation Database	Global	Study-wide	29944	C=0.361	T=0.639
The Genome Aggregation Database	Other	Sub	302	C=0.400	T=0.600
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.345	T=0.654
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.345	T=0.655

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs481440	0.000808	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:53344976	ZYG11B	ENSG00000162378.8	C>T	2.0219e-4	152850	Cortex

Probe ID	Position	Gene	beta	p-value
cg08736216	chr1:53307985	ZYG11A	0.0475291731201685	3.9275e-16
cg24675658	chr1:53192096	ZYG11B	0.0173840135152751	2.1980e-13

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	53365452	53365598	E068	20476
chr1	53391872	53391926	E068	46896
chr1	53370235	53370285	E070	25259
chr1	53370557	53370825	E070	25581
chr1	53370867	53371262	E070	25891
chr1	53365161	53365303	E072	20185
chr1	53365330	53365391	E072	20354
chr1	53391730	53391800	E072	46754
chr1	53391872	53391926	E072	46896
chr1	53365161	53365303	E074	20185
chr1	53365330	53365391	E074	20354
chr1	53365452	53365598	E074	20476
chr1	53390973	53391061	E074	45997
chr1	53391113	53391242	E074	46137
chr1	53391270	53391454	E074	46294
chr1	53391484	53391680	E074	46508
chr1	53391730	53391800	E074	46754
chr1	53391872	53391926	E074	46896

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	53386292	53386407	E067	41316
chr1	53386429	53387720	E067	41453
chr1	53392443	53393970	E067	47467
chr1	53308131	53309356	E068	-35620
chr1	53386292	53386407	E068	41316
chr1	53386429	53387720	E068	41453
chr1	53392443	53393970	E068	47467
chr1	53386292	53386407	E069	41316
chr1	53386429	53387720	E069	41453
chr1	53392443	53393970	E069	47467
chr1	53386292	53386407	E070	41316
chr1	53386429	53387720	E070	41453
chr1	53392443	53393970	E070	47467
chr1	53386292	53386407	E071	41316
chr1	53386429	53387720	E071	41453
chr1	53392443	53393970	E071	47467
chr1	53386292	53386407	E072	41316
chr1	53386429	53387720	E072	41453
chr1	53392443	53393970	E072	47467
chr1	53386429	53387720	E073	41453
chr1	53392443	53393970	E073	47467
chr1	53386292	53386407	E074	41316
chr1	53386429	53387720	E074	41453
chr1	53392443	53393970	E074	47467
chr1	53392443	53393970	E081	47467
chr1	53308131	53309356	E082	-35620
chr1	53386429	53387720	E082	41453
chr1	53392443	53393970	E082	47467

rs481440