rs75562159

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

CAMTA1 : Intron Variant
LOC101928836 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0057 (1718/29954,GnomAD)
A=0078 (2280/29118,TOPMED)
A=0057 (286/5008,1000G)
A=0017 (66/3854,ALSPAC)
A=0018 (67/3708,TWINSUK)

Position: chr1:7444081 (GRCh38.p7) (1p36.23)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 155 Enhancers around

Promoter: 43 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.7444081C>A
GRCh38.p7 chr 1	NC_000001.11:g.7444081C>T
GRCh37.p13 chr 1	NC_000001.10:g.7504141C>A
GRCh37.p13 chr 1	NC_000001.10:g.7504141C>T

Gene: CAMTA1, calmodulin binding transcription activator 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAMTA1 transcript variant 1	NM_015215.3:c.	N/A	Intron Variant
CAMTA1 transcript variant 2	NM_001195563.1:c.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant 3	NM_001242701.1:c.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant 4	NR_038934.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X1	XM_011541083.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X2	XM_011541084.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X3	XM_011541085.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X5	XM_011541086.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X5	XM_011541087.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X6	XM_011541088.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X11	XM_011541089.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X12	XM_011541090.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X10	XM_011541091.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X17	XM_011541092.2:c.	N/A	Intron Variant
CAMTA1 transcript variant X4	XM_017000773.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X6	XM_017000774.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X9	XM_017000775.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X10	XM_017000776.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X8	XM_017000777.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X9	XM_017000778.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X15	XM_017000779.1:c.	N/A	Intron Variant
CAMTA1 transcript variant X18	XM_017000780.1:c.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X21	XM_017000781.1:c.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X22	XR_001737061.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X23	XR_001737062.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X24	XR_001737063.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X25	XR_001737064.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X26	XR_001737065.1:n.	N/A	Genic Downstream Transcript Variant
CAMTA1 transcript variant X27	XR_001737066.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC101928836, uncharacterized LOC101928836(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928836 transcript variant X1	XR_001737884.1:n.	N/A	Upstream Transcript Variant
LOC101928836 transcript variant X4	XR_001737885.1:n.	N/A	Upstream Transcript Variant
LOC101928836 transcript variant X5	XR_001737886.1:n.	N/A	Upstream Transcript Variant
LOC101928836 transcript variant X2	XR_946925.2:n.	N/A	Upstream Transcript Variant
LOC101928836 transcript variant X3	XR_946926.2:n.	N/A	Upstream Transcript Variant
LOC101928836 transcript variant X6	XR_946928.2:n.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.866	A=0.134
1000Genomes	American	Sub	694	C=0.960	A=0.040
1000Genomes	East Asian	Sub	1008	C=0.965	A=0.035
1000Genomes	Europe	Sub	1006	C=0.966	A=0.034
1000Genomes	Global	Study-wide	5008	C=0.943	A=0.057
1000Genomes	South Asian	Sub	978	C=0.990	A=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.983	A=0.017
The Genome Aggregation Database	African	Sub	8710	C=0.867	A=0.133
The Genome Aggregation Database	American	Sub	838	C=0.960	A=0.040
The Genome Aggregation Database	East Asian	Sub	1620	C=0.970	A=0.030
The Genome Aggregation Database	Europe	Sub	18484	C=0.974	A=0.025
The Genome Aggregation Database	Global	Study-wide	29954	C=0.942	A=0.057
The Genome Aggregation Database	Other	Sub	302	C=0.990	A=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.921	A=0.078
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.982	A=0.018

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

P-Value

SNP ID	p-value	Traits	Study
rs75562159	9E-06	alcohol dependence	26365420

eQTL of rs75562159 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 rs75562159 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 )
chr1	16009998	16010180	E067	-48725
chr1	16018008	16018305	E067	-40600
chr1	16024362	16024603	E067	-34302
chr1	16026933	16026987	E067	-31918
chr1	16029593	16030503	E067	-28402
chr1	16030611	16030675	E067	-28230
chr1	16030845	16030889	E067	-28016
chr1	16030983	16031058	E067	-27847
chr1	16031149	16031284	E067	-27621
chr1	16031290	16031611	E067	-27294
chr1	16033232	16033617	E067	-25288
chr1	16038645	16038989	E067	-19916
chr1	16040879	16041430	E067	-17475
chr1	16067554	16068386	E067	8649
chr1	16082740	16083218	E067	23835
chr1	16018008	16018305	E068	-40600
chr1	16024362	16024603	E068	-34302
chr1	16026933	16026987	E068	-31918
chr1	16027069	16027285	E068	-31620
chr1	16027351	16027405	E068	-31500
chr1	16029593	16030503	E068	-28402
chr1	16030611	16030675	E068	-28230
chr1	16030845	16030889	E068	-28016
chr1	16030983	16031058	E068	-27847
chr1	16031149	16031284	E068	-27621
chr1	16038645	16038989	E068	-19916
chr1	16040879	16041430	E068	-17475
chr1	16061835	16062103	E068	2930
chr1	16062208	16062895	E068	3303
chr1	16062903	16063204	E068	3998
chr1	16092007	16092083	E068	33102
chr1	16092089	16092779	E068	33184
chr1	16009289	16009522	E069	-49383
chr1	16009583	16009649	E069	-49256
chr1	16009732	16009838	E069	-49067
chr1	16009923	16009975	E069	-48930
chr1	16009998	16010180	E069	-48725
chr1	16017045	16017085	E069	-41820
chr1	16018008	16018305	E069	-40600
chr1	16018742	16018809	E069	-40096
chr1	16022698	16022744	E069	-36161
chr1	16024362	16024603	E069	-34302
chr1	16026933	16026987	E069	-31918
chr1	16027069	16027285	E069	-31620
chr1	16027351	16027405	E069	-31500
chr1	16029418	16029548	E069	-29357
chr1	16029593	16030503	E069	-28402
chr1	16030611	16030675	E069	-28230
chr1	16030845	16030889	E069	-28016
chr1	16030983	16031058	E069	-27847
chr1	16031149	16031284	E069	-27621
chr1	16062208	16062895	E069	3303
chr1	16009583	16009649	E070	-49256
chr1	16009732	16009838	E070	-49067
chr1	16009923	16009975	E070	-48930
chr1	16009998	16010180	E070	-48725
chr1	16009732	16009838	E071	-49067
chr1	16009923	16009975	E071	-48930
chr1	16009998	16010180	E071	-48725
chr1	16012810	16012860	E071	-46045
chr1	16018008	16018305	E071	-40600
chr1	16018742	16018809	E071	-40096
chr1	16024362	16024603	E071	-34302
chr1	16026933	16026987	E071	-31918
chr1	16027069	16027285	E071	-31620
chr1	16027351	16027405	E071	-31500
chr1	16030611	16030675	E071	-28230
chr1	16030845	16030889	E071	-28016
chr1	16030983	16031058	E071	-27847
chr1	16031149	16031284	E071	-27621
chr1	16031290	16031611	E071	-27294
chr1	16037515	16037555	E071	-21350
chr1	16038645	16038989	E071	-19916
chr1	16062903	16063204	E071	3998
chr1	16064126	16064203	E071	5221
chr1	16064286	16064420	E071	5381
chr1	16081813	16082042	E071	22908
chr1	16082211	16082535	E071	23306
chr1	16082740	16083218	E071	23835
chr1	16009289	16009522	E072	-49383
chr1	16009583	16009649	E072	-49256
chr1	16009732	16009838	E072	-49067
chr1	16009923	16009975	E072	-48930
chr1	16009998	16010180	E072	-48725
chr1	16018008	16018305	E072	-40600
chr1	16018936	16019041	E072	-39864
chr1	16020013	16020214	E072	-38691
chr1	16020227	16020277	E072	-38628
chr1	16020281	16020331	E072	-38574
chr1	16022698	16022744	E072	-36161
chr1	16024362	16024603	E072	-34302
chr1	16026933	16026987	E072	-31918
chr1	16027069	16027285	E072	-31620
chr1	16029593	16030503	E072	-28402
chr1	16030611	16030675	E072	-28230
chr1	16030845	16030889	E072	-28016
chr1	16030983	16031058	E072	-27847
chr1	16031149	16031284	E072	-27621
chr1	16031290	16031611	E072	-27294
chr1	16033232	16033617	E072	-25288
chr1	16038645	16038989	E072	-19916
chr1	16040879	16041430	E072	-17475
chr1	16042500	16042596	E072	-16309
chr1	16062208	16062895	E072	3303
chr1	16067554	16068386	E072	8649
chr1	16082211	16082535	E072	23306
chr1	16082740	16083218	E072	23835
chr1	16018008	16018305	E073	-40600
chr1	16018742	16018809	E073	-40096
chr1	16024362	16024603	E073	-34302
chr1	16026933	16026987	E073	-31918
chr1	16027069	16027285	E073	-31620
chr1	16029593	16030503	E073	-28402
chr1	16030611	16030675	E073	-28230
chr1	16030845	16030889	E073	-28016
chr1	16030983	16031058	E073	-27847
chr1	16031149	16031284	E073	-27621
chr1	16031290	16031611	E073	-27294
chr1	16040879	16041430	E073	-17475
chr1	16062208	16062895	E073	3303
chr1	16062903	16063204	E073	3998
chr1	16075883	16076588	E073	16978
chr1	16022573	16022627	E074	-36278
chr1	16022698	16022744	E074	-36161
chr1	16026933	16026987	E074	-31918
chr1	16027069	16027285	E074	-31620
chr1	16027351	16027405	E074	-31500
chr1	16029418	16029548	E074	-29357
chr1	16029593	16030503	E074	-28402
chr1	16033232	16033617	E074	-25288
chr1	16033828	16033872	E074	-25033
chr1	16033926	16034098	E074	-24807
chr1	16038645	16038989	E074	-19916
chr1	16040879	16041430	E074	-17475
chr1	16062208	16062895	E074	3303
chr1	16062903	16063204	E074	3998
chr1	16067554	16068386	E074	8649
chr1	16082211	16082535	E074	23306
chr1	16082740	16083218	E074	23835
chr1	16092007	16092083	E074	33102
chr1	16092089	16092779	E074	33184
chr1	16009583	16009649	E081	-49256
chr1	16009732	16009838	E081	-49067
chr1	16009923	16009975	E081	-48930
chr1	16009998	16010180	E081	-48725
chr1	16012810	16012860	E081	-46045
chr1	16024362	16024603	E081	-34302
chr1	16026933	16026987	E081	-31918
chr1	16027069	16027285	E081	-31620
chr1	16027351	16027405	E081	-31500
chr1	16029593	16030503	E081	-28402
chr1	16030611	16030675	E081	-28230
chr1	16038645	16038989	E081	-19916
chr1	16086966	16088170	E081	28061
chr1	16038645	16038989	E082	-19916

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	16010434	16010492	E067	-48413
chr1	16010525	16010922	E067	-47983
chr1	16010985	16011183	E067	-47722
chr1	16011192	16011828	E067	-47077
chr1	16010434	16010492	E068	-48413
chr1	16010525	16010922	E068	-47983
chr1	16010985	16011183	E068	-47722
chr1	16011192	16011828	E068	-47077
chr1	16085390	16086459	E068	26485
chr1	16010434	16010492	E069	-48413
chr1	16010525	16010922	E069	-47983
chr1	16010985	16011183	E069	-47722
chr1	16011192	16011828	E069	-47077
chr1	16085390	16086459	E069	26485
chr1	16010434	16010492	E070	-48413
chr1	16010525	16010922	E070	-47983
chr1	16010985	16011183	E070	-47722
chr1	16011192	16011828	E070	-47077
chr1	16010434	16010492	E071	-48413
chr1	16010525	16010922	E071	-47983
chr1	16010985	16011183	E071	-47722
chr1	16011192	16011828	E071	-47077
chr1	16085390	16086459	E071	26485
chr1	16010434	16010492	E072	-48413
chr1	16010525	16010922	E072	-47983
chr1	16010985	16011183	E072	-47722
chr1	16011192	16011828	E072	-47077
chr1	16010434	16010492	E073	-48413
chr1	16010525	16010922	E073	-47983
chr1	16010985	16011183	E073	-47722
chr1	16011192	16011828	E073	-47077
chr1	16085390	16086459	E073	26485
chr1	16010434	16010492	E074	-48413
chr1	16010525	16010922	E074	-47983
chr1	16010985	16011183	E074	-47722
chr1	16011192	16011828	E074	-47077
chr1	16011192	16011828	E081	-47077
chr1	16010434	16010492	E082	-48413
chr1	16010525	16010922	E082	-47983
chr1	16010985	16011183	E082	-47722
chr1	16011192	16011828	E082	-47077
chr1	16085390	16086459	E082	26485
chr1	16086668	16086761	E082	27763