rs6975142

Organism: Homo sapiens

Alleles: A>C / A>T

Gene : Feature

CACNA2D1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0344 (10189/29556,GnomAD)
T=0403 (11734/29118,TOPMED)
T=0370 (1851/5008,1000G)
T=0226 (871/3854,ALSPAC)
T=0231 (855/3708,TWINSUK)

Position: chr7:82388133 (GRCh38.p7) (7q21.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 11 Enhancers around

Promoter: 11 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.82388133A>C
GRCh38.p7 chr 7	NC_000007.14:g.82388133A>T
GRCh37.p13 chr 7	NC_000007.13:g.82017449A>C
GRCh37.p13 chr 7	NC_000007.13:g.82017449A>T
CACNA2D1 RefSeqGene	LRG_437
CACNA2D1 RefSeqGene	LRG_437

Gene: CACNA2D1, calcium voltage-gated channel auxiliary subunit alpha2delta 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA2D1 transcript variant 1	NM_000722.3:c.	N/A	Intron Variant
CACNA2D1 transcript variant 2	NM_001302890.1:c.	N/A	Intron Variant
CACNA2D1 transcript variant X4	XM_005250570.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X6	XM_005250572.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X8	XM_005250573.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X9	XM_005250574.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X1	XM_006716118.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X7	XM_006716119.3:c.	N/A	Intron Variant
CACNA2D1 transcript variant X10	XM_006716120.3:c.	N/A	Intron Variant
CACNA2D1 transcript variant X2	XM_011516570.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X3	XM_011516571.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X5	XM_011516572.2:c.	N/A	Intron Variant
CACNA2D1 transcript variant X11	XM_017012588.1:c.	N/A	Intron Variant
CACNA2D1 transcript variant X14	XM_006716121.3:c.	N/A	Genic Upstream Transcript Variant
CACNA2D1 transcript variant X12	XR_001744873.1:n.	N/A	Intron Variant
CACNA2D1 transcript variant X13	XR_001744874.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.382	T=0.618
1000Genomes	American	Sub	694	A=0.680	T=0.320
1000Genomes	East Asian	Sub	1008	A=0.623	T=0.377
1000Genomes	Europe	Sub	1006	A=0.754	T=0.246
1000Genomes	Global	Study-wide	5008	A=0.630	T=0.370
1000Genomes	South Asian	Sub	978	A=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.774	T=0.226
The Genome Aggregation Database	African	Sub	8602	A=0.415	T=0.585
The Genome Aggregation Database	American	Sub	806	A=0.760	T=0.240
The Genome Aggregation Database	East Asian	Sub	1606	A=0.605	T=0.395
The Genome Aggregation Database	Europe	Sub	18242	A=0.765	T=0.234
The Genome Aggregation Database	Global	Study-wide	29556	A=0.655	T=0.344
The Genome Aggregation Database	Other	Sub	300	A=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.597	T=0.403
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.769	T=0.231

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

P-Value

SNP ID	p-value	Traits	Study
rs6975142	0.000467	alcohol dependence	21314694

eQTL of rs6975142 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 rs6975142 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 )
chr7	87974361	87974601	E068	39929
chr7	87974635	87974954	E068	40203
chr7	87974957	87975033	E068	40525
chr7	87974635	87974954	E069	40203
chr7	87974957	87975033	E069	40525
chr7	87976807	87977200	E070	42375
chr7	87977391	87977441	E070	42959
chr7	87974635	87974954	E071	40203
chr7	87974957	87975033	E071	40525
chr7	87975083	87975248	E071	40651
chr7	87975255	87975396	E071	40823

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	87935876	87936560	E067	1444
chr7	87935709	87935833	E068	1277
chr7	87935876	87936560	E068	1444
chr7	87935709	87935833	E070	1277
chr7	87935876	87936560	E070	1444
chr7	87935709	87935833	E073	1277
chr7	87935876	87936560	E073	1444
chr7	87935709	87935833	E074	1277
chr7	87935876	87936560	E074	1444
chr7	87935709	87935833	E082	1277
chr7	87935876	87936560	E082	1444