rs10489142

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CAMTA1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0211 (6345/29980,GnomAD)
G=0177 (5157/29118,TOPMED)
G=0175 (876/5008,1000G)
G=0263 (1015/3854,ALSPAC)
G=0256 (951/3708,TWINSUK)

Position: chr1:7303250 (GRCh38.p7) (1p36.23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 77 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.7303250A>G
GRCh37.p13 chr 1	NC_000001.10:g.7363310A>G

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	Intron 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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.964	G=0.036
1000Genomes	American	Sub	694	A=0.700	G=0.300
1000Genomes	East Asian	Sub	1008	A=0.736	G=0.264
1000Genomes	Europe	Sub	1006	A=0.769	G=0.231
1000Genomes	Global	Study-wide	5008	A=0.825	G=0.175
1000Genomes	South Asian	Sub	978	A=0.880	G=0.120
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.737	G=0.263
The Genome Aggregation Database	African	Sub	8728	A=0.941	G=0.059
The Genome Aggregation Database	American	Sub	838	A=0.710	G=0.290
The Genome Aggregation Database	East Asian	Sub	1622	A=0.723	G=0.277
The Genome Aggregation Database	Europe	Sub	18490	A=0.726	G=0.273
The Genome Aggregation Database	Global	Study-wide	29980	A=0.788	G=0.211
The Genome Aggregation Database	Other	Sub	302	A=0.730	G=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.822	G=0.177
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.744	G=0.256

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
26194999	Fine-scale population structure of Malays in Peninsular Malaysia and Singapore and implications for association studies.	Hoh BP	Hum Genomics

P-Value

SNP ID	p-value	Traits	Study
rs10489142	0.000716	alcohol dependence	21314694

eQTL of rs10489142 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 rs10489142 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	7351251	7351301	E067	-12009
chr1	7354406	7354566	E067	-8744
chr1	7358795	7360489	E067	-2821
chr1	7372813	7372893	E067	9503
chr1	7373153	7373304	E067	9843
chr1	7373356	7373575	E067	10046
chr1	7401115	7401227	E067	37805
chr1	7401258	7401915	E067	37948
chr1	7326720	7326890	E068	-36420
chr1	7327460	7327520	E068	-35790
chr1	7327687	7327986	E068	-35324
chr1	7358795	7360489	E068	-2821
chr1	7373153	7373304	E068	9843
chr1	7373356	7373575	E068	10046
chr1	7351251	7351301	E069	-12009
chr1	7351390	7352078	E069	-11232
chr1	7352579	7352666	E069	-10644
chr1	7352890	7353052	E069	-10258
chr1	7353154	7353609	E069	-9701
chr1	7358795	7360489	E069	-2821
chr1	7373153	7373304	E069	9843
chr1	7373356	7373575	E069	10046
chr1	7394478	7395088	E069	31168
chr1	7401115	7401227	E069	37805
chr1	7401258	7401915	E069	37948
chr1	7402104	7402154	E069	38794
chr1	7325020	7325122	E070	-38188
chr1	7358795	7360489	E070	-2821
chr1	7394478	7395088	E070	31168
chr1	7395168	7395250	E070	31858
chr1	7400135	7400265	E070	36825
chr1	7401115	7401227	E070	37805
chr1	7401258	7401915	E070	37948
chr1	7402104	7402154	E070	38794
chr1	7351251	7351301	E071	-12009
chr1	7351390	7352078	E071	-11232
chr1	7352890	7353052	E071	-10258
chr1	7353154	7353609	E071	-9701
chr1	7358795	7360489	E071	-2821
chr1	7361507	7361667	E071	-1643
chr1	7373876	7374027	E071	10566
chr1	7374062	7374113	E071	10752
chr1	7401115	7401227	E071	37805
chr1	7401258	7401915	E071	37948
chr1	7351251	7351301	E072	-12009
chr1	7358795	7360489	E072	-2821
chr1	7401115	7401227	E072	37805
chr1	7401258	7401915	E072	37948
chr1	7351251	7351301	E073	-12009
chr1	7351390	7352078	E073	-11232
chr1	7401115	7401227	E073	37805
chr1	7401258	7401915	E073	37948
chr1	7358795	7360489	E074	-2821
chr1	7373876	7374027	E074	10566
chr1	7374062	7374113	E074	10752
chr1	7401115	7401227	E074	37805
chr1	7401258	7401915	E074	37948
chr1	7316909	7317018	E081	-46292
chr1	7317382	7317753	E081	-45557
chr1	7322816	7323553	E081	-39757
chr1	7325020	7325122	E081	-38188
chr1	7325799	7326421	E081	-36889
chr1	7394478	7395088	E081	31168
chr1	7395168	7395250	E081	31858
chr1	7395320	7396007	E081	32010
chr1	7401115	7401227	E081	37805
chr1	7401258	7401915	E081	37948
chr1	7402104	7402154	E081	38794
chr1	7408809	7408902	E081	45499
chr1	7322816	7323553	E082	-39757
chr1	7325020	7325122	E082	-38188
chr1	7325799	7326421	E082	-36889
chr1	7326720	7326890	E082	-36420
chr1	7394478	7395088	E082	31168
chr1	7401115	7401227	E082	37805
chr1	7401258	7401915	E082	37948
chr1	7402104	7402154	E082	38794