rs10490046

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

SLC8A1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0281 (8437/29936,GnomAD)
C=0292 (8528/29116,TOPMED)
C=0286 (1432/5008,1000G)
C=0229 (882/3854,ALSPAC)
C=0216 (800/3708,TWINSUK)

Position: chr2:40403538 (GRCh38.p7) (2p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 99 Enhancers around

Promoter: 25 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.40403538A>C
GRCh37.p13 chr 2	NC_000002.11:g.40630678A>C

Gene: SLC8A1, solute carrier family 8 member A1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC8A1 transcript variant B	NM_001112800.1:c.	N/A	Intron Variant
SLC8A1 transcript variant C	NM_001112801.1:c.	N/A	Intron Variant
SLC8A1 transcript variant D	NM_001112802.1:c.	N/A	Intron Variant
SLC8A1 transcript variant E	NM_001252624.1:c.	N/A	Intron Variant
SLC8A1 transcript variant A	NM_021097.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X30	XM_005264514.3:c.	N/A	Intron Variant
SLC8A1 transcript variant X8	XM_006712081.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X7	XM_006712082.3:c.	N/A	Intron Variant
SLC8A1 transcript variant X12	XM_006712083.3:c.	N/A	Intron Variant
SLC8A1 transcript variant X14	XM_006712084.3:c.	N/A	Intron Variant
SLC8A1 transcript variant X16	XM_006712085.3:c.	N/A	Intron Variant
SLC8A1 transcript variant X3	XM_011533050.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X10	XM_011533054.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X15	XM_011533055.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X17	XM_011533056.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X19	XM_011533057.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X21	XM_011533058.2:c.	N/A	Intron Variant
SLC8A1 transcript variant X1	XM_017004745.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X2	XM_017004746.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X4	XM_017004747.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X5	XM_017004748.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X6	XM_017004749.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X9	XM_017004750.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X11	XM_017004751.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X13	XM_017004752.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X18	XM_017004753.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X20	XM_017004754.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X21	XM_017004755.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X22	XM_017004756.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X23	XM_017004757.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X24	XM_017004758.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X25	XM_017004759.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X26	XM_017004760.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X27	XM_017004761.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X28	XM_017004762.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X29	XM_017004763.1:c.	N/A	Intron Variant
SLC8A1 transcript variant X22	XM_017004764.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.705	C=0.295
1000Genomes	American	Sub	694	A=0.630	C=0.370
1000Genomes	East Asian	Sub	1008	A=0.692	C=0.308
1000Genomes	Europe	Sub	1006	A=0.739	C=0.261
1000Genomes	Global	Study-wide	5008	A=0.714	C=0.286
1000Genomes	South Asian	Sub	978	A=0.780	C=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.771	C=0.229
The Genome Aggregation Database	African	Sub	8720	A=0.701	C=0.299
The Genome Aggregation Database	American	Sub	836	A=0.660	C=0.340
The Genome Aggregation Database	East Asian	Sub	1608	A=0.687	C=0.313
The Genome Aggregation Database	Europe	Sub	18472	A=0.730	C=0.269
The Genome Aggregation Database	Global	Study-wide	29936	A=0.718	C=0.281
The Genome Aggregation Database	Other	Sub	300	A=0.770	C=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.707	C=0.292
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.784	C=0.216

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs10490046	7.23E-05	alcohol consumption	23743675

eQTL of rs10490046 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 rs10490046 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 )
chr2	40592762	40592812	E067	-37866
chr2	40680221	40680344	E067	49543
chr2	40586139	40586189	E068	-44489
chr2	40598523	40599254	E068	-31424
chr2	40622170	40622713	E068	-7965
chr2	40627557	40627653	E068	-3025
chr2	40627671	40627842	E068	-2836
chr2	40627850	40628015	E068	-2663
chr2	40628179	40628311	E068	-2367
chr2	40630069	40630122	E068	-556
chr2	40630190	40630288	E068	-390
chr2	40630466	40631036	E068	0
chr2	40631185	40631520	E068	507
chr2	40632632	40632926	E068	1954
chr2	40645655	40645870	E068	14977
chr2	40645885	40646113	E068	15207
chr2	40646445	40646575	E068	15767
chr2	40646584	40646723	E068	15906
chr2	40646750	40646801	E068	16072
chr2	40658197	40658400	E068	27519
chr2	40658445	40658626	E068	27767
chr2	40658672	40659036	E068	27994
chr2	40661830	40662676	E068	31152
chr2	40662694	40662774	E068	32016
chr2	40662969	40663073	E068	32291
chr2	40663145	40663217	E068	32467
chr2	40663327	40663442	E068	32649
chr2	40664516	40664665	E068	33838
chr2	40666163	40666313	E068	35485
chr2	40666513	40666557	E068	35835
chr2	40666724	40666926	E068	36046
chr2	40672729	40672947	E068	42051
chr2	40646445	40646575	E069	15767
chr2	40646584	40646723	E069	15906
chr2	40647891	40648017	E069	17213
chr2	40590461	40590616	E070	-40062
chr2	40622880	40623078	E070	-7600
chr2	40623158	40623266	E070	-7412
chr2	40623444	40623562	E070	-7116
chr2	40630466	40631036	E070	0
chr2	40631185	40631520	E070	507
chr2	40632632	40632926	E070	1954
chr2	40646445	40646575	E070	15767
chr2	40646584	40646723	E070	15906
chr2	40646750	40646801	E070	16072
chr2	40680221	40680344	E070	49543
chr2	40680346	40680656	E070	49668
chr2	40622170	40622713	E071	-7965
chr2	40622880	40623078	E071	-7600
chr2	40630466	40631036	E071	0
chr2	40631185	40631520	E071	507
chr2	40647891	40648017	E072	17213
chr2	40658197	40658400	E072	27519
chr2	40658445	40658626	E072	27767
chr2	40680221	40680344	E072	49543
chr2	40680346	40680656	E072	49668
chr2	40622170	40622713	E073	-7965
chr2	40622880	40623078	E073	-7600
chr2	40645655	40645870	E073	14977
chr2	40645885	40646113	E073	15207
chr2	40646584	40646723	E073	15906
chr2	40647891	40648017	E073	17213
chr2	40680221	40680344	E073	49543
chr2	40593479	40593611	E081	-37067
chr2	40593919	40594063	E081	-36615
chr2	40594292	40594414	E081	-36264
chr2	40594842	40595132	E081	-35546
chr2	40621074	40621173	E081	-9505
chr2	40621266	40621437	E081	-9241
chr2	40621562	40621733	E081	-8945
chr2	40621758	40622127	E081	-8551
chr2	40622170	40622713	E081	-7965
chr2	40622880	40623078	E081	-7600
chr2	40630466	40631036	E081	0
chr2	40631185	40631520	E081	507
chr2	40636779	40636837	E081	6101
chr2	40636880	40637210	E081	6202
chr2	40643116	40643169	E081	12438
chr2	40645885	40646113	E081	15207
chr2	40654365	40654566	E081	23687
chr2	40665188	40665444	E081	34510
chr2	40675572	40675707	E081	44894
chr2	40680221	40680344	E081	49543
chr2	40680346	40680656	E081	49668
chr2	40590461	40590616	E082	-40062
chr2	40593479	40593611	E082	-37067
chr2	40593919	40594063	E082	-36615
chr2	40621266	40621437	E082	-9241
chr2	40621562	40621733	E082	-8945
chr2	40621758	40622127	E082	-8551
chr2	40622170	40622713	E082	-7965
chr2	40625246	40625328	E082	-5350
chr2	40630466	40631036	E082	0
chr2	40631185	40631520	E082	507
chr2	40632632	40632926	E082	1954
chr2	40645655	40645870	E082	14977
chr2	40645885	40646113	E082	15207
chr2	40646445	40646575	E082	15767
chr2	40646584	40646723	E082	15906

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	40677123	40679808	E067	46445
chr2	40679841	40680126	E067	49163
chr2	40591236	40591565	E068	-39113
chr2	40631735	40632015	E068	1057
chr2	40677123	40679808	E068	46445
chr2	40679841	40680126	E068	49163
chr2	40631735	40632015	E069	1057
chr2	40677123	40679808	E069	46445
chr2	40679841	40680126	E069	49163
chr2	40677123	40679808	E070	46445
chr2	40679841	40680126	E070	49163
chr2	40631735	40632015	E071	1057
chr2	40677123	40679808	E071	46445
chr2	40677123	40679808	E072	46445
chr2	40679841	40680126	E072	49163
chr2	40677123	40679808	E073	46445
chr2	40679841	40680126	E073	49163
chr2	40631735	40632015	E074	1057
chr2	40677123	40679808	E074	46445
chr2	40679841	40680126	E074	49163
chr2	40677123	40679808	E081	46445
chr2	40679841	40680126	E081	49163
chr2	40631735	40632015	E082	1057
chr2	40677123	40679808	E082	46445
chr2	40679841	40680126	E082	49163