rs9789765

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

SLC8A1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0086 (2594/29960,GnomAD)
T=0086 (2531/29116,TOPMED)
T=0180 (901/5008,1000G)
T=0081 (311/3854,ALSPAC)
T=0087 (323/3708,TWINSUK)

Position: chr2:40407694 (GRCh38.p7) (2p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 100 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.40407694A>T
GRCh37.p13 chr 2	NC_000002.11:g.40634834A>T

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=0.971	T=0.029
1000Genomes	American	Sub	694	A=0.820	T=0.180
1000Genomes	East Asian	Sub	1008	A=0.620	T=0.380
1000Genomes	Europe	Sub	1006	A=0.934	T=0.066
1000Genomes	Global	Study-wide	5008	A=0.820	T=0.180
1000Genomes	South Asian	Sub	978	A=0.710	T=0.290
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.919	T=0.081
The Genome Aggregation Database	African	Sub	8720	A=0.957	T=0.043
The Genome Aggregation Database	American	Sub	838	A=0.790	T=0.210
The Genome Aggregation Database	East Asian	Sub	1604	A=0.628	T=0.372
The Genome Aggregation Database	Europe	Sub	18496	A=0.922	T=0.077
The Genome Aggregation Database	Global	Study-wide	29960	A=0.913	T=0.086
The Genome Aggregation Database	Other	Sub	302	A=0.930	T=0.070
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.913	T=0.086
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.913	T=0.087

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
rs9789765	0.000458	alcohol dependence	21314694

eQTL of rs9789765 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 rs9789765 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	-42022
chr2	40680221	40680344	E067	45387
chr2	40586139	40586189	E068	-48645
chr2	40598523	40599254	E068	-35580
chr2	40622170	40622713	E068	-12121
chr2	40627557	40627653	E068	-7181
chr2	40627671	40627842	E068	-6992
chr2	40627850	40628015	E068	-6819
chr2	40628179	40628311	E068	-6523
chr2	40630069	40630122	E068	-4712
chr2	40630190	40630288	E068	-4546
chr2	40630466	40631036	E068	-3798
chr2	40631185	40631520	E068	-3314
chr2	40632632	40632926	E068	-1908
chr2	40645655	40645870	E068	10821
chr2	40645885	40646113	E068	11051
chr2	40646445	40646575	E068	11611
chr2	40646584	40646723	E068	11750
chr2	40646750	40646801	E068	11916
chr2	40658197	40658400	E068	23363
chr2	40658445	40658626	E068	23611
chr2	40658672	40659036	E068	23838
chr2	40661830	40662676	E068	26996
chr2	40662694	40662774	E068	27860
chr2	40662969	40663073	E068	28135
chr2	40663145	40663217	E068	28311
chr2	40663327	40663442	E068	28493
chr2	40664516	40664665	E068	29682
chr2	40666163	40666313	E068	31329
chr2	40666513	40666557	E068	31679
chr2	40666724	40666926	E068	31890
chr2	40672729	40672947	E068	37895
chr2	40646445	40646575	E069	11611
chr2	40646584	40646723	E069	11750
chr2	40647891	40648017	E069	13057
chr2	40590461	40590616	E070	-44218
chr2	40622880	40623078	E070	-11756
chr2	40623158	40623266	E070	-11568
chr2	40623444	40623562	E070	-11272
chr2	40630466	40631036	E070	-3798
chr2	40631185	40631520	E070	-3314
chr2	40632632	40632926	E070	-1908
chr2	40646445	40646575	E070	11611
chr2	40646584	40646723	E070	11750
chr2	40646750	40646801	E070	11916
chr2	40680221	40680344	E070	45387
chr2	40680346	40680656	E070	45512
chr2	40680699	40681048	E070	45865
chr2	40622170	40622713	E071	-12121
chr2	40622880	40623078	E071	-11756
chr2	40630466	40631036	E071	-3798
chr2	40631185	40631520	E071	-3314
chr2	40647891	40648017	E072	13057
chr2	40658197	40658400	E072	23363
chr2	40658445	40658626	E072	23611
chr2	40680221	40680344	E072	45387
chr2	40680346	40680656	E072	45512
chr2	40622170	40622713	E073	-12121
chr2	40622880	40623078	E073	-11756
chr2	40645655	40645870	E073	10821
chr2	40645885	40646113	E073	11051
chr2	40646584	40646723	E073	11750
chr2	40647891	40648017	E073	13057
chr2	40680221	40680344	E073	45387
chr2	40593479	40593611	E081	-41223
chr2	40593919	40594063	E081	-40771
chr2	40594292	40594414	E081	-40420
chr2	40594842	40595132	E081	-39702
chr2	40621074	40621173	E081	-13661
chr2	40621266	40621437	E081	-13397
chr2	40621562	40621733	E081	-13101
chr2	40621758	40622127	E081	-12707
chr2	40622170	40622713	E081	-12121
chr2	40622880	40623078	E081	-11756
chr2	40630466	40631036	E081	-3798
chr2	40631185	40631520	E081	-3314
chr2	40636779	40636837	E081	1945
chr2	40636880	40637210	E081	2046
chr2	40643116	40643169	E081	8282
chr2	40645885	40646113	E081	11051
chr2	40654365	40654566	E081	19531
chr2	40665188	40665444	E081	30354
chr2	40675572	40675707	E081	40738
chr2	40680221	40680344	E081	45387
chr2	40680346	40680656	E081	45512
chr2	40590461	40590616	E082	-44218
chr2	40593479	40593611	E082	-41223
chr2	40593919	40594063	E082	-40771
chr2	40621266	40621437	E082	-13397
chr2	40621562	40621733	E082	-13101
chr2	40621758	40622127	E082	-12707
chr2	40622170	40622713	E082	-12121
chr2	40625246	40625328	E082	-9506
chr2	40630466	40631036	E082	-3798
chr2	40631185	40631520	E082	-3314
chr2	40632632	40632926	E082	-1908
chr2	40645655	40645870	E082	10821
chr2	40645885	40646113	E082	11051
chr2	40646445	40646575	E082	11611
chr2	40646584	40646723	E082	11750

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	40677123	40679808	E067	42289
chr2	40679841	40680126	E067	45007
chr2	40591236	40591565	E068	-43269
chr2	40631735	40632015	E068	-2819
chr2	40677123	40679808	E068	42289
chr2	40679841	40680126	E068	45007
chr2	40631735	40632015	E069	-2819
chr2	40677123	40679808	E069	42289
chr2	40679841	40680126	E069	45007
chr2	40677123	40679808	E070	42289
chr2	40679841	40680126	E070	45007
chr2	40631735	40632015	E071	-2819
chr2	40677123	40679808	E071	42289
chr2	40677123	40679808	E072	42289
chr2	40679841	40680126	E072	45007
chr2	40677123	40679808	E073	42289
chr2	40679841	40680126	E073	45007
chr2	40631735	40632015	E074	-2819
chr2	40677123	40679808	E074	42289
chr2	40679841	40680126	E074	45007
chr2	40677123	40679808	E081	42289
chr2	40679841	40680126	E081	45007
chr2	40631735	40632015	E082	-2819
chr2	40677123	40679808	E082	42289
chr2	40679841	40680126	E082	45007