rs12116935

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SH3D21 : Intron Variant
EVA1B : 5 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0279 (8373/29910,GnomAD)
G=0249 (7278/29118,TOPMED)
G=0235 (1179/5008,1000G)
G=0373 (1436/3854,ALSPAC)
G=0373 (1382/3708,TWINSUK)

Position: chr1:36323945 (GRCh38.p7) (1p34.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 152 Enhancers around

Promoter: 14 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.36323945A>G
GRCh37.p13 chr 1	NC_000001.10:g.36789546A>G

Gene: EVA1B, eva-1 homolog B (C. elegans)(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EVA1B transcript variant 1	NM_018166.2:c.	N/A	5 Prime UTR Variant
EVA1B transcript variant 2	NM_001304762.1:c.	N/A	Genic Upstream Transcript Variant
EVA1B transcript variant 3	NR_130899.1:n.	N/A	Genic Upstream Transcript Variant
EVA1B transcript variant X1	XM_017001627.1:c.	N/A	Genic Upstream Transcript Variant

Gene: SH3D21, SH3 domain containing 21(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SH3D21 transcript variant 1	NM_001162530.1:c.	N/A	Genic Downstream Transcript Variant
SH3D21 transcript variant 2	NM_024676.4:c.	N/A	Genic Downstream Transcript Variant
SH3D21 transcript variant X1	XM_017002340.1:c.	N/A	Intron Variant
SH3D21 transcript variant X2	XM_017002341.1:c.	N/A	Intron Variant
SH3D21 transcript variant X5	XM_017002344.1:c.	N/A	Intron Variant
SH3D21 transcript variant X6	XM_017002345.1:c.	N/A	Intron Variant
SH3D21 transcript variant X7	XM_011542153.2:c.	N/A	Genic Downstream Transcript Variant
SH3D21 transcript variant X3	XM_017002342.1:c.	N/A	Genic Downstream Transcript Variant
SH3D21 transcript variant X4	XM_017002343.1:c.	N/A	Genic Downstream Transcript Variant
SH3D21 transcript variant X8	XM_017002346.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.939	G=0.061
1000Genomes	American	Sub	694	A=0.780	G=0.220
1000Genomes	East Asian	Sub	1008	A=0.920	G=0.080
1000Genomes	Europe	Sub	1006	A=0.579	G=0.421
1000Genomes	Global	Study-wide	5008	A=0.765	G=0.235
1000Genomes	South Asian	Sub	978	A=0.550	G=0.450
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.627	G=0.373
The Genome Aggregation Database	African	Sub	8708	A=0.899	G=0.101
The Genome Aggregation Database	American	Sub	838	A=0.780	G=0.220
The Genome Aggregation Database	East Asian	Sub	1622	A=0.936	G=0.064
The Genome Aggregation Database	Europe	Sub	18440	A=0.615	G=0.384
The Genome Aggregation Database	Global	Study-wide	29910	A=0.720	G=0.279
The Genome Aggregation Database	Other	Sub	302	A=0.640	G=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.750	G=0.249
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.627	G=0.373

PMID	Title	Author	Journal
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs12116935	6.98E-06	alcohol dependence	23691058

eQTL of rs12116935 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:36789546	EVA1B	ENSG00000142694.6	A>G	2.8272e-3	330	Cerebellum
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	5.3713e-11	211	Cerebellum
Chr1:36789546	SH3D21	ENSG00000214193.5	A>G	4.9165e-4	17558	Frontal_Cortex_BA9
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	6.9606e-6	211	Frontal_Cortex_BA9
Chr1:36789546	SH3D21	ENSG00000214193.5	A>G	4.5512e-13	17558	Cortex
Chr1:36789546	EVA1B	ENSG00000142694.6	A>G	5.4099e-6	330	Cortex
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	2.4749e-9	211	Cortex
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	2.1249e-4	211	Cerebellar_Hemisphere
Chr1:36789546	SH3D21	ENSG00000214193.5	A>G	2.8203e-3	17558	Caudate_basal_ganglia
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	2.4587e-5	211	Hippocampus
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	2.8329e-4	211	Putamen_basal_ganglia
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	2.4968e-9	211	Anterior_cingulate_cortex
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	7.6474e-3	211	Nucleus_accumbens_basal_ganglia
Chr1:36789546	RP11-268J15.5	ENSG00000116883.8	A>G	1.1526e-3	211	Amygdala

meQTL of rs12116935 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	36765420	36766053	E067	-23493
chr1	36815792	36815914	E067	26246
chr1	36815967	36816040	E067	26421
chr1	36816043	36817792	E067	26497
chr1	36817835	36818298	E067	28289
chr1	36830886	36831432	E067	41340
chr1	36831687	36832337	E067	42141
chr1	36832362	36832412	E067	42816
chr1	36834499	36835173	E067	44953
chr1	36835243	36835494	E067	45697
chr1	36835545	36835635	E067	45999
chr1	36838282	36838530	E067	48736
chr1	36744744	36744844	E068	-44702
chr1	36744903	36745324	E068	-44222
chr1	36745420	36745678	E068	-43868
chr1	36766162	36766405	E068	-23141
chr1	36766554	36766698	E068	-22848
chr1	36816043	36817792	E068	26497
chr1	36817835	36818298	E068	28289
chr1	36830886	36831432	E068	41340
chr1	36832362	36832412	E068	42816
chr1	36834499	36835173	E068	44953
chr1	36835243	36835494	E068	45697
chr1	36835545	36835635	E068	45999
chr1	36838282	36838530	E068	48736
chr1	36794408	36794659	E069	4862
chr1	36795115	36795165	E069	5569
chr1	36795167	36795238	E069	5621
chr1	36815967	36816040	E069	26421
chr1	36816043	36817792	E069	26497
chr1	36817835	36818298	E069	28289
chr1	36830886	36831432	E069	41340
chr1	36832362	36832412	E069	42816
chr1	36834499	36835173	E069	44953
chr1	36838282	36838530	E069	48736
chr1	36773421	36773525	E070	-16021
chr1	36773545	36773660	E070	-15886
chr1	36794408	36794659	E070	4862
chr1	36815967	36816040	E070	26421
chr1	36816043	36817792	E070	26497
chr1	36817835	36818298	E070	28289
chr1	36818459	36818837	E070	28913
chr1	36830886	36831432	E070	41340
chr1	36832362	36832412	E070	42816
chr1	36832723	36833014	E070	43177
chr1	36745420	36745678	E071	-43868
chr1	36766162	36766405	E071	-23141
chr1	36766554	36766698	E071	-22848
chr1	36766893	36767436	E071	-22110
chr1	36767554	36767620	E071	-21926
chr1	36794408	36794659	E071	4862
chr1	36795115	36795165	E071	5569
chr1	36795167	36795238	E071	5621
chr1	36815464	36815767	E071	25918
chr1	36815792	36815914	E071	26246
chr1	36815967	36816040	E071	26421
chr1	36816043	36817792	E071	26497
chr1	36817835	36818298	E071	28289
chr1	36830886	36831432	E071	41340
chr1	36832362	36832412	E071	42816
chr1	36834499	36835173	E071	44953
chr1	36837847	36837958	E071	48301
chr1	36838085	36838145	E071	48539
chr1	36838282	36838530	E071	48736
chr1	36765420	36766053	E072	-23493
chr1	36766162	36766405	E072	-23141
chr1	36766554	36766698	E072	-22848
chr1	36766893	36767436	E072	-22110
chr1	36767554	36767620	E072	-21926
chr1	36773421	36773525	E072	-16021
chr1	36773545	36773660	E072	-15886
chr1	36773728	36773806	E072	-15740
chr1	36804733	36804817	E072	15187
chr1	36815792	36815914	E072	26246
chr1	36815967	36816040	E072	26421
chr1	36816043	36817792	E072	26497
chr1	36817835	36818298	E072	28289
chr1	36830886	36831432	E072	41340
chr1	36832362	36832412	E072	42816
chr1	36834499	36835173	E072	44953
chr1	36773728	36773806	E073	-15740
chr1	36773947	36773991	E073	-15555
chr1	36774096	36774174	E073	-15372
chr1	36794408	36794659	E073	4862
chr1	36795115	36795165	E073	5569
chr1	36795167	36795238	E073	5621
chr1	36803266	36803457	E073	13720
chr1	36815464	36815767	E073	25918
chr1	36815792	36815914	E073	26246
chr1	36815967	36816040	E073	26421
chr1	36816043	36817792	E073	26497
chr1	36817835	36818298	E073	28289
chr1	36825395	36825499	E073	35849
chr1	36830886	36831432	E073	41340
chr1	36832362	36832412	E073	42816
chr1	36832723	36833014	E073	43177
chr1	36834499	36835173	E073	44953
chr1	36835243	36835494	E073	45697
chr1	36835545	36835635	E073	45999
chr1	36835641	36835785	E073	46095
chr1	36835955	36836085	E073	46409
chr1	36838282	36838530	E073	48736
chr1	36765420	36766053	E074	-23493
chr1	36766162	36766405	E074	-23141
chr1	36766554	36766698	E074	-22848
chr1	36766893	36767436	E074	-22110
chr1	36794408	36794659	E074	4862
chr1	36795115	36795165	E074	5569
chr1	36795167	36795238	E074	5621
chr1	36815967	36816040	E074	26421
chr1	36816043	36817792	E074	26497
chr1	36817835	36818298	E074	28289
chr1	36830886	36831432	E074	41340
chr1	36831687	36832337	E074	42141
chr1	36832362	36832412	E074	42816
chr1	36834499	36835173	E074	44953
chr1	36835243	36835494	E074	45697
chr1	36835545	36835635	E074	45999
chr1	36739684	36740231	E081	-49315
chr1	36773421	36773525	E081	-16021
chr1	36773545	36773660	E081	-15886
chr1	36816043	36817792	E081	26497
chr1	36823735	36823785	E081	34189
chr1	36824243	36824654	E081	34697
chr1	36824976	36825352	E081	35430
chr1	36825395	36825499	E081	35849
chr1	36825509	36825997	E081	35963
chr1	36826174	36826236	E081	36628
chr1	36826922	36827011	E081	37376
chr1	36830490	36830547	E081	40944
chr1	36831687	36832337	E081	42141
chr1	36832362	36832412	E081	42816
chr1	36832723	36833014	E081	43177
chr1	36833076	36833152	E081	43530
chr1	36834499	36835173	E081	44953
chr1	36835243	36835494	E081	45697
chr1	36795115	36795165	E082	5569
chr1	36817835	36818298	E082	28289
chr1	36824243	36824654	E082	34697
chr1	36824976	36825352	E082	35430
chr1	36825395	36825499	E082	35849
chr1	36825509	36825997	E082	35963
chr1	36826174	36826236	E082	36628
chr1	36832362	36832412	E082	42816
chr1	36832723	36833014	E082	43177
chr1	36833076	36833152	E082	43530
chr1	36833474	36833564	E082	43928
chr1	36833585	36833705	E082	44039
chr1	36833834	36833878	E082	44288
chr1	36833910	36833954	E082	44364
chr1	36834259	36834299	E082	44713
chr1	36834499	36835173	E082	44953

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	36770983	36773385	E067	-16161
chr1	36785767	36790329	E068	0
chr1	36770983	36773385	E069	-16161
chr1	36785767	36790329	E069	0
chr1	36770983	36773385	E070	-16161
chr1	36770983	36773385	E071	-16161
chr1	36785767	36790329	E071	0
chr1	36770983	36773385	E072	-16161
chr1	36785767	36790329	E072	0
chr1	36770983	36773385	E073	-16161
chr1	36785767	36790329	E073	0
chr1	36785767	36790329	E074	0
chr1	36770983	36773385	E082	-16161
chr1	36785767	36790329	E082	0