rs11583322

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

STK40 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0307 (9165/29814,GnomAD)
C=0253 (7389/29118,TOPMED)
C=0221 (1105/5008,1000G)
C=0386 (1489/3854,ALSPAC)
C=0380 (1408/3708,TWINSUK)

Position: chr1:36356711 (GRCh38.p7) (1p34.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 188 Enhancers around

Promoter: 29 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.36356711T>C
GRCh37.p13 chr 1	NC_000001.10:g.36822312T>C

Gene: STK40, serine/threonine kinase 40(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
STK40 transcript variant 1	NM_001282546.1:c.	N/A	Intron Variant
STK40 transcript variant 2	NM_001282547.1:c.	N/A	Intron Variant
STK40 transcript variant 3	NM_032017.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.927	C=0.073
1000Genomes	American	Sub	694	T=0.750	C=0.250
1000Genomes	East Asian	Sub	1008	T=0.853	C=0.147
1000Genomes	Europe	Sub	1006	T=0.577	C=0.423
1000Genomes	Global	Study-wide	5008	T=0.779	C=0.221
1000Genomes	South Asian	Sub	978	T=0.730	C=0.270
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.614	C=0.386
The Genome Aggregation Database	African	Sub	8698	T=0.886	C=0.114
The Genome Aggregation Database	American	Sub	832	T=0.780	C=0.220
The Genome Aggregation Database	East Asian	Sub	1616	T=0.820	C=0.180
The Genome Aggregation Database	Europe	Sub	18368	T=0.587	C=0.412
The Genome Aggregation Database	Global	Study-wide	29814	T=0.692	C=0.307
The Genome Aggregation Database	Other	Sub	300	T=0.620	C=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.746	C=0.253
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.620	C=0.380

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs11583322	0.000000011	alcohol dependence	23691058
rs11583322	0.00032	alcohol dependence	20201924

eQTL of rs11583322 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	5.3713e-11	32977	Cerebellum
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	6.9606e-6	32977	Frontal_Cortex_BA9
Chr1:36822312	SH3D21	ENSG00000214193.5	T>C	4.5512e-13	50324	Cortex
Chr1:36822312	EVA1B	ENSG00000142694.6	T>C	5.4099e-6	33096	Cortex
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	2.4749e-9	32977	Cortex
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	2.1249e-4	32977	Cerebellar_Hemisphere
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	1.3454e-2	32977	Caudate_basal_ganglia
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	2.4587e-5	32977	Hippocampus
Chr1:36822312	RP11-268J15.5	ENSG00000116883.8	T>C	2.4968e-9	32977	Anterior_cingulate_cortex

meQTL of rs11583322 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	36815792	36815914	E067	-6398
chr1	36815967	36816040	E067	-6272
chr1	36816043	36817792	E067	-4520
chr1	36817835	36818298	E067	-4014
chr1	36830886	36831432	E067	8574
chr1	36831687	36832337	E067	9375
chr1	36832362	36832412	E067	10050
chr1	36834499	36835173	E067	12187
chr1	36835243	36835494	E067	12931
chr1	36835545	36835635	E067	13233
chr1	36838282	36838530	E067	15970
chr1	36848835	36849085	E067	26523
chr1	36849122	36849166	E067	26810
chr1	36849226	36849307	E067	26914
chr1	36849477	36849583	E067	27165
chr1	36816043	36817792	E068	-4520
chr1	36817835	36818298	E068	-4014
chr1	36830886	36831432	E068	8574
chr1	36832362	36832412	E068	10050
chr1	36834499	36835173	E068	12187
chr1	36835243	36835494	E068	12931
chr1	36835545	36835635	E068	13233
chr1	36838282	36838530	E068	15970
chr1	36848835	36849085	E068	26523
chr1	36849122	36849166	E068	26810
chr1	36849226	36849307	E068	26914
chr1	36849477	36849583	E068	27165
chr1	36794408	36794659	E069	-27653
chr1	36795115	36795165	E069	-27147
chr1	36795167	36795238	E069	-27074
chr1	36815967	36816040	E069	-6272
chr1	36816043	36817792	E069	-4520
chr1	36817835	36818298	E069	-4014
chr1	36830886	36831432	E069	8574
chr1	36832362	36832412	E069	10050
chr1	36834499	36835173	E069	12187
chr1	36838282	36838530	E069	15970
chr1	36848835	36849085	E069	26523
chr1	36849122	36849166	E069	26810
chr1	36849226	36849307	E069	26914
chr1	36849477	36849583	E069	27165
chr1	36861871	36861993	E069	39559
chr1	36773421	36773525	E070	-48787
chr1	36773545	36773660	E070	-48652
chr1	36794408	36794659	E070	-27653
chr1	36815967	36816040	E070	-6272
chr1	36816043	36817792	E070	-4520
chr1	36817835	36818298	E070	-4014
chr1	36818459	36818837	E070	-3475
chr1	36830886	36831432	E070	8574
chr1	36832362	36832412	E070	10050
chr1	36832723	36833014	E070	10411
chr1	36848835	36849085	E070	26523
chr1	36849122	36849166	E070	26810
chr1	36794408	36794659	E071	-27653
chr1	36795115	36795165	E071	-27147
chr1	36795167	36795238	E071	-27074
chr1	36815464	36815767	E071	-6545
chr1	36815792	36815914	E071	-6398
chr1	36815967	36816040	E071	-6272
chr1	36816043	36817792	E071	-4520
chr1	36817835	36818298	E071	-4014
chr1	36830886	36831432	E071	8574
chr1	36832362	36832412	E071	10050
chr1	36834499	36835173	E071	12187
chr1	36837847	36837958	E071	15535
chr1	36838085	36838145	E071	15773
chr1	36838282	36838530	E071	15970
chr1	36848835	36849085	E071	26523
chr1	36849122	36849166	E071	26810
chr1	36849226	36849307	E071	26914
chr1	36849477	36849583	E071	27165
chr1	36862203	36862312	E071	39891
chr1	36773421	36773525	E072	-48787
chr1	36773545	36773660	E072	-48652
chr1	36773728	36773806	E072	-48506
chr1	36804733	36804817	E072	-17495
chr1	36815792	36815914	E072	-6398
chr1	36815967	36816040	E072	-6272
chr1	36816043	36817792	E072	-4520
chr1	36817835	36818298	E072	-4014
chr1	36830886	36831432	E072	8574
chr1	36832362	36832412	E072	10050
chr1	36834499	36835173	E072	12187
chr1	36846612	36846738	E072	24300
chr1	36848835	36849085	E072	26523
chr1	36849122	36849166	E072	26810
chr1	36849226	36849307	E072	26914
chr1	36849477	36849583	E072	27165
chr1	36773728	36773806	E073	-48506
chr1	36773947	36773991	E073	-48321
chr1	36774096	36774174	E073	-48138
chr1	36794408	36794659	E073	-27653
chr1	36795115	36795165	E073	-27147
chr1	36795167	36795238	E073	-27074
chr1	36803266	36803457	E073	-18855
chr1	36815464	36815767	E073	-6545
chr1	36815792	36815914	E073	-6398
chr1	36815967	36816040	E073	-6272
chr1	36816043	36817792	E073	-4520
chr1	36817835	36818298	E073	-4014
chr1	36825395	36825499	E073	3083
chr1	36830886	36831432	E073	8574
chr1	36832362	36832412	E073	10050
chr1	36832723	36833014	E073	10411
chr1	36834499	36835173	E073	12187
chr1	36835243	36835494	E073	12931
chr1	36835545	36835635	E073	13233
chr1	36835641	36835785	E073	13329
chr1	36835955	36836085	E073	13643
chr1	36838282	36838530	E073	15970
chr1	36841741	36842129	E073	19429
chr1	36842142	36842237	E073	19830
chr1	36843218	36843676	E073	20906
chr1	36848835	36849085	E073	26523
chr1	36849122	36849166	E073	26810
chr1	36849226	36849307	E073	26914
chr1	36849477	36849583	E073	27165
chr1	36857014	36857095	E073	34702
chr1	36857288	36857342	E073	34976
chr1	36859702	36859756	E073	37390
chr1	36794408	36794659	E074	-27653
chr1	36795115	36795165	E074	-27147
chr1	36795167	36795238	E074	-27074
chr1	36815967	36816040	E074	-6272
chr1	36816043	36817792	E074	-4520
chr1	36817835	36818298	E074	-4014
chr1	36830886	36831432	E074	8574
chr1	36831687	36832337	E074	9375
chr1	36832362	36832412	E074	10050
chr1	36834499	36835173	E074	12187
chr1	36835243	36835494	E074	12931
chr1	36835545	36835635	E074	13233
chr1	36845938	36846199	E074	23626
chr1	36846339	36846513	E074	24027
chr1	36849226	36849307	E074	26914
chr1	36849477	36849583	E074	27165
chr1	36854250	36854320	E074	31938
chr1	36862203	36862312	E074	39891
chr1	36773421	36773525	E081	-48787
chr1	36773545	36773660	E081	-48652
chr1	36816043	36817792	E081	-4520
chr1	36823735	36823785	E081	1423
chr1	36824243	36824654	E081	1931
chr1	36824976	36825352	E081	2664
chr1	36825395	36825499	E081	3083
chr1	36825509	36825997	E081	3197
chr1	36826174	36826236	E081	3862
chr1	36826922	36827011	E081	4610
chr1	36830490	36830547	E081	8178
chr1	36831687	36832337	E081	9375
chr1	36832362	36832412	E081	10050
chr1	36832723	36833014	E081	10411
chr1	36833076	36833152	E081	10764
chr1	36834499	36835173	E081	12187
chr1	36835243	36835494	E081	12931
chr1	36848835	36849085	E081	26523
chr1	36849122	36849166	E081	26810
chr1	36849226	36849307	E081	26914
chr1	36849477	36849583	E081	27165
chr1	36854250	36854320	E081	31938
chr1	36854729	36854802	E081	32417
chr1	36854977	36855161	E081	32665
chr1	36855473	36855641	E081	33161
chr1	36861871	36861993	E081	39559
chr1	36862203	36862312	E081	39891
chr1	36867630	36867690	E081	45318
chr1	36867882	36867932	E081	45570
chr1	36868094	36868454	E081	45782
chr1	36795115	36795165	E082	-27147
chr1	36817835	36818298	E082	-4014
chr1	36824243	36824654	E082	1931
chr1	36824976	36825352	E082	2664
chr1	36825395	36825499	E082	3083
chr1	36825509	36825997	E082	3197
chr1	36826174	36826236	E082	3862
chr1	36832362	36832412	E082	10050
chr1	36832723	36833014	E082	10411
chr1	36833076	36833152	E082	10764
chr1	36833474	36833564	E082	11162
chr1	36833585	36833705	E082	11273
chr1	36833834	36833878	E082	11522
chr1	36833910	36833954	E082	11598
chr1	36834259	36834299	E082	11947
chr1	36834499	36835173	E082	12187
chr1	36849226	36849307	E082	26914
chr1	36849477	36849583	E082	27165
chr1	36867630	36867690	E082	45318

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	36850096	36853817	E067	27784
chr1	36862763	36864077	E067	40451
chr1	36785767	36790329	E068	-31983
chr1	36850096	36853817	E068	27784
chr1	36862763	36864077	E068	40451
chr1	36866204	36867406	E068	43892
chr1	36785767	36790329	E069	-31983
chr1	36850096	36853817	E069	27784
chr1	36862763	36864077	E069	40451
chr1	36866204	36867406	E069	43892
chr1	36850096	36853817	E070	27784
chr1	36862763	36864077	E070	40451
chr1	36785767	36790329	E071	-31983
chr1	36850096	36853817	E071	27784
chr1	36862763	36864077	E071	40451
chr1	36866204	36867406	E071	43892
chr1	36785767	36790329	E072	-31983
chr1	36850096	36853817	E072	27784
chr1	36862763	36864077	E072	40451
chr1	36785767	36790329	E073	-31983
chr1	36850096	36853817	E073	27784
chr1	36862763	36864077	E073	40451
chr1	36785767	36790329	E074	-31983
chr1	36850096	36853817	E074	27784
chr1	36862763	36864077	E074	40451
chr1	36862763	36864077	E081	40451
chr1	36785767	36790329	E082	-31983
chr1	36850096	36853817	E082	27784
chr1	36862763	36864077	E082	40451