rs4451521

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

STK40 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0010 (310/30002,GnomAD)
C==0016 (489/29118,TOPMED)
C==0015 (76/5008,1000G)
C==0000 (1/3854,ALSPAC)
C==0001 (2/3708,TWINSUK)

Position: chr1:36365663 (GRCh38.p7) (1p34.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 178 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.36365663C>G
GRCh37.p13 chr 1	NC_000001.10:g.36831264C>G

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	C=0.053	G=0.947
1000Genomes	American	Sub	694	C=0.010	G=0.990
1000Genomes	East Asian	Sub	1008	C=0.000	G=1.000
1000Genomes	Europe	Sub	1006	C=0.000	G=1.000
1000Genomes	Global	Study-wide	5008	C=0.015	G=0.985
1000Genomes	South Asian	Sub	978	C=0.000	G=1.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.000	G=1.000
The Genome Aggregation Database	African	Sub	8734	C=0.035	G=0.965
The Genome Aggregation Database	American	Sub	838	C=0.000	G=1.000
The Genome Aggregation Database	East Asian	Sub	1622	C=0.000	G=1.000
The Genome Aggregation Database	Europe	Sub	18506	C=0.000	G=0.999
The Genome Aggregation Database	Global	Study-wide	30002	C=0.010	G=0.989
The Genome Aggregation Database	Other	Sub	302	C=0.000	G=1.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.016	G=0.983
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.001	G=0.999

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
rs4451521	0.000156	alcohol dependence	21314694

eQTL of rs4451521 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 rs4451521 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	-15350
chr1	36815967	36816040	E067	-15224
chr1	36816043	36817792	E067	-13472
chr1	36817835	36818298	E067	-12966
chr1	36830886	36831432	E067	0
chr1	36831687	36832337	E067	423
chr1	36832362	36832412	E067	1098
chr1	36834499	36835173	E067	3235
chr1	36835243	36835494	E067	3979
chr1	36835545	36835635	E067	4281
chr1	36838282	36838530	E067	7018
chr1	36848835	36849085	E067	17571
chr1	36849122	36849166	E067	17858
chr1	36849226	36849307	E067	17962
chr1	36849477	36849583	E067	18213
chr1	36816043	36817792	E068	-13472
chr1	36817835	36818298	E068	-12966
chr1	36830886	36831432	E068	0
chr1	36832362	36832412	E068	1098
chr1	36834499	36835173	E068	3235
chr1	36835243	36835494	E068	3979
chr1	36835545	36835635	E068	4281
chr1	36838282	36838530	E068	7018
chr1	36848835	36849085	E068	17571
chr1	36849122	36849166	E068	17858
chr1	36849226	36849307	E068	17962
chr1	36849477	36849583	E068	18213
chr1	36794408	36794659	E069	-36605
chr1	36795115	36795165	E069	-36099
chr1	36795167	36795238	E069	-36026
chr1	36815967	36816040	E069	-15224
chr1	36816043	36817792	E069	-13472
chr1	36817835	36818298	E069	-12966
chr1	36830886	36831432	E069	0
chr1	36832362	36832412	E069	1098
chr1	36834499	36835173	E069	3235
chr1	36838282	36838530	E069	7018
chr1	36848835	36849085	E069	17571
chr1	36849122	36849166	E069	17858
chr1	36849226	36849307	E069	17962
chr1	36849477	36849583	E069	18213
chr1	36861871	36861993	E069	30607
chr1	36794408	36794659	E070	-36605
chr1	36815967	36816040	E070	-15224
chr1	36816043	36817792	E070	-13472
chr1	36817835	36818298	E070	-12966
chr1	36818459	36818837	E070	-12427
chr1	36830886	36831432	E070	0
chr1	36832362	36832412	E070	1098
chr1	36832723	36833014	E070	1459
chr1	36848835	36849085	E070	17571
chr1	36849122	36849166	E070	17858
chr1	36794408	36794659	E071	-36605
chr1	36795115	36795165	E071	-36099
chr1	36795167	36795238	E071	-36026
chr1	36815464	36815767	E071	-15497
chr1	36815792	36815914	E071	-15350
chr1	36815967	36816040	E071	-15224
chr1	36816043	36817792	E071	-13472
chr1	36817835	36818298	E071	-12966
chr1	36830886	36831432	E071	0
chr1	36832362	36832412	E071	1098
chr1	36834499	36835173	E071	3235
chr1	36837847	36837958	E071	6583
chr1	36838085	36838145	E071	6821
chr1	36838282	36838530	E071	7018
chr1	36848835	36849085	E071	17571
chr1	36849122	36849166	E071	17858
chr1	36849226	36849307	E071	17962
chr1	36849477	36849583	E071	18213
chr1	36862203	36862312	E071	30939
chr1	36804733	36804817	E072	-26447
chr1	36815792	36815914	E072	-15350
chr1	36815967	36816040	E072	-15224
chr1	36816043	36817792	E072	-13472
chr1	36817835	36818298	E072	-12966
chr1	36830886	36831432	E072	0
chr1	36832362	36832412	E072	1098
chr1	36834499	36835173	E072	3235
chr1	36846612	36846738	E072	15348
chr1	36848835	36849085	E072	17571
chr1	36849122	36849166	E072	17858
chr1	36849226	36849307	E072	17962
chr1	36849477	36849583	E072	18213
chr1	36794408	36794659	E073	-36605
chr1	36795115	36795165	E073	-36099
chr1	36795167	36795238	E073	-36026
chr1	36803266	36803457	E073	-27807
chr1	36815464	36815767	E073	-15497
chr1	36815792	36815914	E073	-15350
chr1	36815967	36816040	E073	-15224
chr1	36816043	36817792	E073	-13472
chr1	36817835	36818298	E073	-12966
chr1	36825395	36825499	E073	-5765
chr1	36830886	36831432	E073	0
chr1	36832362	36832412	E073	1098
chr1	36832723	36833014	E073	1459
chr1	36834499	36835173	E073	3235
chr1	36835243	36835494	E073	3979
chr1	36835545	36835635	E073	4281
chr1	36835641	36835785	E073	4377
chr1	36835955	36836085	E073	4691
chr1	36838282	36838530	E073	7018
chr1	36841741	36842129	E073	10477
chr1	36842142	36842237	E073	10878
chr1	36843218	36843676	E073	11954
chr1	36848835	36849085	E073	17571
chr1	36849122	36849166	E073	17858
chr1	36849226	36849307	E073	17962
chr1	36849477	36849583	E073	18213
chr1	36857014	36857095	E073	25750
chr1	36857288	36857342	E073	26024
chr1	36859702	36859756	E073	28438
chr1	36794408	36794659	E074	-36605
chr1	36795115	36795165	E074	-36099
chr1	36795167	36795238	E074	-36026
chr1	36815967	36816040	E074	-15224
chr1	36816043	36817792	E074	-13472
chr1	36817835	36818298	E074	-12966
chr1	36830886	36831432	E074	0
chr1	36831687	36832337	E074	423
chr1	36832362	36832412	E074	1098
chr1	36834499	36835173	E074	3235
chr1	36835243	36835494	E074	3979
chr1	36835545	36835635	E074	4281
chr1	36845938	36846199	E074	14674
chr1	36846339	36846513	E074	15075
chr1	36849226	36849307	E074	17962
chr1	36849477	36849583	E074	18213
chr1	36854250	36854320	E074	22986
chr1	36862203	36862312	E074	30939
chr1	36816043	36817792	E081	-13472
chr1	36823735	36823785	E081	-7479
chr1	36824243	36824654	E081	-6610
chr1	36824976	36825352	E081	-5912
chr1	36825395	36825499	E081	-5765
chr1	36825509	36825997	E081	-5267
chr1	36826174	36826236	E081	-5028
chr1	36826922	36827011	E081	-4253
chr1	36830490	36830547	E081	-717
chr1	36831687	36832337	E081	423
chr1	36832362	36832412	E081	1098
chr1	36832723	36833014	E081	1459
chr1	36833076	36833152	E081	1812
chr1	36834499	36835173	E081	3235
chr1	36835243	36835494	E081	3979
chr1	36848835	36849085	E081	17571
chr1	36849122	36849166	E081	17858
chr1	36849226	36849307	E081	17962
chr1	36849477	36849583	E081	18213
chr1	36854250	36854320	E081	22986
chr1	36854729	36854802	E081	23465
chr1	36854977	36855161	E081	23713
chr1	36855473	36855641	E081	24209
chr1	36861871	36861993	E081	30607
chr1	36862203	36862312	E081	30939
chr1	36867630	36867690	E081	36366
chr1	36867882	36867932	E081	36618
chr1	36868094	36868454	E081	36830
chr1	36795115	36795165	E082	-36099
chr1	36817835	36818298	E082	-12966
chr1	36824243	36824654	E082	-6610
chr1	36824976	36825352	E082	-5912
chr1	36825395	36825499	E082	-5765
chr1	36825509	36825997	E082	-5267
chr1	36826174	36826236	E082	-5028
chr1	36832362	36832412	E082	1098
chr1	36832723	36833014	E082	1459
chr1	36833076	36833152	E082	1812
chr1	36833474	36833564	E082	2210
chr1	36833585	36833705	E082	2321
chr1	36833834	36833878	E082	2570
chr1	36833910	36833954	E082	2646
chr1	36834259	36834299	E082	2995
chr1	36834499	36835173	E082	3235
chr1	36849226	36849307	E082	17962
chr1	36849477	36849583	E082	18213
chr1	36867630	36867690	E082	36366

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	36850096	36853817	E067	18832
chr1	36862763	36864077	E067	31499
chr1	36785767	36790329	E068	-40935
chr1	36850096	36853817	E068	18832
chr1	36862763	36864077	E068	31499
chr1	36866204	36867406	E068	34940
chr1	36785767	36790329	E069	-40935
chr1	36850096	36853817	E069	18832
chr1	36862763	36864077	E069	31499
chr1	36866204	36867406	E069	34940
chr1	36850096	36853817	E070	18832
chr1	36862763	36864077	E070	31499
chr1	36785767	36790329	E071	-40935
chr1	36850096	36853817	E071	18832
chr1	36862763	36864077	E071	31499
chr1	36866204	36867406	E071	34940
chr1	36785767	36790329	E072	-40935
chr1	36850096	36853817	E072	18832
chr1	36862763	36864077	E072	31499
chr1	36785767	36790329	E073	-40935
chr1	36850096	36853817	E073	18832
chr1	36862763	36864077	E073	31499
chr1	36785767	36790329	E074	-40935
chr1	36850096	36853817	E074	18832
chr1	36862763	36864077	E074	31499
chr1	36862763	36864077	E081	31499
chr1	36785767	36790329	E082	-40935
chr1	36850096	36853817	E082	18832
chr1	36862763	36864077	E082	31499