rs642490

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PLEKHB1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0151 (4544/29942,GnomAD)
G=0197 (5757/29118,TOPMED)
G=0164 (819/5008,1000G)
G=0056 (214/3854,ALSPAC)
G=0053 (198/3708,TWINSUK)

Position: chr11:73654570 (GRCh38.p7) (11q13.4)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 232 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.73654570A>G
GRCh37.p13 chr 11	NC_000011.9:g.73365615A>G

Gene: PLEKHB1, pleckstrin homology domain containing B1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLEKHB1 transcript variant 3	NM_001130033.1:c.	N/A	Intron Variant
PLEKHB1 transcript variant 2	NM_001130034.1:c.	N/A	Intron Variant
PLEKHB1 transcript variant 4	NM_001130035.1:c.	N/A	Intron Variant
PLEKHB1 transcript variant 5	NM_001130036.1:c.	N/A	Intron Variant
PLEKHB1 transcript variant 1	NM_021200.2:c.	N/A	Intron Variant
PLEKHB1 transcript variant X1	XM_011545192.2:c.	N/A	Intron Variant
PLEKHB1 transcript variant X2	XM_011545193.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.570	G=0.430
1000Genomes	American	Sub	694	A=0.910	G=0.090
1000Genomes	East Asian	Sub	1008	A=0.975	G=0.025
1000Genomes	Europe	Sub	1006	A=0.929	G=0.071
1000Genomes	Global	Study-wide	5008	A=0.836	G=0.164
1000Genomes	South Asian	Sub	978	A=0.900	G=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.944	G=0.056
The Genome Aggregation Database	African	Sub	8694	A=0.625	G=0.375
The Genome Aggregation Database	American	Sub	838	A=0.950	G=0.050
The Genome Aggregation Database	East Asian	Sub	1620	A=0.994	G=0.006
The Genome Aggregation Database	Europe	Sub	18488	A=0.935	G=0.064
The Genome Aggregation Database	Global	Study-wide	29942	A=0.848	G=0.151
The Genome Aggregation Database	Other	Sub	302	A=0.870	G=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.802	G=0.197
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.947	G=0.053

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
rs642490	0.000628	alcohol dependence	21314694

eQTL of rs642490 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 rs642490 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 )
chr11	73361427	73361500	E067	-4115
chr11	73361616	73361682	E067	-3933
chr11	73361784	73361855	E067	-3760
chr11	73362439	73362537	E067	-3078
chr11	73362711	73362765	E067	-2850
chr11	73362839	73363910	E067	-1705
chr11	73363994	73364249	E067	-1366
chr11	73364331	73364518	E067	-1097
chr11	73364552	73364709	E067	-906
chr11	73364791	73364880	E067	-735
chr11	73365136	73365340	E067	-275
chr11	73365374	73365469	E067	-146
chr11	73365531	73365581	E067	-34
chr11	73365591	73365654	E067	0
chr11	73365831	73365881	E067	216
chr11	73365939	73365979	E067	324
chr11	73371078	73371376	E067	5463
chr11	73371490	73371550	E067	5875
chr11	73374326	73374408	E067	8711
chr11	73374457	73374507	E067	8842
chr11	73374577	73374671	E067	8962
chr11	73374827	73374907	E067	9212
chr11	73374941	73375231	E067	9326
chr11	73375276	73375349	E067	9661
chr11	73344161	73344311	E068	-21304
chr11	73344403	73344453	E068	-21162
chr11	73344467	73344535	E068	-21080
chr11	73345132	73345529	E068	-20086
chr11	73357849	73357938	E068	-7677
chr11	73357950	73358206	E068	-7409
chr11	73360602	73360681	E068	-4934
chr11	73361427	73361500	E068	-4115
chr11	73361616	73361682	E068	-3933
chr11	73361784	73361855	E068	-3760
chr11	73362439	73362537	E068	-3078
chr11	73362711	73362765	E068	-2850
chr11	73363994	73364249	E068	-1366
chr11	73364331	73364518	E068	-1097
chr11	73364552	73364709	E068	-906
chr11	73364791	73364880	E068	-735
chr11	73365136	73365340	E068	-275
chr11	73365374	73365469	E068	-146
chr11	73365531	73365581	E068	-34
chr11	73365591	73365654	E068	0
chr11	73371078	73371376	E068	5463
chr11	73371490	73371550	E068	5875
chr11	73373904	73374090	E068	8289
chr11	73374129	73374205	E068	8514
chr11	73374326	73374408	E068	8711
chr11	73374457	73374507	E068	8842
chr11	73374577	73374671	E068	8962
chr11	73374827	73374907	E068	9212
chr11	73374941	73375231	E068	9326
chr11	73375276	73375349	E068	9661
chr11	73375421	73375533	E068	9806
chr11	73375660	73375759	E068	10045
chr11	73375871	73375921	E068	10256
chr11	73375986	73376159	E068	10371
chr11	73344161	73344311	E069	-21304
chr11	73344403	73344453	E069	-21162
chr11	73344467	73344535	E069	-21080
chr11	73357950	73358206	E069	-7409
chr11	73360472	73360560	E069	-5055
chr11	73360602	73360681	E069	-4934
chr11	73360819	73360873	E069	-4742
chr11	73361020	73361134	E069	-4481
chr11	73361427	73361500	E069	-4115
chr11	73361616	73361682	E069	-3933
chr11	73361784	73361855	E069	-3760
chr11	73362439	73362537	E069	-3078
chr11	73362711	73362765	E069	-2850
chr11	73363994	73364249	E069	-1366
chr11	73364331	73364518	E069	-1097
chr11	73364552	73364709	E069	-906
chr11	73364791	73364880	E069	-735
chr11	73365136	73365340	E069	-275
chr11	73365374	73365469	E069	-146
chr11	73365531	73365581	E069	-34
chr11	73365591	73365654	E069	0
chr11	73370862	73370933	E069	5247
chr11	73370943	73370983	E069	5328
chr11	73371490	73371550	E069	5875
chr11	73374129	73374205	E069	8514
chr11	73374326	73374408	E069	8711
chr11	73374457	73374507	E069	8842
chr11	73374577	73374671	E069	8962
chr11	73374827	73374907	E069	9212
chr11	73374941	73375231	E069	9326
chr11	73375276	73375349	E069	9661
chr11	73375421	73375533	E069	9806
chr11	73375660	73375759	E069	10045
chr11	73375871	73375921	E069	10256
chr11	73375986	73376159	E069	10371
chr11	73362839	73363910	E070	-1705
chr11	73336262	73336405	E071	-29210
chr11	73336790	73337175	E071	-28440
chr11	73344161	73344311	E071	-21304
chr11	73344403	73344453	E071	-21162
chr11	73344467	73344535	E071	-21080
chr11	73344711	73344829	E071	-20786
chr11	73360472	73360560	E071	-5055
chr11	73360602	73360681	E071	-4934
chr11	73360819	73360873	E071	-4742
chr11	73361020	73361134	E071	-4481
chr11	73361427	73361500	E071	-4115
chr11	73361616	73361682	E071	-3933
chr11	73361784	73361855	E071	-3760
chr11	73362439	73362537	E071	-3078
chr11	73362711	73362765	E071	-2850
chr11	73363994	73364249	E071	-1366
chr11	73364331	73364518	E071	-1097
chr11	73364552	73364709	E071	-906
chr11	73364791	73364880	E071	-735
chr11	73365136	73365340	E071	-275
chr11	73365374	73365469	E071	-146
chr11	73365531	73365581	E071	-34
chr11	73365591	73365654	E071	0
chr11	73365831	73365881	E071	216
chr11	73365939	73365979	E071	324
chr11	73366383	73366439	E071	768
chr11	73370389	73370490	E071	4774
chr11	73370553	73370711	E071	4938
chr11	73370770	73370855	E071	5155
chr11	73370862	73370933	E071	5247
chr11	73370943	73370983	E071	5328
chr11	73371078	73371376	E071	5463
chr11	73371490	73371550	E071	5875
chr11	73374326	73374408	E071	8711
chr11	73374457	73374507	E071	8842
chr11	73374577	73374671	E071	8962
chr11	73374827	73374907	E071	9212
chr11	73374941	73375231	E071	9326
chr11	73396980	73397163	E071	31365
chr11	73336790	73337175	E072	-28440
chr11	73337409	73337459	E072	-28156
chr11	73344161	73344311	E072	-21304
chr11	73344403	73344453	E072	-21162
chr11	73344467	73344535	E072	-21080
chr11	73344711	73344829	E072	-20786
chr11	73357950	73358206	E072	-7409
chr11	73360602	73360681	E072	-4934
chr11	73360819	73360873	E072	-4742
chr11	73361020	73361134	E072	-4481
chr11	73361427	73361500	E072	-4115
chr11	73361616	73361682	E072	-3933
chr11	73361784	73361855	E072	-3760
chr11	73362439	73362537	E072	-3078
chr11	73362711	73362765	E072	-2850
chr11	73363994	73364249	E072	-1366
chr11	73364331	73364518	E072	-1097
chr11	73364552	73364709	E072	-906
chr11	73364791	73364880	E072	-735
chr11	73365136	73365340	E072	-275
chr11	73365374	73365469	E072	-146
chr11	73365531	73365581	E072	-34
chr11	73365591	73365654	E072	0
chr11	73371078	73371376	E072	5463
chr11	73371490	73371550	E072	5875
chr11	73374577	73374671	E072	8962
chr11	73374827	73374907	E072	9212
chr11	73374941	73375231	E072	9326
chr11	73375276	73375349	E072	9661
chr11	73375421	73375533	E072	9806
chr11	73375660	73375759	E072	10045
chr11	73357849	73357938	E073	-7677
chr11	73357950	73358206	E073	-7409
chr11	73360182	73360271	E073	-5344
chr11	73360472	73360560	E073	-5055
chr11	73360602	73360681	E073	-4934
chr11	73360819	73360873	E073	-4742
chr11	73361020	73361134	E073	-4481
chr11	73361427	73361500	E073	-4115
chr11	73361616	73361682	E073	-3933
chr11	73361784	73361855	E073	-3760
chr11	73362439	73362537	E073	-3078
chr11	73362711	73362765	E073	-2850
chr11	73362839	73363910	E073	-1705
chr11	73363994	73364249	E073	-1366
chr11	73364331	73364518	E073	-1097
chr11	73364552	73364709	E073	-906
chr11	73364791	73364880	E073	-735
chr11	73365136	73365340	E073	-275
chr11	73365374	73365469	E073	-146
chr11	73365531	73365581	E073	-34
chr11	73365591	73365654	E073	0
chr11	73365831	73365881	E073	216
chr11	73365939	73365979	E073	324
chr11	73371490	73371550	E073	5875
chr11	73374577	73374671	E073	8962
chr11	73374827	73374907	E073	9212
chr11	73374941	73375231	E073	9326
chr11	73375276	73375349	E073	9661
chr11	73375421	73375533	E073	9806
chr11	73375660	73375759	E073	10045
chr11	73336790	73337175	E074	-28440
chr11	73344161	73344311	E074	-21304
chr11	73344403	73344453	E074	-21162
chr11	73344467	73344535	E074	-21080
chr11	73344711	73344829	E074	-20786
chr11	73357950	73358206	E074	-7409
chr11	73360819	73360873	E074	-4742
chr11	73361020	73361134	E074	-4481
chr11	73361427	73361500	E074	-4115
chr11	73361616	73361682	E074	-3933
chr11	73361784	73361855	E074	-3760
chr11	73362439	73362537	E074	-3078
chr11	73362711	73362765	E074	-2850
chr11	73363994	73364249	E074	-1366
chr11	73364331	73364518	E074	-1097
chr11	73364552	73364709	E074	-906
chr11	73364791	73364880	E074	-735
chr11	73365136	73365340	E074	-275
chr11	73365374	73365469	E074	-146
chr11	73365531	73365581	E074	-34
chr11	73365591	73365654	E074	0
chr11	73365831	73365881	E074	216
chr11	73365939	73365979	E074	324
chr11	73366383	73366439	E074	768
chr11	73370389	73370490	E074	4774
chr11	73370553	73370711	E074	4938
chr11	73370770	73370855	E074	5155
chr11	73370862	73370933	E074	5247
chr11	73370943	73370983	E074	5328
chr11	73371078	73371376	E074	5463
chr11	73371490	73371550	E074	5875
chr11	73374941	73375231	E074	9326
chr11	73375276	73375349	E074	9661
chr11	73375421	73375533	E074	9806
chr11	73375660	73375759	E074	10045
chr11	73375871	73375921	E074	10256
chr11	73375986	73376159	E074	10371
chr11	73357950	73358206	E081	-7409