rs16826852

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CAP1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0111 (3345/29970,GnomAD)
G=0115 (3348/29118,TOPMED)
G=0162 (809/5008,1000G)
G=0104 (400/3854,ALSPAC)
G=0096 (357/3708,TWINSUK)

Position: chr1:40065422 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 190 Enhancers around

Promoter: 30 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.40065422A>G
GRCh37.p13 chr 1	NC_000001.10:g.40531094A>G

Gene: CAP1, CAP, adenylate cyclase-associated protein 1 (yeast)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAP1 transcript variant 2	NM_001105530.1:c.	N/A	Intron Variant
CAP1 transcript variant 1	NM_006367.3:c.	N/A	Intron Variant
CAP1 transcript variant X2	XM_005270368.1:c.	N/A	Intron Variant
CAP1 transcript variant X4	XM_011540509.1:c.	N/A	Intron Variant
CAP1 transcript variant X2	XM_011540510.1:c.	N/A	Intron Variant
CAP1 transcript variant X11	XM_011540511.1:c.	N/A	Intron Variant
CAP1 transcript variant X12	XM_011540512.1:c.	N/A	Intron Variant
CAP1 transcript variant X13	XM_011540513.2:c.	N/A	Intron Variant
CAP1 transcript variant X14	XM_011540514.1:c.	N/A	Intron Variant
CAP1 transcript variant X3	XM_011540515.1:c.	N/A	Intron Variant
CAP1 transcript variant X1	XM_017000067.1:c.	N/A	Intron Variant
CAP1 transcript variant X3	XM_017000068.1:c.	N/A	Intron Variant
CAP1 transcript variant X1	XM_017000069.1:c.	N/A	Intron Variant
CAP1 transcript variant X7	XM_017000070.1:c.	N/A	Intron Variant
CAP1 transcript variant X8	XM_017000071.1:c.	N/A	Intron Variant
CAP1 transcript variant X9	XM_017000072.1:c.	N/A	Intron Variant
CAP1 transcript variant X10	XM_017000073.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.832	G=0.168
1000Genomes	American	Sub	694	A=0.920	G=0.080
1000Genomes	East Asian	Sub	1008	A=0.747	G=0.253
1000Genomes	Europe	Sub	1006	A=0.917	G=0.083
1000Genomes	Global	Study-wide	5008	A=0.838	G=0.162
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.896	G=0.104
The Genome Aggregation Database	African	Sub	8726	A=0.860	G=0.140
The Genome Aggregation Database	American	Sub	836	A=0.900	G=0.100
The Genome Aggregation Database	East Asian	Sub	1618	A=0.783	G=0.217
The Genome Aggregation Database	Europe	Sub	18488	A=0.909	G=0.090
The Genome Aggregation Database	Global	Study-wide	29970	A=0.888	G=0.111
The Genome Aggregation Database	Other	Sub	302	A=0.960	G=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.885	G=0.115
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.904	G=0.096

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
rs16826852	0.000647	alcohol dependence	21314694

eQTL of rs16826852 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 rs16826852 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	40512987	40513213	E067	-17881
chr1	40513387	40513455	E067	-17639
chr1	40513520	40513659	E067	-17435
chr1	40514011	40514096	E067	-16998
chr1	40514667	40514768	E067	-16326
chr1	40515068	40515248	E067	-15846
chr1	40515263	40515696	E067	-15398
chr1	40515738	40515876	E067	-15218
chr1	40516476	40516848	E067	-14246
chr1	40521869	40521909	E067	-9185
chr1	40522173	40522247	E067	-8847
chr1	40522252	40522292	E067	-8802
chr1	40522847	40523094	E067	-8000
chr1	40523180	40523428	E067	-7666
chr1	40526167	40526264	E067	-4830
chr1	40526289	40526366	E067	-4728
chr1	40549927	40549969	E067	18833
chr1	40550097	40550222	E067	19003
chr1	40510906	40511170	E068	-19924
chr1	40511556	40511724	E068	-19370
chr1	40512987	40513213	E068	-17881
chr1	40513387	40513455	E068	-17639
chr1	40513520	40513659	E068	-17435
chr1	40514011	40514096	E068	-16998
chr1	40514667	40514768	E068	-16326
chr1	40515068	40515248	E068	-15846
chr1	40515263	40515696	E068	-15398
chr1	40515738	40515876	E068	-15218
chr1	40521869	40521909	E068	-9185
chr1	40522173	40522247	E068	-8847
chr1	40522252	40522292	E068	-8802
chr1	40523958	40524004	E068	-7090
chr1	40524076	40524146	E068	-6948
chr1	40524300	40524769	E068	-6325
chr1	40524776	40526066	E068	-5028
chr1	40527414	40527477	E068	-3617
chr1	40549422	40549502	E068	18328
chr1	40549927	40549969	E068	18833
chr1	40550097	40550222	E068	19003
chr1	40550337	40550393	E068	19243
chr1	40550466	40550809	E068	19372
chr1	40497884	40498378	E069	-32716
chr1	40502110	40502218	E069	-28876
chr1	40502299	40502647	E069	-28447
chr1	40502768	40502853	E069	-28241
chr1	40512987	40513213	E069	-17881
chr1	40513387	40513455	E069	-17639
chr1	40514667	40514768	E069	-16326
chr1	40515068	40515248	E069	-15846
chr1	40515263	40515696	E069	-15398
chr1	40515738	40515876	E069	-15218
chr1	40516476	40516848	E069	-14246
chr1	40521869	40521909	E069	-9185
chr1	40522173	40522247	E069	-8847
chr1	40522252	40522292	E069	-8802
chr1	40522847	40523094	E069	-8000
chr1	40523180	40523428	E069	-7666
chr1	40523958	40524004	E069	-7090
chr1	40524076	40524146	E069	-6948
chr1	40532784	40532931	E069	1690
chr1	40532933	40533086	E069	1839
chr1	40549927	40549969	E069	18833
chr1	40550097	40550222	E069	19003
chr1	40561540	40561802	E069	30446
chr1	40502110	40502218	E070	-28876
chr1	40502299	40502647	E070	-28447
chr1	40502768	40502853	E070	-28241
chr1	40502929	40502985	E070	-28109
chr1	40503665	40503705	E070	-27389
chr1	40503760	40503895	E070	-27199
chr1	40503926	40503976	E070	-27118
chr1	40504421	40504735	E070	-26359
chr1	40522847	40523094	E070	-8000
chr1	40523180	40523428	E070	-7666
chr1	40561540	40561802	E070	30446
chr1	40497884	40498378	E071	-32716
chr1	40501889	40502042	E071	-29052
chr1	40502110	40502218	E071	-28876
chr1	40502299	40502647	E071	-28447
chr1	40509211	40509329	E071	-21765
chr1	40511556	40511724	E071	-19370
chr1	40512212	40512434	E071	-18660
chr1	40512987	40513213	E071	-17881
chr1	40513387	40513455	E071	-17639
chr1	40513520	40513659	E071	-17435
chr1	40514667	40514768	E071	-16326
chr1	40515068	40515248	E071	-15846
chr1	40515263	40515696	E071	-15398
chr1	40515738	40515876	E071	-15218
chr1	40522173	40522247	E071	-8847
chr1	40522252	40522292	E071	-8802
chr1	40522847	40523094	E071	-8000
chr1	40523180	40523428	E071	-7666
chr1	40523958	40524004	E071	-7090
chr1	40524076	40524146	E071	-6948
chr1	40524300	40524769	E071	-6325
chr1	40524776	40526066	E071	-5028
chr1	40526167	40526264	E071	-4830
chr1	40526289	40526366	E071	-4728
chr1	40531508	40531585	E071	414
chr1	40532784	40532931	E071	1690
chr1	40549927	40549969	E071	18833
chr1	40550097	40550222	E071	19003
chr1	40550337	40550393	E071	19243
chr1	40550466	40550809	E071	19372
chr1	40550959	40551053	E071	19865
chr1	40561540	40561802	E071	30446
chr1	40497884	40498378	E072	-32716
chr1	40502110	40502218	E072	-28876
chr1	40502299	40502647	E072	-28447
chr1	40502768	40502853	E072	-28241
chr1	40502929	40502985	E072	-28109
chr1	40510906	40511170	E072	-19924
chr1	40514667	40514768	E072	-16326
chr1	40515068	40515248	E072	-15846
chr1	40515263	40515696	E072	-15398
chr1	40515738	40515876	E072	-15218
chr1	40521869	40521909	E072	-9185
chr1	40522173	40522247	E072	-8847
chr1	40522252	40522292	E072	-8802
chr1	40522847	40523094	E072	-8000
chr1	40523180	40523428	E072	-7666
chr1	40523958	40524004	E072	-7090
chr1	40526167	40526264	E072	-4830
chr1	40549927	40549969	E072	18833
chr1	40550097	40550222	E072	19003
chr1	40561540	40561802	E072	30446
chr1	40502110	40502218	E073	-28876
chr1	40502299	40502647	E073	-28447
chr1	40502768	40502853	E073	-28241
chr1	40514667	40514768	E073	-16326
chr1	40515068	40515248	E073	-15846
chr1	40515263	40515696	E073	-15398
chr1	40515738	40515876	E073	-15218
chr1	40522173	40522247	E073	-8847
chr1	40522252	40522292	E073	-8802
chr1	40522847	40523094	E073	-8000
chr1	40523180	40523428	E073	-7666
chr1	40549422	40549502	E073	18328
chr1	40549927	40549969	E073	18833
chr1	40510906	40511170	E074	-19924
chr1	40511556	40511724	E074	-19370
chr1	40512987	40513213	E074	-17881
chr1	40513387	40513455	E074	-17639
chr1	40514667	40514768	E074	-16326
chr1	40515068	40515248	E074	-15846
chr1	40515263	40515696	E074	-15398
chr1	40515738	40515876	E074	-15218
chr1	40521869	40521909	E074	-9185
chr1	40522173	40522247	E074	-8847
chr1	40522252	40522292	E074	-8802
chr1	40522847	40523094	E074	-8000
chr1	40523180	40523428	E074	-7666
chr1	40523958	40524004	E074	-7090
chr1	40524076	40524146	E074	-6948
chr1	40524300	40524769	E074	-6325
chr1	40549927	40549969	E074	18833
chr1	40550097	40550222	E074	19003
chr1	40550337	40550393	E074	19243
chr1	40550466	40550809	E074	19372
chr1	40550959	40551053	E074	19865
chr1	40486300	40486350	E081	-44744
chr1	40486379	40486711	E081	-44383
chr1	40501209	40501277	E081	-29817
chr1	40501351	40501448	E081	-29646
chr1	40501889	40502042	E081	-29052
chr1	40502110	40502218	E081	-28876
chr1	40502299	40502647	E081	-28447
chr1	40502768	40502853	E081	-28241
chr1	40502929	40502985	E081	-28109
chr1	40503665	40503705	E081	-27389
chr1	40503760	40503895	E081	-27199
chr1	40503926	40503976	E081	-27118
chr1	40504421	40504735	E081	-26359
chr1	40509211	40509329	E081	-21765
chr1	40510906	40511170	E081	-19924
chr1	40561540	40561802	E081	30446
chr1	40500306	40500410	E082	-30684
chr1	40500510	40501034	E082	-30060
chr1	40501209	40501277	E082	-29817
chr1	40501889	40502042	E082	-29052
chr1	40502110	40502218	E082	-28876
chr1	40502299	40502647	E082	-28447
chr1	40502768	40502853	E082	-28241
chr1	40502929	40502985	E082	-28109
chr1	40503665	40503705	E082	-27389
chr1	40503760	40503895	E082	-27199
chr1	40503926	40503976	E082	-27118
chr1	40504421	40504735	E082	-26359
chr1	40561540	40561802	E082	30446

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	40504789	40507357	E067	-23737
chr1	40507396	40507500	E067	-23594
chr1	40562445	40563750	E067	31351
chr1	40504789	40507357	E068	-23737
chr1	40507396	40507500	E068	-23594
chr1	40562445	40563750	E068	31351
chr1	40504789	40507357	E069	-23737
chr1	40507396	40507500	E069	-23594
chr1	40562445	40563750	E069	31351
chr1	40504789	40507357	E070	-23737
chr1	40507396	40507500	E070	-23594
chr1	40562445	40563750	E070	31351
chr1	40504789	40507357	E071	-23737
chr1	40507396	40507500	E071	-23594
chr1	40562445	40563750	E071	31351
chr1	40504789	40507357	E072	-23737
chr1	40507396	40507500	E072	-23594
chr1	40562445	40563750	E072	31351
chr1	40504789	40507357	E073	-23737
chr1	40507396	40507500	E073	-23594
chr1	40562445	40563750	E073	31351
chr1	40504789	40507357	E074	-23737
chr1	40507396	40507500	E074	-23594
chr1	40562445	40563750	E074	31351
chr1	40504789	40507357	E081	-23737
chr1	40507396	40507500	E081	-23594
chr1	40562445	40563750	E081	31351
chr1	40504789	40507357	E082	-23737
chr1	40507396	40507500	E082	-23594
chr1	40562445	40563750	E082	31351