rs13223209

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PDE1C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0216 (6470/29922,GnomAD)
G==0220 (6420/29118,TOPMED)
G==0275 (1378/5008,1000G)
G==0133 (512/3854,ALSPAC)
G==0157 (583/3708,TWINSUK)

Position: chr7:31910150 (GRCh38.p7) (7p14.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 301 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.31910150G>A
GRCh37.p13 chr 7	NC_000007.13:g.31949763G>A

Gene: PDE1C, phosphodiesterase 1C(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDE1C transcript variant 1	NM_001191056.3:c.	N/A	Intron Variant
PDE1C transcript variant 2	NM_001191057.3:c.	N/A	Intron Variant
PDE1C transcript variant 3	NM_001191058.3:c.	N/A	Intron Variant
PDE1C transcript variant 5	NM_001191059.3:c.	N/A	Intron Variant
PDE1C transcript variant 6	NM_001322055.1:c.	N/A	Intron Variant
PDE1C transcript variant 7	NM_001322056.1:c.	N/A	Intron Variant
PDE1C transcript variant 8	NM_001322057.1:c.	N/A	Intron Variant
PDE1C transcript variant 9	NM_001322058.1:c.	N/A	Intron Variant
PDE1C transcript variant 10	NM_001322059.1:c.	N/A	Intron Variant
PDE1C transcript variant 4	NM_005020.4:c.	N/A	Intron Variant
PDE1C transcript variant X1	XM_017012264.1:c.	N/A	Intron Variant
PDE1C transcript variant X4	XM_017012265.1:c.	N/A	Intron Variant
PDE1C transcript variant X5	XM_017012266.1:c.	N/A	Intron Variant
PDE1C transcript variant X6	XM_017012267.1:c.	N/A	Intron Variant
PDE1C transcript variant X2	XR_001744802.1:n.	N/A	Intron Variant
PDE1C transcript variant X3	XR_001744803.1:n.	N/A	Intron Variant
PDE1C transcript variant X7	XR_001744804.1:n.	N/A	Intron Variant
PDE1C transcript variant X8	XR_001744805.1:n.	N/A	Intron Variant
PDE1C transcript variant X9	XR_001744806.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.375	A=0.625
1000Genomes	American	Sub	694	G=0.150	A=0.850
1000Genomes	East Asian	Sub	1008	G=0.344	A=0.656
1000Genomes	Europe	Sub	1006	G=0.170	A=0.830
1000Genomes	Global	Study-wide	5008	G=0.275	A=0.725
1000Genomes	South Asian	Sub	978	G=0.270	A=0.730
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.133	A=0.867
The Genome Aggregation Database	African	Sub	8702	G=0.327	A=0.673
The Genome Aggregation Database	American	Sub	836	G=0.100	A=0.900
The Genome Aggregation Database	East Asian	Sub	1610	G=0.294	A=0.706
The Genome Aggregation Database	Europe	Sub	18472	G=0.163	A=0.836
The Genome Aggregation Database	Global	Study-wide	29922	G=0.216	A=0.783
The Genome Aggregation Database	Other	Sub	302	G=0.170	A=0.830
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.220	A=0.779
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.157	A=0.843

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
rs13223209	0.000859	alcohol dependence	21314694

eQTL of rs13223209 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 rs13223209 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 )
chr7	31913532	31913711	E067	-36052
chr7	31921634	31921775	E067	-27988
chr7	31921845	31922126	E067	-27637
chr7	31922257	31922326	E067	-27437
chr7	31922668	31922776	E067	-26987
chr7	31922877	31922927	E067	-26836
chr7	31923075	31923191	E067	-26572
chr7	31923221	31924241	E067	-25522
chr7	31924408	31924777	E067	-24986
chr7	31924886	31925205	E067	-24558
chr7	31925446	31925579	E067	-24184
chr7	31925802	31926325	E067	-23438
chr7	31935954	31936014	E067	-13749
chr7	31936059	31936109	E067	-13654
chr7	31936124	31936207	E067	-13556
chr7	31936244	31936304	E067	-13459
chr7	31936500	31936630	E067	-13133
chr7	31936655	31936738	E067	-13025
chr7	31952752	31952807	E067	2989
chr7	31952873	31952937	E067	3110
chr7	31964028	31964202	E067	14265
chr7	31964262	31964368	E067	14499
chr7	31973707	31973839	E067	23944
chr7	31974364	31974444	E067	24601
chr7	31974677	31974770	E067	24914
chr7	31974810	31975159	E067	25047
chr7	31995994	31996408	E067	46231
chr7	31996805	31997004	E067	47042
chr7	31997035	31997288	E067	47272
chr7	31997472	31997884	E067	47709
chr7	31921136	31921212	E068	-28551
chr7	31921634	31921775	E068	-27988
chr7	31921845	31922126	E068	-27637
chr7	31922257	31922326	E068	-27437
chr7	31922877	31922927	E068	-26836
chr7	31923075	31923191	E068	-26572
chr7	31923221	31924241	E068	-25522
chr7	31934760	31934810	E068	-14953
chr7	31934883	31934933	E068	-14830
chr7	31935023	31935105	E068	-14658
chr7	31935313	31935400	E068	-14363
chr7	31935576	31935721	E068	-14042
chr7	31936500	31936630	E068	-13133
chr7	31936655	31936738	E068	-13025
chr7	31974810	31975159	E068	25047
chr7	31996805	31997004	E068	47042
chr7	31997035	31997288	E068	47272
chr7	31914716	31914803	E069	-34960
chr7	31914909	31915058	E069	-34705
chr7	31915142	31915341	E069	-34422
chr7	31915543	31915604	E069	-34159
chr7	31915660	31915710	E069	-34053
chr7	31915721	31915839	E069	-33924
chr7	31916736	31916786	E069	-32977
chr7	31916985	31917065	E069	-32698
chr7	31921136	31921212	E069	-28551
chr7	31921634	31921775	E069	-27988
chr7	31921845	31922126	E069	-27637
chr7	31922257	31922326	E069	-27437
chr7	31922877	31922927	E069	-26836
chr7	31923075	31923191	E069	-26572
chr7	31923221	31924241	E069	-25522
chr7	31924408	31924777	E069	-24986
chr7	31924886	31925205	E069	-24558
chr7	31929128	31929250	E069	-20513
chr7	31929301	31929351	E069	-20412
chr7	31929795	31930276	E069	-19487
chr7	31930517	31930716	E069	-19047
chr7	31930734	31930864	E069	-18899
chr7	31931651	31931701	E069	-18062
chr7	31931787	31931828	E069	-17935
chr7	31931838	31931940	E069	-17823
chr7	31932110	31932160	E069	-17603
chr7	31933220	31933457	E069	-16306
chr7	31933617	31933703	E069	-16060
chr7	31933795	31933845	E069	-15918
chr7	31933988	31934251	E069	-15512
chr7	31934392	31934487	E069	-15276
chr7	31934760	31934810	E069	-14953
chr7	31964028	31964202	E069	14265
chr7	31964262	31964368	E069	14499
chr7	31973253	31973397	E069	23490
chr7	31973707	31973839	E069	23944
chr7	31974364	31974444	E069	24601
chr7	31974677	31974770	E069	24914
chr7	31974810	31975159	E069	25047
chr7	31975403	31975743	E069	25640
chr7	31975989	31976039	E069	26226
chr7	31976220	31976507	E069	26457
chr7	31992957	31993007	E069	43194
chr7	31993208	31993320	E069	43445
chr7	31993711	31993761	E069	43948
chr7	31993941	31994053	E069	44178
chr7	31996805	31997004	E069	47042
chr7	31997035	31997288	E069	47272
chr7	31997472	31997884	E069	47709
chr7	31997905	31998137	E069	48142
chr7	31933220	31933457	E070	-16306
chr7	31933617	31933703	E070	-16060
chr7	31933795	31933845	E070	-15918
chr7	31913532	31913711	E071	-36052
chr7	31913807	31914200	E071	-35563
chr7	31914716	31914803	E071	-34960
chr7	31914909	31915058	E071	-34705
chr7	31915142	31915341	E071	-34422
chr7	31915543	31915604	E071	-34159
chr7	31915660	31915710	E071	-34053
chr7	31915721	31915839	E071	-33924
chr7	31916736	31916786	E071	-32977
chr7	31916985	31917065	E071	-32698
chr7	31920878	31920958	E071	-28805
chr7	31921136	31921212	E071	-28551
chr7	31921634	31921775	E071	-27988
chr7	31921845	31922126	E071	-27637
chr7	31922257	31922326	E071	-27437
chr7	31922668	31922776	E071	-26987
chr7	31922877	31922927	E071	-26836
chr7	31923075	31923191	E071	-26572
chr7	31924408	31924777	E071	-24986
chr7	31924886	31925205	E071	-24558
chr7	31925446	31925579	E071	-24184
chr7	31925802	31926325	E071	-23438
chr7	31926458	31926514	E071	-23249
chr7	31926960	31927047	E071	-22716
chr7	31927094	31927144	E071	-22619
chr7	31928803	31928880	E071	-20883
chr7	31928902	31928987	E071	-20776
chr7	31929128	31929250	E071	-20513
chr7	31929301	31929351	E071	-20412
chr7	31929795	31930276	E071	-19487
chr7	31930517	31930716	E071	-19047
chr7	31930734	31930864	E071	-18899
chr7	31931651	31931701	E071	-18062
chr7	31931787	31931828	E071	-17935
chr7	31931838	31931940	E071	-17823
chr7	31932110	31932160	E071	-17603
chr7	31932305	31932475	E071	-17288
chr7	31932763	31932813	E071	-16950
chr7	31933220	31933457	E071	-16306
chr7	31933617	31933703	E071	-16060
chr7	31933795	31933845	E071	-15918
chr7	31933988	31934251	E071	-15512
chr7	31934392	31934487	E071	-15276
chr7	31934760	31934810	E071	-14953
chr7	31935576	31935721	E071	-14042
chr7	31936655	31936738	E071	-13025
chr7	31938788	31938875	E071	-10888
chr7	31939024	31939138	E071	-10625
chr7	31954563	31954613	E071	4800
chr7	31954956	31955006	E071	5193
chr7	31955019	31955102	E071	5256
chr7	31963151	31963201	E071	13388
chr7	31963310	31963350	E071	13547
chr7	31963371	31963439	E071	13608
chr7	31964028	31964202	E071	14265
chr7	31964262	31964368	E071	14499
chr7	31964481	31965020	E071	14718
chr7	31974364	31974444	E071	24601
chr7	31974677	31974770	E071	24914
chr7	31974810	31975159	E071	25047
chr7	31975403	31975743	E071	25640
chr7	31975989	31976039	E071	26226
chr7	31976220	31976507	E071	26457
chr7	31976631	31976728	E071	26868
chr7	31976829	31976879	E071	27066
chr7	31977071	31977310	E071	27308
chr7	31979831	31979881	E071	30068
chr7	31979944	31980090	E071	30181
chr7	31980156	31980227	E071	30393
chr7	31981724	31981778	E071	31961
chr7	31983803	31983866	E071	34040
chr7	31993208	31993320	E071	43445
chr7	31993711	31993761	E071	43948
chr7	31993941	31994053	E071	44178
chr7	31994841	31994907	E071	45078
chr7	31996805	31997004	E071	47042
chr7	31997035	31997288	E071	47272
chr7	31997472	31997884	E071	47709
chr7	31997905	31998137	E071	48142
chr7	31914909	31915058	E072	-34705
chr7	31915142	31915341	E072	-34422
chr7	31916736	31916786	E072	-32977
chr7	31921634	31921775	E072	-27988
chr7	31921845	31922126	E072	-27637
chr7	31922257	31922326	E072	-27437
chr7	31922668	31922776	E072	-26987
chr7	31922877	31922927	E072	-26836
chr7	31923075	31923191	E072	-26572
chr7	31924886	31925205	E072	-24558
chr7	31931787	31931828	E072	-17935
chr7	31931838	31931940	E072	-17823
chr7	31932110	31932160	E072	-17603
chr7	31933220	31933457	E072	-16306
chr7	31933617	31933703	E072	-16060
chr7	31933795	31933845	E072	-15918
chr7	31943786	31943836	E072	-5927
chr7	31953210	31953280	E072	3447
chr7	31953363	31953591	E072	3600
chr7	31974810	31975159	E072	25047
chr7	31975403	31975743	E072	25640
chr7	31983803	31983866	E072	34040
chr7	31993711	31993761	E072	43948
chr7	31994841	31994907	E072	45078
chr7	31995396	31995511	E072	45633
chr7	31996805	31997004	E072	47042
chr7	31997035	31997288	E072	47272
chr7	31997472	31997884	E072	47709
chr7	31997905	31998137	E072	48142
chr7	31921845	31922126	E073	-27637
chr7	31922257	31922326	E073	-27437
chr7	31922877	31922927	E073	-26836
chr7	31923075	31923191	E073	-26572
chr7	31923221	31924241	E073	-25522
chr7	31933220	31933457	E073	-16306
chr7	31933617	31933703	E073	-16060
chr7	31933795	31933845	E073	-15918
chr7	31933988	31934251	E073	-15512
chr7	31996805	31997004	E073	47042
chr7	31997035	31997288	E073	47272
chr7	31913532	31913711	E074	-36052
chr7	31913807	31914200	E074	-35563
chr7	31914716	31914803	E074	-34960
chr7	31914909	31915058	E074	-34705
chr7	31915142	31915341	E074	-34422
chr7	31915543	31915604	E074	-34159
chr7	31915660	31915710	E074	-34053
chr7	31915721	31915839	E074	-33924
chr7	31916736	31916786	E074	-32977
chr7	31916985	31917065	E074	-32698
chr7	31917224	31917268	E074	-32495
chr7	31921845	31922126	E074	-27637
chr7	31922257	31922326	E074	-27437
chr7	31922668	31922776	E074	-26987
chr7	31922877	31922927	E074	-26836
chr7	31923075	31923191	E074	-26572
chr7	31923221	31924241	E074	-25522
chr7	31924408	31924777	E074	-24986
chr7	31924886	31925205	E074	-24558
chr7	31925446	31925579	E074	-24184
chr7	31925802	31926325	E074	-23438
chr7	31926458	31926514	E074	-23249
chr7	31926960	31927047	E074	-22716
chr7	31927094	31927144	E074	-22619
chr7	31930517	31930716	E074	-19047
chr7	31930734	31930864	E074	-18899
chr7	31931651	31931701	E074	-18062
chr7	31931787	31931828	E074	-17935
chr7	31931838	31931940	E074	-17823
chr7	31932110	31932160	E074	-17603
chr7	31932305	31932475	E074	-17288
chr7	31932763	31932813	E074	-16950
chr7	31933988	31934251	E074	-15512
chr7	31934392	31934487	E074	-15276
chr7	31934760	31934810	E074	-14953
chr7	31934883	31934933	E074	-14830
chr7	31946487	31946756	E074	-3007
chr7	31954563	31954613	E074	4800
chr7	31954956	31955006	E074	5193
chr7	31955019	31955102	E074	5256
chr7	31962136	31962876	E074	12373
chr7	31964028	31964202	E074	14265
chr7	31964262	31964368	E074	14499
chr7	31974677	31974770	E074	24914
chr7	31974810	31975159	E074	25047
chr7	31975403	31975743	E074	25640
chr7	31975989	31976039	E074	26226
chr7	31976220	31976507	E074	26457
chr7	31976631	31976728	E074	26868
chr7	31976829	31976879	E074	27066
chr7	31978285	31978653	E074	28522
chr7	31978735	31978999	E074	28972
chr7	31979308	31979364	E074	29545
chr7	31979831	31979881	E074	30068
chr7	31979944	31980090	E074	30181
chr7	31980156	31980227	E074	30393
chr7	31980540	31980584	E074	30777
chr7	31981724	31981778	E074	31961
chr7	31993711	31993761	E074	43948
chr7	31993941	31994053	E074	44178
chr7	31994143	31994354	E074	44380
chr7	31995994	31996408	E074	46231
chr7	31996805	31997004	E074	47042
chr7	31997035	31997288	E074	47272
chr7	31997472	31997884	E074	47709
chr7	31921634	31921775	E081	-27988
chr7	31921845	31922126	E081	-27637
chr7	31923221	31924241	E081	-25522
chr7	31933617	31933703	E081	-16060
chr7	31933795	31933845	E081	-15918
chr7	31933988	31934251	E081	-15512
chr7	31934392	31934487	E081	-15276
chr7	31934760	31934810	E081	-14953
chr7	31934883	31934933	E081	-14830
chr7	31952752	31952807	E081	2989
chr7	31952873	31952937	E081	3110
chr7	31962136	31962876	E081	12373
chr7	31963151	31963201	E081	13388
chr7	31964028	31964202	E081	14265
chr7	31964262	31964368	E081	14499
chr7	31964481	31965020	E081	14718
chr7	31923221	31924241	E082	-25522