rs10392

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PPP1R16B : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0160 (4795/29944,GnomAD)
A=0162 (4737/29118,TOPMED)
A=0204 (1024/5008,1000G)
A=0174 (670/3854,ALSPAC)
A=0183 (679/3708,TWINSUK)

Position: chr20:38922292 (GRCh38.p7) (20q11.23)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 424 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.38922292G>A
GRCh37.p13 chr 20	NC_000020.10:g.37550935G>A

Gene: PPP1R16B, protein phosphatase 1 regulatory subunit 16B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PPP1R16B transcript variant 1	NM_015568.3:c.	N/A	3 Prime UTR Variant
PPP1R16B transcript variant 2	NM_001172735.2:c.	N/A	3 Prime UTR Variant
PPP1R16B transcript variant X1	XM_011528768.2:c.	N/A	3 Prime UTR Variant
PPP1R16B transcript variant X2	XM_017027785.1:c.	N/A	3 Prime UTR Variant
PPP1R16B transcript variant X3	XM_011528769.2:c.	N/A	3 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.918	A=0.082
1000Genomes	American	Sub	694	G=0.740	A=0.260
1000Genomes	East Asian	Sub	1008	G=0.675	A=0.325
1000Genomes	Europe	Sub	1006	G=0.795	A=0.205
1000Genomes	Global	Study-wide	5008	G=0.796	A=0.204
1000Genomes	South Asian	Sub	978	G=0.790	A=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.826	A=0.174
The Genome Aggregation Database	African	Sub	8730	G=0.896	A=0.104
The Genome Aggregation Database	American	Sub	838	G=0.780	A=0.220
The Genome Aggregation Database	East Asian	Sub	1616	G=0.688	A=0.312
The Genome Aggregation Database	Europe	Sub	18458	G=0.830	A=0.169
The Genome Aggregation Database	Global	Study-wide	29944	G=0.839	A=0.160
The Genome Aggregation Database	Other	Sub	302	G=0.740	A=0.260
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.837	A=0.162
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.817	A=0.183

PMID	Title	Author	Journal
28714907	Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis.	Treutlein J	Genes (Basel)

P-Value

SNP ID	p-value	Traits	Study
rs10392	8E-07	alcohol dependence	28714907

eQTL of rs10392 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 rs10392 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 )
chr20	37502406	37502458	E067	-48477
chr20	37502663	37502770	E067	-48165
chr20	37502806	37502986	E067	-47949
chr20	37504883	37505430	E067	-45505
chr20	37505522	37505629	E067	-45306
chr20	37505769	37505885	E067	-45050
chr20	37506175	37506225	E067	-44710
chr20	37506255	37506314	E067	-44621
chr20	37506351	37506396	E067	-44539
chr20	37506940	37507047	E067	-43888
chr20	37507106	37507151	E067	-43784
chr20	37507265	37507326	E067	-43609
chr20	37507435	37507502	E067	-43433
chr20	37507548	37507907	E067	-43028
chr20	37509508	37509613	E067	-41322
chr20	37509698	37509977	E067	-40958
chr20	37510000	37510181	E067	-40754
chr20	37510215	37510411	E067	-40524
chr20	37510511	37510747	E067	-40188
chr20	37510788	37510838	E067	-40097
chr20	37510861	37510904	E067	-40031
chr20	37510946	37511071	E067	-39864
chr20	37511239	37511363	E067	-39572
chr20	37511590	37511688	E067	-39247
chr20	37511763	37511852	E067	-39083
chr20	37511860	37512432	E067	-38503
chr20	37512528	37512588	E067	-38347
chr20	37512622	37512662	E067	-38273
chr20	37512745	37512825	E067	-38110
chr20	37512880	37513087	E067	-37848
chr20	37514020	37514192	E067	-36743
chr20	37515247	37515323	E067	-35612
chr20	37515336	37515513	E067	-35422
chr20	37515592	37515681	E067	-35254
chr20	37515792	37515884	E067	-35051
chr20	37515999	37516060	E067	-34875
chr20	37516144	37516204	E067	-34731
chr20	37516825	37517131	E067	-33804
chr20	37517218	37517287	E067	-33648
chr20	37517727	37517777	E067	-33158
chr20	37517975	37518015	E067	-32920
chr20	37518236	37518314	E067	-32621
chr20	37518414	37518658	E067	-32277
chr20	37518724	37518804	E067	-32131
chr20	37518891	37519444	E067	-31491
chr20	37519658	37519761	E067	-31174
chr20	37520755	37521165	E067	-29770
chr20	37521209	37521672	E067	-29263
chr20	37521684	37523252	E067	-27683
chr20	37523537	37523587	E067	-27348
chr20	37529060	37529120	E067	-21815
chr20	37529358	37529412	E067	-21523
chr20	37529462	37529605	E067	-21330
chr20	37529677	37529925	E067	-21010
chr20	37592010	37592067	E067	41075
chr20	37592121	37592161	E067	41186
chr20	37502406	37502458	E068	-48477
chr20	37502663	37502770	E068	-48165
chr20	37502806	37502986	E068	-47949
chr20	37504883	37505430	E068	-45505
chr20	37505522	37505629	E068	-45306
chr20	37505769	37505885	E068	-45050
chr20	37506175	37506225	E068	-44710
chr20	37506255	37506314	E068	-44621
chr20	37506351	37506396	E068	-44539
chr20	37506940	37507047	E068	-43888
chr20	37507106	37507151	E068	-43784
chr20	37507265	37507326	E068	-43609
chr20	37507435	37507502	E068	-43433
chr20	37507548	37507907	E068	-43028
chr20	37508307	37508352	E068	-42583
chr20	37508408	37508499	E068	-42436
chr20	37508548	37508641	E068	-42294
chr20	37508720	37508770	E068	-42165
chr20	37509307	37509364	E068	-41571
chr20	37509508	37509613	E068	-41322
chr20	37509698	37509977	E068	-40958
chr20	37510000	37510181	E068	-40754
chr20	37510215	37510411	E068	-40524
chr20	37510511	37510747	E068	-40188
chr20	37510788	37510838	E068	-40097
chr20	37510861	37510904	E068	-40031
chr20	37510946	37511071	E068	-39864
chr20	37511239	37511363	E068	-39572
chr20	37511590	37511688	E068	-39247
chr20	37511763	37511852	E068	-39083
chr20	37511860	37512432	E068	-38503
chr20	37512528	37512588	E068	-38347
chr20	37512622	37512662	E068	-38273
chr20	37512745	37512825	E068	-38110
chr20	37512880	37513087	E068	-37848
chr20	37514020	37514192	E068	-36743
chr20	37515247	37515323	E068	-35612
chr20	37515336	37515513	E068	-35422
chr20	37515592	37515681	E068	-35254
chr20	37515792	37515884	E068	-35051
chr20	37515999	37516060	E068	-34875
chr20	37516144	37516204	E068	-34731
chr20	37516825	37517131	E068	-33804
chr20	37517218	37517287	E068	-33648
chr20	37517727	37517777	E068	-33158
chr20	37517975	37518015	E068	-32920
chr20	37518236	37518314	E068	-32621
chr20	37518414	37518658	E068	-32277
chr20	37518724	37518804	E068	-32131
chr20	37518891	37519444	E068	-31491
chr20	37519658	37519761	E068	-31174
chr20	37520364	37520414	E068	-30521
chr20	37520755	37521165	E068	-29770
chr20	37521209	37521672	E068	-29263
chr20	37521684	37523252	E068	-27683
chr20	37529060	37529120	E068	-21815
chr20	37529358	37529412	E068	-21523
chr20	37529462	37529605	E068	-21330
chr20	37529677	37529925	E068	-21010
chr20	37592010	37592067	E068	41075
chr20	37592121	37592161	E068	41186
chr20	37502406	37502458	E069	-48477
chr20	37502663	37502770	E069	-48165
chr20	37502806	37502986	E069	-47949
chr20	37504883	37505430	E069	-45505
chr20	37505522	37505629	E069	-45306
chr20	37505769	37505885	E069	-45050
chr20	37506175	37506225	E069	-44710
chr20	37506255	37506314	E069	-44621
chr20	37506351	37506396	E069	-44539
chr20	37506940	37507047	E069	-43888
chr20	37507106	37507151	E069	-43784
chr20	37507265	37507326	E069	-43609
chr20	37507435	37507502	E069	-43433
chr20	37507548	37507907	E069	-43028
chr20	37507924	37508002	E069	-42933
chr20	37508152	37508202	E069	-42733
chr20	37508307	37508352	E069	-42583
chr20	37508408	37508499	E069	-42436
chr20	37508548	37508641	E069	-42294
chr20	37508720	37508770	E069	-42165
chr20	37509508	37509613	E069	-41322
chr20	37509698	37509977	E069	-40958
chr20	37510000	37510181	E069	-40754
chr20	37510215	37510411	E069	-40524
chr20	37510511	37510747	E069	-40188
chr20	37510788	37510838	E069	-40097
chr20	37510861	37510904	E069	-40031
chr20	37510946	37511071	E069	-39864
chr20	37511239	37511363	E069	-39572
chr20	37511590	37511688	E069	-39247
chr20	37511763	37511852	E069	-39083
chr20	37511860	37512432	E069	-38503
chr20	37512528	37512588	E069	-38347
chr20	37512622	37512662	E069	-38273
chr20	37512745	37512825	E069	-38110
chr20	37512880	37513087	E069	-37848
chr20	37514020	37514192	E069	-36743
chr20	37515247	37515323	E069	-35612
chr20	37515336	37515513	E069	-35422
chr20	37515592	37515681	E069	-35254
chr20	37515792	37515884	E069	-35051
chr20	37515999	37516060	E069	-34875
chr20	37516144	37516204	E069	-34731
chr20	37516825	37517131	E069	-33804
chr20	37517218	37517287	E069	-33648
chr20	37517727	37517777	E069	-33158
chr20	37517975	37518015	E069	-32920
chr20	37518236	37518314	E069	-32621
chr20	37518414	37518658	E069	-32277
chr20	37518724	37518804	E069	-32131
chr20	37518891	37519444	E069	-31491
chr20	37519658	37519761	E069	-31174
chr20	37520364	37520414	E069	-30521
chr20	37520755	37521165	E069	-29770
chr20	37521209	37521672	E069	-29263
chr20	37521684	37523252	E069	-27683
chr20	37523537	37523587	E069	-27348
chr20	37529060	37529120	E069	-21815
chr20	37529358	37529412	E069	-21523
chr20	37529462	37529605	E069	-21330
chr20	37529677	37529925	E069	-21010
chr20	37521209	37521672	E070	-29263
chr20	37521684	37523252	E070	-27683
chr20	37559991	37560087	E070	9056
chr20	37560199	37560262	E070	9264
chr20	37560344	37560394	E070	9409
chr20	37560400	37560499	E070	9465
chr20	37560638	37560737	E070	9703
chr20	37502406	37502458	E071	-48477
chr20	37502663	37502770	E071	-48165
chr20	37502806	37502986	E071	-47949
chr20	37504883	37505430	E071	-45505
chr20	37505522	37505629	E071	-45306
chr20	37505769	37505885	E071	-45050
chr20	37506175	37506225	E071	-44710
chr20	37506255	37506314	E071	-44621
chr20	37506351	37506396	E071	-44539
chr20	37506940	37507047	E071	-43888
chr20	37507106	37507151	E071	-43784
chr20	37507265	37507326	E071	-43609
chr20	37507435	37507502	E071	-43433
chr20	37507548	37507907	E071	-43028
chr20	37509508	37509613	E071	-41322
chr20	37509698	37509977	E071	-40958
chr20	37510000	37510181	E071	-40754
chr20	37510215	37510411	E071	-40524
chr20	37510511	37510747	E071	-40188
chr20	37510788	37510838	E071	-40097
chr20	37510861	37510904	E071	-40031
chr20	37510946	37511071	E071	-39864
chr20	37511239	37511363	E071	-39572
chr20	37511590	37511688	E071	-39247
chr20	37511763	37511852	E071	-39083
chr20	37511860	37512432	E071	-38503
chr20	37512528	37512588	E071	-38347
chr20	37512622	37512662	E071	-38273
chr20	37512745	37512825	E071	-38110
chr20	37512880	37513087	E071	-37848
chr20	37514020	37514192	E071	-36743
chr20	37515247	37515323	E071	-35612
chr20	37515336	37515513	E071	-35422
chr20	37515592	37515681	E071	-35254
chr20	37515792	37515884	E071	-35051
chr20	37515999	37516060	E071	-34875
chr20	37516144	37516204	E071	-34731
chr20	37516825	37517131	E071	-33804
chr20	37517218	37517287	E071	-33648
chr20	37517727	37517777	E071	-33158
chr20	37517975	37518015	E071	-32920
chr20	37518236	37518314	E071	-32621
chr20	37518414	37518658	E071	-32277
chr20	37518724	37518804	E071	-32131
chr20	37518891	37519444	E071	-31491
chr20	37519658	37519761	E071	-31174
chr20	37520364	37520414	E071	-30521
chr20	37520755	37521165	E071	-29770
chr20	37521209	37521672	E071	-29263
chr20	37521684	37523252	E071	-27683
chr20	37523537	37523587	E071	-27348
chr20	37529060	37529120	E071	-21815
chr20	37529358	37529412	E071	-21523
chr20	37529462	37529605	E071	-21330
chr20	37529677	37529925	E071	-21010
chr20	37502406	37502458	E072	-48477
chr20	37502663	37502770	E072	-48165
chr20	37502806	37502986	E072	-47949
chr20	37504883	37505430	E072	-45505
chr20	37506175	37506225	E072	-44710
chr20	37506255	37506314	E072	-44621
chr20	37506351	37506396	E072	-44539
chr20	37506940	37507047	E072	-43888
chr20	37507106	37507151	E072	-43784
chr20	37507265	37507326	E072	-43609
chr20	37507435	37507502	E072	-43433
chr20	37507548	37507907	E072	-43028
chr20	37507924	37508002	E072	-42933
chr20	37508152	37508202	E072	-42733
chr20	37508307	37508352	E072	-42583
chr20	37508408	37508499	E072	-42436
chr20	37508548	37508641	E072	-42294
chr20	37508720	37508770	E072	-42165
chr20	37509508	37509613	E072	-41322
chr20	37509698	37509977	E072	-40958
chr20	37510000	37510181	E072	-40754
chr20	37510215	37510411	E072	-40524
chr20	37510511	37510747	E072	-40188
chr20	37510788	37510838	E072	-40097
chr20	37510861	37510904	E072	-40031
chr20	37510946	37511071	E072	-39864
chr20	37511239	37511363	E072	-39572
chr20	37514020	37514192	E072	-36743
chr20	37515247	37515323	E072	-35612
chr20	37515336	37515513	E072	-35422
chr20	37515592	37515681	E072	-35254
chr20	37515792	37515884	E072	-35051
chr20	37515999	37516060	E072	-34875
chr20	37516144	37516204	E072	-34731
chr20	37516825	37517131	E072	-33804
chr20	37517218	37517287	E072	-33648
chr20	37517727	37517777	E072	-33158
chr20	37517975	37518015	E072	-32920
chr20	37518236	37518314	E072	-32621
chr20	37518414	37518658	E072	-32277
chr20	37518724	37518804	E072	-32131
chr20	37518891	37519444	E072	-31491
chr20	37519658	37519761	E072	-31174
chr20	37520364	37520414	E072	-30521
chr20	37520755	37521165	E072	-29770
chr20	37521209	37521672	E072	-29263
chr20	37521684	37523252	E072	-27683
chr20	37529060	37529120	E072	-21815
chr20	37529358	37529412	E072	-21523
chr20	37529462	37529605	E072	-21330
chr20	37529677	37529925	E072	-21010
chr20	37592010	37592067	E072	41075
chr20	37592121	37592161	E072	41186
chr20	37502406	37502458	E073	-48477
chr20	37502663	37502770	E073	-48165
chr20	37502806	37502986	E073	-47949
chr20	37504883	37505430	E073	-45505
chr20	37505522	37505629	E073	-45306
chr20	37505769	37505885	E073	-45050
chr20	37506940	37507047	E073	-43888
chr20	37507106	37507151	E073	-43784
chr20	37507265	37507326	E073	-43609
chr20	37507435	37507502	E073	-43433
chr20	37507548	37507907	E073	-43028
chr20	37507924	37508002	E073	-42933
chr20	37509508	37509613	E073	-41322
chr20	37509698	37509977	E073	-40958
chr20	37510000	37510181	E073	-40754
chr20	37510215	37510411	E073	-40524
chr20	37510511	37510747	E073	-40188
chr20	37510788	37510838	E073	-40097
chr20	37510861	37510904	E073	-40031
chr20	37510946	37511071	E073	-39864
chr20	37511239	37511363	E073	-39572
chr20	37511590	37511688	E073	-39247
chr20	37511763	37511852	E073	-39083
chr20	37511860	37512432	E073	-38503
chr20	37512528	37512588	E073	-38347
chr20	37512622	37512662	E073	-38273
chr20	37512745	37512825	E073	-38110
chr20	37512880	37513087	E073	-37848
chr20	37514020	37514192	E073	-36743
chr20	37515247	37515323	E073	-35612
chr20	37515336	37515513	E073	-35422
chr20	37515592	37515681	E073	-35254
chr20	37515792	37515884	E073	-35051
chr20	37515999	37516060	E073	-34875
chr20	37516144	37516204	E073	-34731
chr20	37516825	37517131	E073	-33804
chr20	37517218	37517287	E073	-33648
chr20	37517727	37517777	E073	-33158
chr20	37517975	37518015	E073	-32920
chr20	37518236	37518314	E073	-32621
chr20	37518414	37518658	E073	-32277
chr20	37518724	37518804	E073	-32131
chr20	37518891	37519444	E073	-31491
chr20	37519658	37519761	E073	-31174
chr20	37521209	37521672	E073	-29263
chr20	37521684	37523252	E073	-27683
chr20	37504883	37505430	E074	-45505
chr20	37505522	37505629	E074	-45306
chr20	37505769	37505885	E074	-45050
chr20	37506175	37506225	E074	-44710
chr20	37506255	37506314	E074	-44621
chr20	37506351	37506396	E074	-44539
chr20	37506940	37507047	E074	-43888
chr20	37507106	37507151	E074	-43784
chr20	37507265	37507326	E074	-43609
chr20	37507435	37507502	E074	-43433
chr20	37507548	37507907	E074	-43028
chr20	37507924	37508002	E074	-42933
chr20	37508152	37508202	E074	-42733
chr20	37508307	37508352	E074	-42583
chr20	37508408	37508499	E074	-42436
chr20	37508548	37508641	E074	-42294
chr20	37509698	37509977	E074	-40958
chr20	37510000	37510181	E074	-40754
chr20	37510215	37510411	E074	-40524
chr20	37510511	37510747	E074	-40188
chr20	37510788	37510838	E074	-40097
chr20	37510861	37510904	E074	-40031
chr20	37510946	37511071	E074	-39864
chr20	37511239	37511363	E074	-39572
chr20	37511590	37511688	E074	-39247
chr20	37511763	37511852	E074	-39083
chr20	37511860	37512432	E074	-38503
chr20	37512528	37512588	E074	-38347
chr20	37512622	37512662	E074	-38273
chr20	37512745	37512825	E074	-38110
chr20	37512880	37513087	E074	-37848
chr20	37514020	37514192	E074	-36743
chr20	37515247	37515323	E074	-35612
chr20	37515336	37515513	E074	-35422
chr20	37515592	37515681	E074	-35254
chr20	37515792	37515884	E074	-35051
chr20	37515999	37516060	E074	-34875
chr20	37516144	37516204	E074	-34731
chr20	37516825	37517131	E074	-33804
chr20	37517218	37517287	E074	-33648
chr20	37517727	37517777	E074	-33158
chr20	37517975	37518015	E074	-32920
chr20	37518236	37518314	E074	-32621
chr20	37518414	37518658	E074	-32277
chr20	37518724	37518804	E074	-32131
chr20	37518891	37519444	E074	-31491
chr20	37519658	37519761	E074	-31174
chr20	37520364	37520414	E074	-30521
chr20	37520755	37521165	E074	-29770
chr20	37521209	37521672	E074	-29263
chr20	37521684	37523252	E074	-27683
chr20	37523537	37523587	E074	-27348
chr20	37529060	37529120	E074	-21815
chr20	37529358	37529412	E074	-21523
chr20	37529462	37529605	E074	-21330
chr20	37529677	37529925	E074	-21010
chr20	37592010	37592067	E074	41075
chr20	37592121	37592161	E074	41186
chr20	37504883	37505430	E081	-45505
chr20	37505522	37505629	E081	-45306
chr20	37510788	37510838	E081	-40097
chr20	37510861	37510904	E081	-40031
chr20	37510946	37511071	E081	-39864
chr20	37511239	37511363	E081	-39572
chr20	37511590	37511688	E081	-39247
chr20	37511763	37511852	E081	-39083
chr20	37511860	37512432	E081	-38503
chr20	37512528	37512588	E081	-38347
chr20	37512622	37512662	E081	-38273
chr20	37512745	37512825	E081	-38110
chr20	37512880	37513087	E081	-37848
chr20	37521684	37523252	E081	-27683
chr20	37523537	37523587	E081	-27348
chr20	37523650	37523794	E081	-27141
chr20	37504883	37505430	E082	-45505
chr20	37511590	37511688	E082	-39247
chr20	37511763	37511852	E082	-39083
chr20	37511860	37512432	E082	-38503
chr20	37512528	37512588	E082	-38347
chr20	37512622	37512662	E082	-38273
chr20	37512745	37512825	E082	-38110
chr20	37523537	37523587	E082	-27348
chr20	37523650	37523794	E082	-27141
chr20	37561041	37561168	E082	10106
chr20	37561192	37561896	E082	10257

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	37554376	37556121	E067	3441
chr20	37590116	37591765	E067	39181
chr20	37554376	37556121	E068	3441
chr20	37590116	37591765	E068	39181
chr20	37554376	37556121	E069	3441
chr20	37590116	37591765	E069	39181
chr20	37554376	37556121	E070	3441
chr20	37590116	37591765	E070	39181
chr20	37554376	37556121	E071	3441
chr20	37590116	37591765	E071	39181
chr20	37554376	37556121	E072	3441
chr20	37590116	37591765	E072	39181
chr20	37554376	37556121	E073	3441
chr20	37590116	37591765	E073	39181
chr20	37554376	37556121	E074	3441
chr20	37590116	37591765	E074	39181
chr20	37590116	37591765	E081	39181
chr20	37554376	37556121	E082	3441
chr20	37590116	37591765	E082	39181