rs10928056

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

KAZN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0076 (2298/29906,GnomAD)
A=0069 (2018/29118,TOPMED)
A=0160 (802/5008,1000G)
A=0044 (170/3854,ALSPAC)
A=0048 (179/3708,TWINSUK)

Position: chr1:14259153 (GRCh38.p7) (1p36.21)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 97 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.14259153G>A
GRCh37.p13 chr 1	NC_000001.10:g.14585648G>A

Gene: KAZN, kazrin, periplakin interacting protein(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KAZN transcript variant D	NM_001017999.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant B	NM_001018000.3:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant C	NM_001018001.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant A	NM_015209.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant E	NM_201628.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X3	XM_005245795.4:c.	N/A	Intron Variant
KAZN transcript variant X1	XM_011541074.2:c.	N/A	Intron Variant
KAZN transcript variant X6	XM_011541080.2:c.	N/A	Intron Variant
KAZN transcript variant X8	XM_017000768.1:c.	N/A	Intron Variant
KAZN transcript variant X9	XM_017000769.1:c.	N/A	Intron Variant
KAZN transcript variant X10	XM_017000770.1:c.	N/A	Intron Variant
KAZN transcript variant X2	XM_011541075.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X4	XM_011541076.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X5	XM_011541077.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X7	XM_011541081.2:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X10	XM_017000771.1:c.	N/A	Genic Upstream Transcript Variant
KAZN transcript variant X12	XM_017000772.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.969	A=0.031
1000Genomes	American	Sub	694	G=0.780	A=0.220
1000Genomes	East Asian	Sub	1008	G=0.614	A=0.386
1000Genomes	Europe	Sub	1006	G=0.950	A=0.050
1000Genomes	Global	Study-wide	5008	G=0.840	A=0.160
1000Genomes	South Asian	Sub	978	G=0.830	A=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.956	A=0.044
The Genome Aggregation Database	African	Sub	8700	G=0.962	A=0.038
The Genome Aggregation Database	American	Sub	836	G=0.740	A=0.260
The Genome Aggregation Database	East Asian	Sub	1604	G=0.610	A=0.390
The Genome Aggregation Database	Europe	Sub	18464	G=0.940	A=0.059
The Genome Aggregation Database	Global	Study-wide	29906	G=0.923	A=0.076
The Genome Aggregation Database	Other	Sub	302	G=0.920	A=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.930	A=0.069
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.952	A=0.048

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs10928056	0.00082	alcohol dependence	20201924

eQTL of rs10928056 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 rs10928056 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	14578641	14578691	E067	-6957
chr1	14580180	14580522	E067	-5126
chr1	14580536	14580759	E067	-4889
chr1	14580764	14581116	E067	-4532
chr1	14585260	14585328	E067	-320
chr1	14585578	14586229	E067	0
chr1	14586422	14586606	E067	774
chr1	14587134	14587241	E067	1486
chr1	14564903	14565713	E068	-19935
chr1	14582384	14582446	E068	-3202
chr1	14582764	14582843	E068	-2805
chr1	14585260	14585328	E068	-320
chr1	14585578	14586229	E068	0
chr1	14586422	14586606	E068	774
chr1	14587134	14587241	E068	1486
chr1	14589252	14589339	E068	3604
chr1	14589442	14589551	E068	3794
chr1	14589654	14589704	E068	4006
chr1	14608959	14609019	E068	23311
chr1	14609086	14609239	E068	23438
chr1	14609257	14609427	E068	23609
chr1	14580180	14580522	E069	-5126
chr1	14585260	14585328	E069	-320
chr1	14586422	14586606	E069	774
chr1	14587134	14587241	E069	1486
chr1	14589654	14589704	E069	4006
chr1	14611819	14612022	E069	26171
chr1	14538584	14538639	E070	-47009
chr1	14538642	14538836	E070	-46812
chr1	14580180	14580522	E070	-5126
chr1	14589866	14590162	E070	4218
chr1	14590269	14590415	E070	4621
chr1	14564903	14565713	E071	-19935
chr1	14578641	14578691	E071	-6957
chr1	14580180	14580522	E071	-5126
chr1	14580536	14580759	E071	-4889
chr1	14580764	14581116	E071	-4532
chr1	14585578	14586229	E071	0
chr1	14586422	14586606	E071	774
chr1	14587134	14587241	E071	1486
chr1	14608959	14609019	E071	23311
chr1	14609086	14609239	E071	23438
chr1	14609257	14609427	E071	23609
chr1	14564903	14565713	E072	-19935
chr1	14580180	14580522	E072	-5126
chr1	14580536	14580759	E072	-4889
chr1	14580764	14581116	E072	-4532
chr1	14585578	14586229	E072	0
chr1	14586422	14586606	E072	774
chr1	14587134	14587241	E072	1486
chr1	14589252	14589339	E072	3604
chr1	14589442	14589551	E072	3794
chr1	14589654	14589704	E072	4006
chr1	14589866	14590162	E072	4218
chr1	14590269	14590415	E072	4621
chr1	14608959	14609019	E072	23311
chr1	14609086	14609239	E072	23438
chr1	14609257	14609427	E072	23609
chr1	14609433	14609667	E072	23785
chr1	14585260	14585328	E073	-320
chr1	14585578	14586229	E073	0
chr1	14586422	14586606	E073	774
chr1	14587134	14587241	E073	1486
chr1	14564903	14565713	E074	-19935
chr1	14580180	14580522	E074	-5126
chr1	14580536	14580759	E074	-4889
chr1	14580764	14581116	E074	-4532
chr1	14585260	14585328	E074	-320
chr1	14585578	14586229	E074	0
chr1	14586422	14586606	E074	774
chr1	14587134	14587241	E074	1486
chr1	14589252	14589339	E081	3604
chr1	14589442	14589551	E081	3794
chr1	14589654	14589704	E081	4006
chr1	14589866	14590162	E081	4218
chr1	14590269	14590415	E081	4621
chr1	14590681	14590731	E081	5033
chr1	14590753	14590793	E081	5105
chr1	14592075	14592270	E081	6427
chr1	14599494	14599628	E081	13846
chr1	14600207	14600898	E081	14559
chr1	14601832	14601882	E081	16184
chr1	14602069	14602795	E081	16421
chr1	14618827	14618905	E081	33179
chr1	14618983	14619495	E081	33335
chr1	14619514	14619572	E081	33866
chr1	14620106	14620160	E081	34458
chr1	14620572	14620782	E081	34924
chr1	14627643	14628342	E081	41995
chr1	14589866	14590162	E082	4218
chr1	14590269	14590415	E082	4621
chr1	14599494	14599628	E082	13846
chr1	14600207	14600898	E082	14559
chr1	14601832	14601882	E082	16184
chr1	14602069	14602795	E082	16421
chr1	14618827	14618905	E082	33179
chr1	14627643	14628342	E082	41995