rs6923822

Organism: Homo sapiens

Alleles: G>A / G>C

Gene : Feature

PTPRK : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0198 (5951/29960,GnomAD)
A=0227 (6633/29118,TOPMED)
A=0156 (783/5008,1000G)
A=0181 (699/3854,ALSPAC)
A=0163 (606/3708,TWINSUK)

Position: chr6:128518325 (GRCh38.p7) (6q22.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 95 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.128518325G>A
GRCh38.p7 chr 6	NC_000006.12:g.128518325G>C
GRCh37.p13 chr 6	NC_000006.11:g.128839470G>A
GRCh37.p13 chr 6	NC_000006.11:g.128839470G>C
GRCh38.p7 chr 6 alt locus HSCHR6_1_CTG8	NT_187556.1:g.867659G>A
GRCh38.p7 chr 6 alt locus HSCHR6_1_CTG8	NT_187556.1:g.867659G>C

Gene: PTPRK, protein tyrosine phosphatase, receptor type K(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRK transcript variant 1	NM_001135648.2:c.	N/A	Intron Variant
PTPRK transcript variant 3	NM_001291981.1:c.	N/A	Intron Variant
PTPRK transcript variant 4	NM_001291982.1:c.	N/A	Intron Variant
PTPRK transcript variant 5	NM_001291983.1:c.	N/A	Intron Variant
PTPRK transcript variant 6	NM_001291984.1:c.	N/A	Intron Variant
PTPRK transcript variant 2	NM_002844.3:c.	N/A	Intron Variant
PTPRK transcript variant X4	XM_006715537.2:c.	N/A	Intron Variant
PTPRK transcript variant X1	XM_011536014.2:c.	N/A	Intron Variant
PTPRK transcript variant X2	XM_011536015.2:c.	N/A	Intron Variant
PTPRK transcript variant X3	XM_011536016.2:c.	N/A	Intron Variant
PTPRK transcript variant X5	XM_011536017.2:c.	N/A	Intron Variant
PTPRK transcript variant X6	XM_011536018.2:c.	N/A	Intron Variant
PTPRK transcript variant X11	XM_011536020.2:c.	N/A	Intron Variant
PTPRK transcript variant X12	XM_011536021.2:c.	N/A	Intron Variant
PTPRK transcript variant X7	XM_017011145.1:c.	N/A	Intron Variant
PTPRK transcript variant X8	XM_017011146.1:c.	N/A	Intron Variant
PTPRK transcript variant X9	XM_017011147.1:c.	N/A	Intron Variant
PTPRK transcript variant X10	XM_017011148.1:c.	N/A	Intron Variant
PTPRK transcript variant X13	XM_017011149.1:c.	N/A	Genic Upstream Transcript Variant
PTPRK transcript variant X14	XM_017011150.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.669	A=0.331
1000Genomes	American	Sub	694	G=0.920	A=0.080
1000Genomes	East Asian	Sub	1008	G=0.984	A=0.016
1000Genomes	Europe	Sub	1006	G=0.852	A=0.148
1000Genomes	Global	Study-wide	5008	G=0.844	A=0.156
1000Genomes	South Asian	Sub	978	G=0.880	A=0.120
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.819	A=0.181
The Genome Aggregation Database	African	Sub	8712	G=0.664	A=0.336
The Genome Aggregation Database	American	Sub	838	G=0.920	A=0.08,
The Genome Aggregation Database	East Asian	Sub	1622	G=0.990	A=0.010
The Genome Aggregation Database	Europe	Sub	18486	G=0.842	A=0.158
The Genome Aggregation Database	Global	Study-wide	29960	G=0.801	A=0.198
The Genome Aggregation Database	Other	Sub	302	G=0.950	A=0.05,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.772	A=0.227
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.837	A=0.163

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs6923822	9.11E-05	alcohol consumption	23743675

eQTL of rs6923822 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 rs6923822 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 )
chr6	101851588	101851732	E081	37263

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	101841734	101842160	E067	27409
chr6	101842527	101842628	E067	28202
chr6	101843000	101843088	E067	28675
chr6	101846590	101847183	E067	32265
chr6	101847185	101847563	E067	32860
chr6	101847572	101848166	E067	33247
chr6	101849550	101850441	E067	35225
chr6	101850590	101850966	E067	36265
chr6	101851093	101851189	E067	36768
chr6	101851282	101851560	E067	36957
chr6	101841734	101842160	E068	27409
chr6	101846590	101847183	E068	32265
chr6	101847185	101847563	E068	32860
chr6	101847572	101848166	E068	33247
chr6	101849550	101850441	E068	35225
chr6	101850590	101850966	E068	36265
chr6	101851093	101851189	E068	36768
chr6	101851282	101851560	E068	36957
chr6	101841734	101842160	E069	27409
chr6	101842527	101842628	E069	28202
chr6	101843000	101843088	E069	28675
chr6	101846590	101847183	E069	32265
chr6	101847185	101847563	E069	32860
chr6	101847572	101848166	E069	33247
chr6	101849550	101850441	E069	35225
chr6	101850590	101850966	E069	36265
chr6	101851093	101851189	E069	36768
chr6	101851282	101851560	E069	36957
chr6	101842527	101842628	E070	28202
chr6	101846590	101847183	E070	32265
chr6	101849550	101850441	E070	35225
chr6	101850590	101850966	E070	36265
chr6	101851093	101851189	E070	36768
chr6	101851282	101851560	E070	36957
chr6	101841734	101842160	E071	27409
chr6	101842527	101842628	E071	28202
chr6	101846590	101847183	E071	32265
chr6	101847185	101847563	E071	32860
chr6	101847572	101848166	E071	33247
chr6	101849550	101850441	E071	35225
chr6	101850590	101850966	E071	36265
chr6	101841734	101842160	E072	27409
chr6	101842527	101842628	E072	28202
chr6	101843000	101843088	E072	28675
chr6	101843372	101843484	E072	29047
chr6	101843698	101843752	E072	29373
chr6	101844382	101844507	E072	30057
chr6	101844551	101844711	E072	30226
chr6	101846590	101847183	E072	32265
chr6	101847185	101847563	E072	32860
chr6	101847572	101848166	E072	33247
chr6	101849550	101850441	E072	35225
chr6	101850590	101850966	E072	36265
chr6	101851093	101851189	E072	36768
chr6	101851282	101851560	E072	36957
chr6	101839897	101840860	E073	25572
chr6	101841734	101842160	E073	27409
chr6	101842527	101842628	E073	28202
chr6	101843000	101843088	E073	28675
chr6	101843372	101843484	E073	29047
chr6	101843698	101843752	E073	29373
chr6	101846590	101847183	E073	32265
chr6	101847185	101847563	E073	32860
chr6	101847572	101848166	E073	33247
chr6	101849550	101850441	E073	35225
chr6	101850590	101850966	E073	36265
chr6	101851093	101851189	E073	36768
chr6	101851282	101851560	E073	36957
chr6	101841734	101842160	E074	27409
chr6	101847185	101847563	E074	32860
chr6	101847572	101848166	E074	33247
chr6	101849550	101850441	E074	35225
chr6	101850590	101850966	E074	36265
chr6	101851093	101851189	E074	36768
chr6	101842527	101842628	E081	28202
chr6	101843000	101843088	E081	28675
chr6	101843372	101843484	E081	29047
chr6	101843698	101843752	E081	29373
chr6	101844551	101844711	E081	30226
chr6	101845220	101845349	E081	30895
chr6	101847572	101848166	E081	33247
chr6	101840889	101841701	E082	26564
chr6	101841734	101842160	E082	27409
chr6	101842527	101842628	E082	28202
chr6	101843000	101843088	E082	28675
chr6	101843372	101843484	E082	29047
chr6	101843698	101843752	E082	29373
chr6	101844382	101844507	E082	30057
chr6	101844551	101844711	E082	30226
chr6	101845220	101845349	E082	30895
chr6	101846590	101847183	E082	32265
chr6	101847185	101847563	E082	32860
chr6	101847572	101848166	E082	33247
chr6	101849550	101850441	E082	35225
chr6	101851093	101851189	E082	36768