rs12229663

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

PTPRR : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0243 (7266/29900,GnomAD)
G=0235 (1179/5008,1000G)
G=0219 (845/3854,ALSPAC)
G=0226 (837/3708,TWINSUK)

Position: chr12:70856216 (GRCh38.p7) (12q15)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 49 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.70856216A>G
GRCh38.p7 chr 12	NC_000012.12:g.70856216A>T
GRCh37.p13 chr 12	NC_000012.11:g.71249996A>G
GRCh37.p13 chr 12	NC_000012.11:g.71249996A>T

Gene: PTPRR, protein tyrosine phosphatase, receptor type R(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRR transcript variant 1	NM_002849.3:c.	N/A	Intron Variant
PTPRR transcript variant 3	NM_001207015.1:c.	N/A	Genic Upstream Transcript Variant
PTPRR transcript variant 4	NM_001207016.1:c.	N/A	Genic Upstream Transcript Variant
PTPRR transcript variant 2	NM_130846.2:c.	N/A	Genic Upstream Transcript Variant
PTPRR transcript variant 5	NR_073474.1:n.	N/A	Genic Upstream Transcript Variant
PTPRR transcript variant X1	XM_011538615.2:c.	N/A	Intron Variant
PTPRR transcript variant X2	XR_001748830.1:n.	N/A	Intron Variant
PTPRR transcript variant X4	XR_944652.1:n.	N/A	Intron Variant
PTPRR transcript variant X3	XR_001748831.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.811	G=0.189
1000Genomes	American	Sub	694	A=0.870	G=0.130
1000Genomes	East Asian	Sub	1008	A=0.599	G=0.401
1000Genomes	Europe	Sub	1006	A=0.769	G=0.231
1000Genomes	Global	Study-wide	5008	A=0.765	G=0.235
1000Genomes	South Asian	Sub	978	A=0.790	G=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.781	G=0.219
The Genome Aggregation Database	African	Sub	8708	A=0.792	G=0.208
The Genome Aggregation Database	American	Sub	836	A=0.870	G=0.130
The Genome Aggregation Database	East Asian	Sub	1594	A=0.577	G=0.423
The Genome Aggregation Database	Europe	Sub	18460	A=0.749	G=0.250
The Genome Aggregation Database	Global	Study-wide	29900	A=0.757	G=0.243
The Genome Aggregation Database	Other	Sub	302	A=0.810	G=0.190
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.774	G=0.226

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs12229663	0.000429	alcohol dependence	24277619

eQTL of rs12229663 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 rs12229663 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 )
chr12	94854948	94855009	E067	-29971
chr12	94852160	94852262	E068	-32718
chr12	94926352	94927156	E068	41372
chr12	94926352	94927156	E069	41372
chr12	94851844	94851894	E070	-33086
chr12	94854948	94855009	E070	-29971
chr12	94855154	94855276	E070	-29704
chr12	94926352	94927156	E070	41372
chr12	94927277	94927327	E070	42297
chr12	94927630	94927680	E070	42650
chr12	94927738	94927788	E070	42758
chr12	94927881	94928059	E070	42901
chr12	94928165	94928219	E070	43185
chr12	94928255	94928330	E070	43275
chr12	94928472	94928598	E070	43492
chr12	94928634	94928704	E070	43654
chr12	94928754	94928850	E070	43774
chr12	94929588	94929672	E070	44608
chr12	94929884	94929934	E070	44904
chr12	94930017	94930077	E070	45037
chr12	94930163	94930247	E070	45183
chr12	94930356	94930550	E070	45376
chr12	94854948	94855009	E071	-29971
chr12	94926352	94927156	E071	41372
chr12	94854948	94855009	E072	-29971
chr12	94926352	94927156	E072	41372
chr12	94926352	94927156	E074	41372
chr12	94854948	94855009	E081	-29971
chr12	94926352	94927156	E081	41372
chr12	94927277	94927327	E081	42297
chr12	94927881	94928059	E081	42901
chr12	94928165	94928219	E081	43185
chr12	94928255	94928330	E081	43275
chr12	94928472	94928598	E081	43492
chr12	94928634	94928704	E081	43654
chr12	94928754	94928850	E081	43774
chr12	94929588	94929672	E081	44608
chr12	94929884	94929934	E081	44904
chr12	94930017	94930077	E081	45037
chr12	94930163	94930247	E081	45183
chr12	94930356	94930550	E081	45376
chr12	94926352	94927156	E082	41372
chr12	94928472	94928598	E082	43492
chr12	94928634	94928704	E082	43654
chr12	94928754	94928850	E082	43774
chr12	94929588	94929672	E082	44608
chr12	94929884	94929934	E082	44904
chr12	94930017	94930077	E082	45037
chr12	94930163	94930247	E082	45183

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	94852539	94854834	E067	-30146
chr12	94852539	94854834	E068	-30146
chr12	94852539	94854834	E069	-30146
chr12	94852539	94854834	E070	-30146
chr12	94852539	94854834	E071	-30146
chr12	94852539	94854834	E072	-30146
chr12	94852539	94854834	E073	-30146
chr12	94852539	94854834	E074	-30146
chr12	94852539	94854834	E081	-30146
chr12	94852539	94854834	E082	-30146