rs10889272

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PATJ : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0468 (14004/29904,GnomAD)
T=0479 (13972/29118,TOPMED)
C==0466 (2335/5008,1000G)
C==0362 (1397/3854,ALSPAC)
C==0355 (1317/3708,TWINSUK)

Position: chr1:61936877 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 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.61936877C>T
GRCh37.p13 chr 1	NC_000001.10:g.62402549C>T

Gene: PATJ, PATJ, crumbs cell polarity complex component(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PATJ transcript	NM_176877.2:c.	N/A	Intron Variant
PATJ transcript variant X6	XM_005270341.3:c.	N/A	Intron Variant
PATJ transcript variant X14	XM_005270347.1:c.	N/A	Intron Variant
PATJ transcript variant X15	XM_006710278.3:c.	N/A	Intron Variant
PATJ transcript variant X1	XM_011540462.2:c.	N/A	Intron Variant
PATJ transcript variant X2	XM_011540463.2:c.	N/A	Intron Variant
PATJ transcript variant X3	XM_011540464.2:c.	N/A	Intron Variant
PATJ transcript variant X4	XM_011540465.2:c.	N/A	Intron Variant
PATJ transcript variant X5	XM_011540466.2:c.	N/A	Intron Variant
PATJ transcript variant X8	XM_011540467.2:c.	N/A	Intron Variant
PATJ transcript variant X11	XM_011540468.2:c.	N/A	Intron Variant
PATJ transcript variant X12	XM_011540469.2:c.	N/A	Intron Variant
PATJ transcript variant X7	XM_016999998.1:c.	N/A	Intron Variant
PATJ transcript variant X9	XM_016999999.1:c.	N/A	Intron Variant
PATJ transcript variant X11	XM_017000000.1:c.	N/A	Intron Variant
PATJ transcript variant X18	XM_017000001.1:c.	N/A	Intron Variant
PATJ transcript variant X17	XM_011540470.1:c.	N/A	Genic Downstream Transcript Variant
PATJ transcript variant X13	XR_001736900.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.797	T=0.203
1000Genomes	American	Sub	694	C=0.290	T=0.710
1000Genomes	East Asian	Sub	1008	C=0.219	T=0.781
1000Genomes	Europe	Sub	1006	C=0.399	T=0.601
1000Genomes	Global	Study-wide	5008	C=0.466	T=0.534
1000Genomes	South Asian	Sub	978	C=0.470	T=0.530
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.362	T=0.638
The Genome Aggregation Database	African	Sub	8696	C=0.724	T=0.276
The Genome Aggregation Database	American	Sub	834	C=0.260	T=0.740
The Genome Aggregation Database	East Asian	Sub	1616	C=0.165	T=0.835
The Genome Aggregation Database	Europe	Sub	18456	C=0.385	T=0.615
The Genome Aggregation Database	Global	Study-wide	29904	C=0.468	T=0.531
The Genome Aggregation Database	Other	Sub	302	C=0.390	T=0.610
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.520	T=0.479
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.355	T=0.645

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs10889272	0.0001	alcoholism (heaviness of drinking)	21529783

eQTL of rs10889272 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 rs10889272 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	62417398	62418254	E070	14849
chr1	62418344	62418429	E070	15795
chr1	62418880	62419046	E070	16331
chr1	62417398	62418254	E071	14849
chr1	62418344	62418429	E071	15795