SNP Detail Info-rs17241135

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TRAPPC13 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0239 (7168/29902,GnomAD)
A=0208 (6077/29118,TOPMED)
A=0167 (834/5008,1000G)
A=0304 (1171/3854,ALSPAC)
A=0293 (1085/3708,TWINSUK)

Position: chr5:65653767 (GRCh38.p7) (5q12.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 23 Enhancers around

Promoter: 19 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.65653767G>A
GRCh37.p13 chr 5	NC_000005.9:g.64949594G>A

Molecule type	Change	Amino acid[Codon]	SO Term
TRAPPC13 transcript variant 1	NM_001093755.1:c.	N/A	Intron Variant
TRAPPC13 transcript variant 3	NM_001093756.1:c.	N/A	Intron Variant
TRAPPC13 transcript variant 5	NM_001243737.1:c.	N/A	Intron Variant
TRAPPC13 transcript variant 2	NM_024941.3:c.	N/A	Intron Variant
TRAPPC13 transcript variant 4	NR_003545.1:n.	N/A	Genic Downstream Transcript Variant
TRAPPC13 transcript variant X1	XM_011543652.2:c.	N/A	Intron Variant
TRAPPC13 transcript variant X2	XM_017009890.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.834	A=0.166
1000Genomes	American	Sub	694	G=0.860	A=0.140
1000Genomes	East Asian	Sub	1008	G=0.943	A=0.057
1000Genomes	Europe	Sub	1006	G=0.732	A=0.268
1000Genomes	Global	Study-wide	5008	G=0.833	A=0.167
1000Genomes	South Asian	Sub	978	G=0.800	A=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.696	A=0.304
The Genome Aggregation Database	African	Sub	8702	G=0.830	A=0.170
The Genome Aggregation Database	American	Sub	836	G=0.850	A=0.150
The Genome Aggregation Database	East Asian	Sub	1618	G=0.930	A=0.070
The Genome Aggregation Database	Europe	Sub	18444	G=0.707	A=0.292
The Genome Aggregation Database	Global	Study-wide	29902	G=0.760	A=0.239
The Genome Aggregation Database	Other	Sub	302	G=0.790	A=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.791	A=0.208
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.707	A=0.293

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs17241135	0.000963	alcohol dependence	21314694

eQTL of rs17241135 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr5:64949594	PPWD1	ENSG00000113593.7	G>A	1.2421e-5	90528	Cerebellum
Chr5:64949594	PPWD1	ENSG00000113593.7	G>A	3.2091e-6	90528	Cortex
Chr5:64949594	PPWD1	ENSG00000113593.7	G>A	2.0563e-4	90528	Cerebellar_Hemisphere
Chr5:64949594	PPWD1	ENSG00000113593.7	G>A	2.6941e-5	90528	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr5	64914662	64914829	E067	-34765
chr5	64990963	64991043	E067	41369
chr5	64991111	64992062	E067	41517
chr5	64978245	64978295	E068	28651
chr5	64990963	64991043	E068	41369
chr5	64992622	64992676	E068	43028
chr5	64990963	64991043	E069	41369
chr5	64991111	64992062	E069	41517
chr5	64990963	64991043	E071	41369
chr5	64991111	64992062	E071	41517
chr5	64992622	64992676	E071	43028
chr5	64959752	64960367	E072	10158
chr5	64990963	64991043	E072	41369
chr5	64991111	64992062	E072	41517
chr5	64992622	64992676	E072	43028
chr5	64990963	64991043	E073	41369
chr5	64991111	64992062	E073	41517
chr5	64992622	64992676	E073	43028
chr5	64990963	64991043	E074	41369
chr5	64991111	64992062	E074	41517
chr5	64922703	64922800	E081	-26794
chr5	64992622	64992676	E081	43028
chr5	64922703	64922800	E082	-26794

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	64919385	64919687	E067	-29907
chr5	64919739	64921522	E067	-28072
chr5	64919385	64919687	E068	-29907
chr5	64919739	64921522	E068	-28072
chr5	64919385	64919687	E069	-29907
chr5	64919739	64921522	E069	-28072
chr5	64919385	64919687	E070	-29907
chr5	64919739	64921522	E070	-28072
chr5	64919385	64919687	E071	-29907
chr5	64919739	64921522	E071	-28072
chr5	64919385	64919687	E072	-29907
chr5	64919739	64921522	E072	-28072
chr5	64919385	64919687	E073	-29907
chr5	64919739	64921522	E073	-28072
chr5	64919385	64919687	E074	-29907
chr5	64919739	64921522	E074	-28072
chr5	64919385	64919687	E081	-29907
chr5	64919385	64919687	E082	-29907
chr5	64919739	64921522	E082	-28072

rs17241135