SNP Detail Info-rs360595

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SYCP1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0390 (11644/29824,GnomAD)
A=0358 (10428/29118,TOPMED)
A=0362 (1811/5008,1000G)
A=0463 (1785/3854,ALSPAC)
A=0470 (1743/3708,TWINSUK)

Position: chr1:114930585 (GRCh38.p7) (1p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 6 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.114930585G>A
GRCh37.p13 chr 1	NC_000001.10:g.115473206G>A

Molecule type	Change	Amino acid[Codon]	SO Term
SYCP1 transcript variant 2	NM_001282541.1:c.	N/A	Intron Variant
SYCP1 transcript variant 3	NM_001282542.1:c.	N/A	Intron Variant
SYCP1 transcript variant 1	NM_003176.3:c.	N/A	Intron Variant
SYCP1 transcript variant 4	NR_104211.1:n.	N/A	Intron Variant
SYCP1 transcript variant X3	XM_005271155.3:c.	N/A	Intron Variant
SYCP1 transcript variant X4	XM_005271156.1:c.	N/A	Intron Variant
SYCP1 transcript variant X1	XM_006710859.1:c.	N/A	Intron Variant
SYCP1 transcript variant X6	XM_011542037.2:c.	N/A	Intron Variant
SYCP1 transcript variant X7	XM_011542038.2:c.	N/A	Intron Variant
SYCP1 transcript variant X2	XM_017002184.1:c.	N/A	Intron Variant
SYCP1 transcript variant X5	XM_017002185.1:c.	N/A	Intron Variant
SYCP1 transcript variant X8	XM_011542039.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.814	A=0.186
1000Genomes	American	Sub	694	G=0.610	A=0.390
1000Genomes	East Asian	Sub	1008	G=0.470	A=0.530
1000Genomes	Europe	Sub	1006	G=0.552	A=0.448
1000Genomes	Global	Study-wide	5008	G=0.638	A=0.362
1000Genomes	South Asian	Sub	978	G=0.680	A=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.537	A=0.463
The Genome Aggregation Database	African	Sub	8702	G=0.793	A=0.207
The Genome Aggregation Database	American	Sub	836	G=0.590	A=0.410
The Genome Aggregation Database	East Asian	Sub	1608	G=0.506	A=0.494
The Genome Aggregation Database	Europe	Sub	18376	G=0.534	A=0.465
The Genome Aggregation Database	Global	Study-wide	29824	G=0.609	A=0.390
The Genome Aggregation Database	Other	Sub	302	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.641	A=0.358
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.530	A=0.470

PMID	Title	Author	Journal
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

SNP ID	p-value	Traits	Study
rs360595	9.11E-05	alcohol consumption	23953852

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:115473206	TSPAN2	ENSG00000134198.5	G>A	5.2445e-13	-158915	Cerebellum

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

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	115444588	115444648	E068	-28558
chr1	115444653	115444740	E068	-28466
chr1	115444922	115445006	E068	-28200
chr1	115444588	115444648	E071	-28558
chr1	115444653	115444740	E071	-28466
chr1	115444922	115445006	E071	-28200

rs360595