rs529989

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

SYT6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0400 (11948/29854,GnomAD)
C==0427 (12456/29118,TOPMED)
C==0351 (1758/5008,1000G)
C==0435 (1675/3854,ALSPAC)
C==0445 (1651/3708,TWINSUK)

Position: chr1:114135326 (GRCh38.p7) (1p13.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 24 Enhancers around

Promoter: 45 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.114135326C>A
GRCh37.p13 chr 1	NC_000001.10:g.114677948C>A

Molecule type	Change	Amino acid[Codon]	SO Term
SYT6 transcript variant 3	NM_001270805.1:c.	N/A	Intron Variant
SYT6 transcript variant 2	NM_205848.3:c.	N/A	Intron Variant
SYT6 transcript variant X5	XM_017000371.1:c.	N/A	Intron Variant
SYT6 transcript variant X6	XR_001736985.1:n.	N/A	Intron Variant
SYT6 transcript variant X1	XR_946547.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.406	A=0.594
1000Genomes	American	Sub	694	C=0.320	A=0.680
1000Genomes	East Asian	Sub	1008	C=0.238	A=0.762
1000Genomes	Europe	Sub	1006	C=0.437	A=0.563
1000Genomes	Global	Study-wide	5008	C=0.351	A=0.649
1000Genomes	South Asian	Sub	978	C=0.330	A=0.670
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.435	A=0.565
The Genome Aggregation Database	African	Sub	8688	C=0.404	A=0.596
The Genome Aggregation Database	American	Sub	836	C=0.290	A=0.710
The Genome Aggregation Database	East Asian	Sub	1612	C=0.246	A=0.754
The Genome Aggregation Database	Europe	Sub	18416	C=0.416	A=0.583
The Genome Aggregation Database	Global	Study-wide	29854	C=0.400	A=0.599
The Genome Aggregation Database	Other	Sub	302	C=0.460	A=0.540
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.427	A=0.572
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.445	A=0.555

PMID	Title	Author	Journal
23942779	A genome-wide association study of behavioral disinhibition.	McGue M	Behav Genet

SNP ID	p-value	Traits	Study
rs529989	4.7E-05	nicotine use	23942779

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	114646649	114646927	E068	-31021
chr1	114657208	114657488	E068	-20460
chr1	114665520	114666208	E068	-11740
chr1	114657208	114657488	E069	-20460
chr1	114664704	114664764	E069	-13184
chr1	114660932	114661001	E070	-16947
chr1	114661085	114661216	E070	-16732
chr1	114690592	114690680	E070	12644
chr1	114691499	114691549	E070	13551
chr1	114665520	114666208	E071	-11740
chr1	114668123	114668187	E071	-9761
chr1	114708803	114708868	E071	30855
chr1	114708803	114708868	E074	30855
chr1	114636781	114637191	E081	-40757
chr1	114660584	114660874	E081	-17074
chr1	114660932	114661001	E081	-16947
chr1	114661085	114661216	E081	-16732
chr1	114665309	114665425	E081	-12523
chr1	114690592	114690680	E081	12644
chr1	114691860	114692201	E081	13912
chr1	114692620	114692884	E081	14672
chr1	114692620	114692884	E082	14672
chr1	114699591	114699672	E082	21643
chr1	114699687	114699749	E082	21739

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	114695042	114695242	E067	17094
chr1	114695318	114695630	E067	17370
chr1	114695665	114695966	E067	17717
chr1	114695970	114696086	E067	18022
chr1	114696107	114696236	E067	18159
chr1	114696288	114696393	E067	18340
chr1	114696461	114696580	E067	18513
chr1	114694848	114694988	E068	16900
chr1	114695042	114695242	E068	17094
chr1	114695318	114695630	E068	17370
chr1	114695665	114695966	E068	17717
chr1	114695970	114696086	E068	18022
chr1	114696288	114696393	E068	18340
chr1	114696461	114696580	E068	18513
chr1	114694848	114694988	E069	16900
chr1	114695318	114695630	E069	17370
chr1	114695665	114695966	E069	17717
chr1	114694220	114694295	E070	16272
chr1	114694848	114694988	E070	16900
chr1	114695042	114695242	E070	17094
chr1	114695318	114695630	E070	17370
chr1	114695665	114695966	E070	17717
chr1	114694220	114694295	E071	16272
chr1	114694848	114694988	E071	16900
chr1	114695042	114695242	E071	17094
chr1	114695318	114695630	E071	17370
chr1	114695042	114695242	E072	17094
chr1	114695318	114695630	E072	17370
chr1	114695042	114695242	E073	17094
chr1	114695318	114695630	E073	17370
chr1	114695042	114695242	E074	17094
chr1	114695318	114695630	E074	17370
chr1	114695665	114695966	E074	17717
chr1	114695970	114696086	E074	18022
chr1	114696107	114696236	E074	18159
chr1	114696288	114696393	E074	18340
chr1	114696461	114696580	E074	18513
chr1	114693898	114693972	E082	15950
chr1	114695042	114695242	E082	17094
chr1	114695318	114695630	E082	17370
chr1	114695665	114695966	E082	17717
chr1	114695970	114696086	E082	18022
chr1	114696107	114696236	E082	18159
chr1	114696288	114696393	E082	18340
chr1	114696461	114696580	E082	18513