SNP Detail Info-rs10494769

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

NEK7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0048 (1454/29940,GnomAD)
G=0041 (1200/29118,TOPMED)
G=0080 (403/5008,1000G)
G=0037 (142/3854,ALSPAC)
G=0037 (138/3708,TWINSUK)

Position: chr1:198305231 (GRCh38.p7) (1q31.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 42 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.198305231A>G
GRCh37.p13 chr 1	NC_000001.10:g.198274361A>G

Molecule type	Change	Amino acid[Codon]	SO Term
NEK7 transcript	NM_133494.2:c.	N/A	Intron Variant
NEK7 transcript variant X6	XM_011509209.1:c.	N/A	Intron Variant
NEK7 transcript variant X1	XM_017000344.1:c.	N/A	Intron Variant
NEK7 transcript variant X2	XM_017000345.1:c.	N/A	Intron Variant
NEK7 transcript variant X3	XM_017000346.1:c.	N/A	Intron Variant
NEK7 transcript variant X4	XM_017000347.1:c.	N/A	Genic Downstream Transcript Variant
NEK7 transcript variant X5	XM_017000348.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.990	G=0.010
1000Genomes	American	Sub	694	A=0.880	G=0.120
1000Genomes	East Asian	Sub	1008	A=0.820	G=0.180
1000Genomes	Europe	Sub	1006	A=0.958	G=0.042
1000Genomes	Global	Study-wide	5008	A=0.920	G=0.080
1000Genomes	South Asian	Sub	978	A=0.910	G=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.963	G=0.037
The Genome Aggregation Database	African	Sub	8728	A=0.983	G=0.017
The Genome Aggregation Database	American	Sub	836	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1612	A=0.859	G=0.141
The Genome Aggregation Database	Europe	Sub	18462	A=0.950	G=0.049
The Genome Aggregation Database	Global	Study-wide	29940	A=0.951	G=0.048
The Genome Aggregation Database	Other	Sub	302	A=0.960	G=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.958	G=0.041
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.963	G=0.037

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

SNP ID	p-value	Traits	Study
rs10494769	0.000284	nicotine dependence	17158188

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	198234177	198234919	E067	-39442
chr1	198265159	198265390	E067	-8971
chr1	198285283	198285333	E067	10922
chr1	198286417	198286550	E067	12056
chr1	198234177	198234919	E068	-39442
chr1	198264401	198264696	E068	-9665
chr1	198265159	198265390	E068	-8971
chr1	198234177	198234919	E069	-39442
chr1	198273569	198273879	E069	-482
chr1	198285283	198285333	E069	10922
chr1	198245499	198245631	E070	-28730
chr1	198245734	198245788	E070	-28573
chr1	198265159	198265390	E070	-8971
chr1	198267867	198268155	E070	-6206
chr1	198285881	198286086	E070	11520
chr1	198286417	198286550	E070	12056
chr1	198287370	198287455	E070	13009
chr1	198237858	198238218	E071	-36143
chr1	198238244	198239007	E071	-35354
chr1	198264401	198264696	E071	-9665
chr1	198273569	198273879	E071	-482
chr1	198234177	198234919	E072	-39442
chr1	198238244	198239007	E072	-35354
chr1	198273569	198273879	E072	-482
chr1	198285283	198285333	E072	10922
chr1	198285881	198286086	E072	11520
chr1	198286417	198286550	E072	12056
chr1	198234177	198234919	E073	-39442
chr1	198234177	198234919	E074	-39442
chr1	198237627	198237687	E074	-36674
chr1	198237858	198238218	E074	-36143
chr1	198285881	198286086	E074	11520
chr1	198286417	198286550	E074	12056
chr1	198257408	198257532	E081	-16829
chr1	198264401	198264696	E081	-9665
chr1	198265159	198265390	E081	-8971
chr1	198267867	198268155	E081	-6206
chr1	198302038	198302078	E081	27677
chr1	198256992	198257340	E082	-17021
chr1	198257408	198257532	E082	-16829
chr1	198265159	198265390	E082	-8971
chr1	198267867	198268155	E082	-6206

rs10494769