SNP Detail Info-rs12407433

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

NEK7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0078 (2346/29936,GnomAD)
T=0087 (2543/29118,TOPMED)
T=0109 (545/5008,1000G)
T=0038 (148/3854,ALSPAC)
T=0039 (144/3708,TWINSUK)

Position: chr1:198305778 (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.198305778A>T
GRCh37.p13 chr 1	NC_000001.10:g.198274908A>T

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=0.889	T=0.111
1000Genomes	American	Sub	694	A=0.870	T=0.130
1000Genomes	East Asian	Sub	1008	A=0.820	T=0.180
1000Genomes	Europe	Sub	1006	A=0.956	T=0.044
1000Genomes	Global	Study-wide	5008	A=0.891	T=0.109
1000Genomes	South Asian	Sub	978	A=0.910	T=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.962	T=0.038
The Genome Aggregation Database	African	Sub	8710	A=0.884	T=0.116
The Genome Aggregation Database	American	Sub	836	A=0.800	T=0.200
The Genome Aggregation Database	East Asian	Sub	1612	A=0.857	T=0.143
The Genome Aggregation Database	Europe	Sub	18476	A=0.950	T=0.050
The Genome Aggregation Database	Global	Study-wide	29936	A=0.921	T=0.078
The Genome Aggregation Database	Other	Sub	302	A=0.940	T=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.912	T=0.087
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.961	T=0.039

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
rs12407433	0.000733	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	-39989
chr1	198265159	198265390	E067	-9518
chr1	198285283	198285333	E067	10375
chr1	198286417	198286550	E067	11509
chr1	198234177	198234919	E068	-39989
chr1	198264401	198264696	E068	-10212
chr1	198265159	198265390	E068	-9518
chr1	198234177	198234919	E069	-39989
chr1	198273569	198273879	E069	-1029
chr1	198285283	198285333	E069	10375
chr1	198245499	198245631	E070	-29277
chr1	198245734	198245788	E070	-29120
chr1	198265159	198265390	E070	-9518
chr1	198267867	198268155	E070	-6753
chr1	198285881	198286086	E070	10973
chr1	198286417	198286550	E070	11509
chr1	198287370	198287455	E070	12462
chr1	198237858	198238218	E071	-36690
chr1	198238244	198239007	E071	-35901
chr1	198264401	198264696	E071	-10212
chr1	198273569	198273879	E071	-1029
chr1	198234177	198234919	E072	-39989
chr1	198238244	198239007	E072	-35901
chr1	198273569	198273879	E072	-1029
chr1	198285283	198285333	E072	10375
chr1	198285881	198286086	E072	10973
chr1	198286417	198286550	E072	11509
chr1	198234177	198234919	E073	-39989
chr1	198234177	198234919	E074	-39989
chr1	198237627	198237687	E074	-37221
chr1	198237858	198238218	E074	-36690
chr1	198285881	198286086	E074	10973
chr1	198286417	198286550	E074	11509
chr1	198257408	198257532	E081	-17376
chr1	198264401	198264696	E081	-10212
chr1	198265159	198265390	E081	-9518
chr1	198267867	198268155	E081	-6753
chr1	198302038	198302078	E081	27130
chr1	198256992	198257340	E082	-17568
chr1	198257408	198257532	E082	-17376
chr1	198265159	198265390	E082	-9518
chr1	198267867	198268155	E082	-6753

rs12407433