rs1475423

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

NEK7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0047 (1432/29926,GnomAD)
T=0040 (1181/29118,TOPMED)
T=0073 (368/5008,1000G)
T=0039 (151/3854,ALSPAC)
T=0040 (147/3708,TWINSUK)

Position: chr1:198254360 (GRCh38.p7) (1q31.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 59 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.198254360A>T
GRCh37.p13 chr 1	NC_000001.10:g.198223490A>T

Gene: NEK7, NIMA related kinase 7(plus strand)

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	Intron Variant
NEK7 transcript variant X5	XM_017000348.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.989	T=0.011
1000Genomes	American	Sub	694	A=0.930	T=0.070
1000Genomes	East Asian	Sub	1008	A=0.824	T=0.176
1000Genomes	Europe	Sub	1006	A=0.956	T=0.044
1000Genomes	Global	Study-wide	5008	A=0.927	T=0.073
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=0.961	T=0.039
The Genome Aggregation Database	African	Sub	8722	A=0.984	T=0.016
The Genome Aggregation Database	American	Sub	836	A=0.870	T=0.130
The Genome Aggregation Database	East Asian	Sub	1606	A=0.861	T=0.139
The Genome Aggregation Database	Europe	Sub	18460	A=0.948	T=0.051
The Genome Aggregation Database	Global	Study-wide	29926	A=0.952	T=0.047
The Genome Aggregation Database	Other	Sub	302	A=0.960	T=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.959	T=0.040
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.960	T=0.040

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

P-Value

SNP ID	p-value	Traits	Study
rs1475423	0.000188	nicotine dependence	17158188

eQTL of rs1475423 in Brain tissues (GTEx Analysis Release V7)

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

meQTL of rs1475423 in Fetal Brain

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

Genomic View

Chromatin Interaction

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	198174227	198174397	E067	-49093
chr1	198203658	198204004	E067	-19486
chr1	198204103	198204252	E067	-19238
chr1	198234177	198234919	E067	10687
chr1	198265159	198265390	E067	41669
chr1	198174227	198174397	E068	-49093
chr1	198189034	198189228	E068	-34262
chr1	198189316	198189460	E068	-34030
chr1	198189685	198189908	E068	-33582
chr1	198203658	198204004	E068	-19486
chr1	198214303	198214587	E068	-8903
chr1	198214672	198214830	E068	-8660
chr1	198234177	198234919	E068	10687
chr1	198264401	198264696	E068	40911
chr1	198265159	198265390	E068	41669
chr1	198174227	198174397	E069	-49093
chr1	198198124	198198322	E069	-25168
chr1	198203658	198204004	E069	-19486
chr1	198204103	198204252	E069	-19238
chr1	198215381	198215887	E069	-7603
chr1	198234177	198234919	E069	10687
chr1	198174227	198174397	E070	-49093
chr1	198215381	198215887	E070	-7603
chr1	198245499	198245631	E070	22009
chr1	198245734	198245788	E070	22244
chr1	198265159	198265390	E070	41669
chr1	198267867	198268155	E070	44377
chr1	198174227	198174397	E071	-49093
chr1	198203658	198204004	E071	-19486
chr1	198204103	198204252	E071	-19238
chr1	198237858	198238218	E071	14368
chr1	198238244	198239007	E071	14754
chr1	198264401	198264696	E071	40911
chr1	198203658	198204004	E072	-19486
chr1	198204103	198204252	E072	-19238
chr1	198234177	198234919	E072	10687
chr1	198238244	198239007	E072	14754
chr1	198203658	198204004	E073	-19486
chr1	198204103	198204252	E073	-19238
chr1	198234177	198234919	E073	10687
chr1	198203658	198204004	E074	-19486
chr1	198204103	198204252	E074	-19238
chr1	198214144	198214259	E074	-9231
chr1	198214303	198214587	E074	-8903
chr1	198214672	198214830	E074	-8660
chr1	198234177	198234919	E074	10687
chr1	198237627	198237687	E074	14137
chr1	198237858	198238218	E074	14368
chr1	198174227	198174397	E081	-49093
chr1	198214303	198214587	E081	-8903
chr1	198214672	198214830	E081	-8660
chr1	198257408	198257532	E081	33918
chr1	198264401	198264696	E081	40911
chr1	198265159	198265390	E081	41669
chr1	198267867	198268155	E081	44377
chr1	198256992	198257340	E082	33502
chr1	198257408	198257532	E082	33918
chr1	198265159	198265390	E082	41669
chr1	198267867	198268155	E082	44377