SNP Detail Info-rs16842754

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

NEK7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0085 (2491/29118,TOPMED)
A=0109 (548/5008,1000G)
A=0038 (147/3854,ALSPAC)
A=0038 (141/3708,TWINSUK)

Position: chr1:198308005 (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.198308005C>A
GRCh37.p13 chr 1	NC_000001.10:g.198277135C>A

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	C=0.887	A=0.113
1000Genomes	American	Sub	694	C=0.870	A=0.130
1000Genomes	East Asian	Sub	1008	C=0.819	A=0.181
1000Genomes	Europe	Sub	1006	C=0.956	A=0.044
1000Genomes	Global	Study-wide	5008	C=0.891	A=0.109
1000Genomes	South Asian	Sub	978	C=0.910	A=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.962	A=0.038
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.914	A=0.085
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.962	A=0.038

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
rs16842754	0.000525	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	-42216
chr1	198265159	198265390	E067	-11745
chr1	198285283	198285333	E067	8148
chr1	198286417	198286550	E067	9282
chr1	198234177	198234919	E068	-42216
chr1	198264401	198264696	E068	-12439
chr1	198265159	198265390	E068	-11745
chr1	198234177	198234919	E069	-42216
chr1	198273569	198273879	E069	-3256
chr1	198285283	198285333	E069	8148
chr1	198245499	198245631	E070	-31504
chr1	198245734	198245788	E070	-31347
chr1	198265159	198265390	E070	-11745
chr1	198267867	198268155	E070	-8980
chr1	198285881	198286086	E070	8746
chr1	198286417	198286550	E070	9282
chr1	198287370	198287455	E070	10235
chr1	198237858	198238218	E071	-38917
chr1	198238244	198239007	E071	-38128
chr1	198264401	198264696	E071	-12439
chr1	198273569	198273879	E071	-3256
chr1	198234177	198234919	E072	-42216
chr1	198238244	198239007	E072	-38128
chr1	198273569	198273879	E072	-3256
chr1	198285283	198285333	E072	8148
chr1	198285881	198286086	E072	8746
chr1	198286417	198286550	E072	9282
chr1	198234177	198234919	E073	-42216
chr1	198234177	198234919	E074	-42216
chr1	198237627	198237687	E074	-39448
chr1	198237858	198238218	E074	-38917
chr1	198285881	198286086	E074	8746
chr1	198286417	198286550	E074	9282
chr1	198257408	198257532	E081	-19603
chr1	198264401	198264696	E081	-12439
chr1	198265159	198265390	E081	-11745
chr1	198267867	198268155	E081	-8980
chr1	198302038	198302078	E081	24903
chr1	198256992	198257340	E082	-19795
chr1	198257408	198257532	E082	-19603
chr1	198265159	198265390	E082	-11745
chr1	198267867	198268155	E082	-8980

rs16842754