rs3764213

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

NIPA2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0204 (6125/29918,GnomAD)
G=0200 (5849/29118,TOPMED)
G=0227 (1139/5008,1000G)
G=0158 (610/3854,ALSPAC)
G=0167 (619/3708,TWINSUK)

Position: chr15:22845401 (GRCh38.p7) (15q11.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 90 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.22845401G>C
GRCh37.p13 chr 15	NC_000015.9:g.23027667C>G
NIPA2 RefSeqGene	NG_021303.1:g.11761G>C

Gene: NIPA2, non imprinted in Prader-Willi/Angelman syndrome 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NIPA2 transcript variant 2	NM_001008860.2:c.	N/A	Intron Variant
NIPA2 transcript variant 3	NM_001008892.2:c.	N/A	Intron Variant
NIPA2 transcript variant 4	NM_001008894.2:c.	N/A	Intron Variant
NIPA2 transcript variant 6	NM_001184888.1:c.	N/A	Intron Variant
NIPA2 transcript variant 5	NM_001184889.1:c.	N/A	Intron Variant
NIPA2 transcript variant 1	NM_030922.6:c.	N/A	Intron Variant
NIPA2 transcript variant X1	XM_005272546.3:c.	N/A	Intron Variant
NIPA2 transcript variant X3	XM_005272547.4:c.	N/A	Intron Variant
NIPA2 transcript variant X11	XM_005272548.3:c.	N/A	Intron Variant
NIPA2 transcript variant X10	XM_005272550.3:c.	N/A	Intron Variant
NIPA2 transcript variant X20	XM_005272552.3:c.	N/A	Intron Variant
NIPA2 transcript variant X22	XM_005272553.4:c.	N/A	Intron Variant
NIPA2 transcript variant X6	XM_006720364.2:c.	N/A	Intron Variant
NIPA2 transcript variant X18	XM_006720365.2:c.	N/A	Intron Variant
NIPA2 transcript variant X23	XM_006720366.3:c.	N/A	Intron Variant
NIPA2 transcript variant X25	XM_006720367.1:c.	N/A	Intron Variant
NIPA2 transcript variant X4	XM_011543877.2:c.	N/A	Intron Variant
NIPA2 transcript variant X12	XM_011543878.2:c.	N/A	Intron Variant
NIPA2 transcript variant X14	XM_011543879.2:c.	N/A	Intron Variant
NIPA2 transcript variant X13	XM_011543880.2:c.	N/A	Intron Variant
NIPA2 transcript variant X5	XM_017022645.1:c.	N/A	Intron Variant
NIPA2 transcript variant X7	XM_017022646.1:c.	N/A	Intron Variant
NIPA2 transcript variant X8	XM_017022647.1:c.	N/A	Intron Variant
NIPA2 transcript variant X9	XM_017022648.1:c.	N/A	Intron Variant
NIPA2 transcript variant X11	XM_017022649.1:c.	N/A	Intron Variant
NIPA2 transcript variant X15	XM_017022650.1:c.	N/A	Intron Variant
NIPA2 transcript variant X16	XM_017022651.1:c.	N/A	Intron Variant
NIPA2 transcript variant X17	XM_017022652.1:c.	N/A	Intron Variant
NIPA2 transcript variant X19	XM_017022653.1:c.	N/A	Intron Variant
NIPA2 transcript variant X21	XM_017022654.1:c.	N/A	Intron Variant
NIPA2 transcript variant X26	XM_017022655.1:c.	N/A	Intron Variant
NIPA2 transcript variant X27	XM_017022656.1:c.	N/A	Intron Variant
NIPA2 transcript variant X28	XM_017022657.1:c.	N/A	Intron Variant
NIPA2 transcript variant X29	XM_017022658.1:c.	N/A	Intron Variant
NIPA2 transcript variant X30	XM_017022659.1:c.	N/A	Intron Variant
NIPA2 transcript variant X31	XM_017022660.1:c.	N/A	Intron Variant
NIPA2 transcript variant X32	XM_017022661.1:c.	N/A	Intron Variant
NIPA2 transcript variant X33	XM_017022662.1:c.	N/A	Intron Variant
NIPA2 transcript variant X34	XM_017022663.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.769	C=0.231
1000Genomes	American	Sub	694	G=0.690	C=0.310
1000Genomes	East Asian	Sub	1008	G=0.758	C=0.242
1000Genomes	Europe	Sub	1006	G=0.820	C=0.180
1000Genomes	Global	Study-wide	5008	G=0.773	C=0.227
1000Genomes	South Asian	Sub	978	G=0.800	C=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.842	C=0.158
The Genome Aggregation Database	African	Sub	8708	G=0.774	C=0.226
The Genome Aggregation Database	American	Sub	832	G=0.660	C=0.340
The Genome Aggregation Database	East Asian	Sub	1614	G=0.733	C=0.267
The Genome Aggregation Database	Europe	Sub	18462	G=0.817	C=0.182
The Genome Aggregation Database	Global	Study-wide	29918	G=0.795	C=0.204
The Genome Aggregation Database	Other	Sub	302	G=0.760	C=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.799	C=0.200
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.833	C=0.167

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs3764213	9.31E-05	nicotine smoking	19268276

eQTL of rs3764213 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 rs3764213 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 )
chr15	22978893	22978943	E067	-48724
chr15	22979056	22979163	E067	-48504
chr15	22979181	22979311	E067	-48356
chr15	22994608	22994867	E067	-32800
chr15	23011309	23011373	E067	-16294
chr15	23011615	23011797	E067	-15870
chr15	23031742	23031849	E067	4075
chr15	23031990	23032030	E067	4323
chr15	23032268	23032475	E067	4601
chr15	22984490	22985628	E068	-42039
chr15	22985698	22985758	E068	-41909
chr15	22994608	22994867	E068	-32800
chr15	23031990	23032030	E068	4323
chr15	23032268	23032475	E068	4601
chr15	23056895	23057235	E068	29228
chr15	23066020	23066070	E068	38353
chr15	23066076	23066116	E068	38409
chr15	22984295	22984431	E069	-43236
chr15	22984490	22985628	E069	-42039
chr15	22985698	22985758	E069	-41909
chr15	22986146	22986199	E069	-41468
chr15	22994608	22994867	E069	-32800
chr15	22996487	22996864	E069	-30803
chr15	23060970	23061117	E069	33303
chr15	23061138	23061365	E069	33471
chr15	23031990	23032030	E070	4323
chr15	23032268	23032475	E070	4601
chr15	22984490	22985628	E071	-42039
chr15	22985698	22985758	E071	-41909
chr15	22994608	22994867	E071	-32800
chr15	23011185	23011225	E071	-16442
chr15	23011309	23011373	E071	-16294
chr15	23011615	23011797	E071	-15870
chr15	23031648	23031713	E071	3981
chr15	23031742	23031849	E071	4075
chr15	23031990	23032030	E071	4323
chr15	23032268	23032475	E071	4601
chr15	23060970	23061117	E071	33303
chr15	23061138	23061365	E071	33471
chr15	23064674	23064793	E071	37007
chr15	22983620	22983695	E072	-43972
chr15	22983781	22983831	E072	-43836
chr15	22983909	22983972	E072	-43695
chr15	22984490	22985628	E072	-42039
chr15	22985698	22985758	E072	-41909
chr15	22994608	22994867	E072	-32800
chr15	22995101	22995168	E072	-32499
chr15	23011185	23011225	E072	-16442
chr15	23011309	23011373	E072	-16294
chr15	23060970	23061117	E072	33303
chr15	23061138	23061365	E072	33471
chr15	23066020	23066070	E072	38353
chr15	23066076	23066116	E072	38409
chr15	23067619	23067687	E072	39952
chr15	23077153	23077246	E072	49486
chr15	23077303	23077521	E072	49636
chr15	22984490	22985628	E073	-42039
chr15	22985698	22985758	E073	-41909
chr15	23060970	23061117	E073	33303
chr15	23061138	23061365	E073	33471
chr15	23066020	23066070	E073	38353
chr15	23066076	23066116	E073	38409
chr15	22984490	22985628	E074	-42039
chr15	22985698	22985758	E074	-41909
chr15	22994608	22994867	E074	-32800
chr15	22995101	22995168	E074	-32499
chr15	23011185	23011225	E074	-16442
chr15	23011309	23011373	E074	-16294
chr15	23011615	23011797	E074	-15870
chr15	23032268	23032475	E074	4601
chr15	23060970	23061117	E074	33303
chr15	23061138	23061365	E074	33471
chr15	23066020	23066070	E074	38353
chr15	23066076	23066116	E074	38409
chr15	22996487	22996864	E081	-30803
chr15	22997378	22997461	E081	-30206
chr15	22997590	22997693	E081	-29974
chr15	22997930	22997997	E081	-29670
chr15	23031181	23031237	E081	3514
chr15	23031495	23031545	E081	3828
chr15	23031648	23031713	E081	3981
chr15	23031742	23031849	E081	4075
chr15	23031990	23032030	E081	4323
chr15	23032268	23032475	E081	4601
chr15	22996487	22996864	E082	-30803
chr15	23031495	23031545	E082	3828
chr15	23031648	23031713	E082	3981
chr15	23031742	23031849	E082	4075
chr15	23031990	23032030	E082	4323
chr15	23032268	23032475	E082	4601

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	23033335	23035603	E067	5668
chr15	23032793	23033294	E068	5126
chr15	23033335	23035603	E068	5668
chr15	23033335	23035603	E069	5668
chr15	23032793	23033294	E070	5126
chr15	23033335	23035603	E070	5668
chr15	23032793	23033294	E071	5126
chr15	23033335	23035603	E071	5668
chr15	23032793	23033294	E072	5126
chr15	23033335	23035603	E072	5668
chr15	23032793	23033294	E073	5126
chr15	23033335	23035603	E073	5668
chr15	23032793	23033294	E074	5126
chr15	23033335	23035603	E074	5668
chr15	23032793	23033294	E081	5126
chr15	23032793	23033294	E082	5126
chr15	23033335	23035603	E082	5668