rs10490162

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NRXN1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0141 (4223/29848,GnomAD)
C=0136 (3973/29116,TOPMED)
C=0231 (1159/5008,1000G)
C=0110 (424/3854,ALSPAC)
C=0113 (419/3708,TWINSUK)

Position: chr2:51020519 (GRCh38.p7) (2p16.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 65 Enhancers around

Promoter: 126 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.51020519T>C
GRCh37.p13 chr 2	NC_000002.11:g.51247657T>C
NRXN1 RefSeqGene	NG_011878.1:g.17018A>G

Gene: NRXN1, neurexin 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NRXN1 transcript variant alpha2	NM_001135659.1:c.	N/A	Intron Variant
NRXN1 transcript variant alpha1	NM_004801.4:c.	N/A	Intron Variant
NRXN1 transcript variant gamma1	NM_001320156.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant gamma2	NM_001320157.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant beta	NM_138735.2:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X10	XM_005264642.3:c.	N/A	Intron Variant
NRXN1 transcript variant X23	XM_005264643.3:c.	N/A	Intron Variant
NRXN1 transcript variant X31	XM_006712137.3:c.	N/A	Intron Variant
NRXN1 transcript variant X43	XM_006712140.3:c.	N/A	Intron Variant
NRXN1 transcript variant X7	XM_011533167.2:c.	N/A	Intron Variant
NRXN1 transcript variant X12	XM_011533171.2:c.	N/A	Intron Variant
NRXN1 transcript variant X14	XM_011533172.2:c.	N/A	Intron Variant
NRXN1 transcript variant X20	XM_011533174.2:c.	N/A	Intron Variant
NRXN1 transcript variant X24	XM_011533175.2:c.	N/A	Intron Variant
NRXN1 transcript variant X29	XM_011533177.2:c.	N/A	Intron Variant
NRXN1 transcript variant X30	XM_011533178.2:c.	N/A	Intron Variant
NRXN1 transcript variant X39	XM_011533180.2:c.	N/A	Intron Variant
NRXN1 transcript variant X1	XM_017005303.1:c.	N/A	Intron Variant
NRXN1 transcript variant X2	XM_017005304.1:c.	N/A	Intron Variant
NRXN1 transcript variant X3	XM_017005305.1:c.	N/A	Intron Variant
NRXN1 transcript variant X4	XM_017005306.1:c.	N/A	Intron Variant
NRXN1 transcript variant X5	XM_017005307.1:c.	N/A	Intron Variant
NRXN1 transcript variant X6	XM_017005308.1:c.	N/A	Intron Variant
NRXN1 transcript variant X8	XM_017005309.1:c.	N/A	Intron Variant
NRXN1 transcript variant X9	XM_017005310.1:c.	N/A	Intron Variant
NRXN1 transcript variant X11	XM_017005311.1:c.	N/A	Intron Variant
NRXN1 transcript variant X13	XM_017005312.1:c.	N/A	Intron Variant
NRXN1 transcript variant X15	XM_017005313.1:c.	N/A	Intron Variant
NRXN1 transcript variant X16	XM_017005314.1:c.	N/A	Intron Variant
NRXN1 transcript variant X17	XM_017005315.1:c.	N/A	Intron Variant
NRXN1 transcript variant X18	XM_017005316.1:c.	N/A	Intron Variant
NRXN1 transcript variant X19	XM_017005317.1:c.	N/A	Intron Variant
NRXN1 transcript variant X21	XM_017005318.1:c.	N/A	Intron Variant
NRXN1 transcript variant X22	XM_017005319.1:c.	N/A	Intron Variant
NRXN1 transcript variant X25	XM_017005320.1:c.	N/A	Intron Variant
NRXN1 transcript variant X26	XM_017005321.1:c.	N/A	Intron Variant
NRXN1 transcript variant X27	XM_017005322.1:c.	N/A	Intron Variant
NRXN1 transcript variant X28	XM_017005323.1:c.	N/A	Intron Variant
NRXN1 transcript variant X32	XM_017005324.1:c.	N/A	Intron Variant
NRXN1 transcript variant X33	XM_017005325.1:c.	N/A	Intron Variant
NRXN1 transcript variant X34	XM_017005326.1:c.	N/A	Intron Variant
NRXN1 transcript variant X35	XM_017005327.1:c.	N/A	Intron Variant
NRXN1 transcript variant X36	XM_017005328.1:c.	N/A	Intron Variant
NRXN1 transcript variant X37	XM_017005329.1:c.	N/A	Intron Variant
NRXN1 transcript variant X38	XM_017005330.1:c.	N/A	Intron Variant
NRXN1 transcript variant X40	XM_017005331.1:c.	N/A	Intron Variant
NRXN1 transcript variant X41	XM_017005332.1:c.	N/A	Intron Variant
NRXN1 transcript variant X42	XM_017005333.1:c.	N/A	Intron Variant
NRXN1 transcript variant X44	XM_011533183.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X45	XM_017005334.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X46	XM_017005335.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X47	XM_017005336.1:c.	N/A	Genic Upstream Transcript Variant
NRXN1 transcript variant X48	XM_017005337.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.899	C=0.101
1000Genomes	American	Sub	694	T=0.630	C=0.370
1000Genomes	East Asian	Sub	1008	T=0.546	C=0.454
1000Genomes	Europe	Sub	1006	T=0.884	C=0.116
1000Genomes	Global	Study-wide	5008	T=0.769	C=0.231
1000Genomes	South Asian	Sub	978	T=0.800	C=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.890	C=0.110
The Genome Aggregation Database	African	Sub	8712	T=0.900	C=0.100
The Genome Aggregation Database	American	Sub	830	T=0.580	C=0.420
The Genome Aggregation Database	East Asian	Sub	1594	T=0.565	C=0.435
The Genome Aggregation Database	Europe	Sub	18410	T=0.875	C=0.124
The Genome Aggregation Database	Global	Study-wide	29848	T=0.858	C=0.141
The Genome Aggregation Database	Other	Sub	302	T=0.920	C=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.863	C=0.136
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.887	C=0.113

PMID	Title	Author	Journal
21687627	Neurexin-1 and frontal lobe white matter: an overlapping intermediate phenotype for schizophrenia and autism spectrum disorders.	Voineskos AN	PLoS One
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet
18270208	Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers.	Nussbaum J	Hum Mol Genet
24633560	Identification of candidate single-nucleotide polymorphisms in NRXN1 related to antipsychotic treatment response in patients with schizophrenia.	Jenkins A	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs10490162	5.66E-05	nicotine dependence	17158188

eQTL of rs10490162 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 rs10490162 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 )
chr2	51228070	51228356	E067	-19301
chr2	51240153	51241327	E067	-6330
chr2	51241335	51241472	E067	-6185
chr2	51227282	51227401	E068	-20256
chr2	51228070	51228356	E068	-19301
chr2	51228435	51228551	E068	-19106
chr2	51238679	51238729	E068	-8928
chr2	51242027	51242088	E068	-5569
chr2	51242151	51242230	E068	-5427
chr2	51227282	51227401	E069	-20256
chr2	51228070	51228356	E069	-19301
chr2	51228435	51228551	E069	-19106
chr2	51238679	51238729	E069	-8928
chr2	51240153	51241327	E069	-6330
chr2	51241335	51241472	E069	-6185
chr2	51242027	51242088	E069	-5569
chr2	51242151	51242230	E069	-5427
chr2	51206492	51206551	E070	-41106
chr2	51238679	51238729	E070	-8928
chr2	51240153	51241327	E070	-6330
chr2	51241335	51241472	E070	-6185
chr2	51242027	51242088	E070	-5569
chr2	51242151	51242230	E070	-5427
chr2	51246270	51246320	E070	-1337
chr2	51227282	51227401	E071	-20256
chr2	51228070	51228356	E071	-19301
chr2	51228435	51228551	E071	-19106
chr2	51238679	51238729	E071	-8928
chr2	51241335	51241472	E071	-6185
chr2	51242027	51242088	E071	-5569
chr2	51242151	51242230	E071	-5427
chr2	51228070	51228356	E072	-19301
chr2	51238679	51238729	E072	-8928
chr2	51240153	51241327	E073	-6330
chr2	51241335	51241472	E073	-6185
chr2	51242027	51242088	E073	-5569
chr2	51242151	51242230	E073	-5427
chr2	51245135	51245459	E073	-2198
chr2	51227282	51227401	E074	-20256
chr2	51230851	51231029	E074	-16628
chr2	51231066	51231171	E074	-16486
chr2	51231191	51231256	E074	-16401
chr2	51240153	51241327	E074	-6330
chr2	51241335	51241472	E074	-6185
chr2	51206492	51206551	E081	-41106
chr2	51219684	51219740	E081	-27917
chr2	51219873	51219939	E081	-27718
chr2	51227282	51227401	E081	-20256
chr2	51238679	51238729	E081	-8928
chr2	51240153	51241327	E081	-6330
chr2	51241335	51241472	E081	-6185
chr2	51242027	51242088	E081	-5569
chr2	51242151	51242230	E081	-5427
chr2	51245031	51245086	E081	-2571
chr2	51245135	51245459	E081	-2198
chr2	51206492	51206551	E082	-41106
chr2	51219684	51219740	E082	-27917
chr2	51219873	51219939	E082	-27718
chr2	51227282	51227401	E082	-20256
chr2	51228070	51228356	E082	-19301
chr2	51242027	51242088	E082	-5569
chr2	51242151	51242230	E082	-5427
chr2	51245031	51245086	E082	-2571
chr2	51245135	51245459	E082	-2198
chr2	51260665	51260715	E082	13008

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	51252834	51252886	E067	5177
chr2	51252923	51252976	E067	5266
chr2	51253059	51253296	E067	5402
chr2	51253370	51253432	E067	5713
chr2	51253491	51253614	E067	5834
chr2	51253649	51253711	E067	5992
chr2	51253894	51253959	E067	6237
chr2	51253997	51254090	E067	6340
chr2	51255773	51255891	E067	8116
chr2	51256078	51256142	E067	8421
chr2	51256146	51256214	E067	8489
chr2	51257511	51257649	E067	9854
chr2	51258098	51258162	E067	10441
chr2	51258220	51258274	E067	10563
chr2	51258632	51260408	E067	10975
chr2	51252834	51252886	E068	5177
chr2	51252923	51252976	E068	5266
chr2	51253059	51253296	E068	5402
chr2	51253370	51253432	E068	5713
chr2	51253491	51253614	E068	5834
chr2	51253649	51253711	E068	5992
chr2	51253894	51253959	E068	6237
chr2	51253997	51254090	E068	6340
chr2	51257511	51257649	E068	9854
chr2	51258098	51258162	E068	10441
chr2	51258220	51258274	E068	10563
chr2	51258632	51260408	E068	10975
chr2	51253370	51253432	E069	5713
chr2	51253491	51253614	E069	5834
chr2	51253649	51253711	E069	5992
chr2	51253894	51253959	E069	6237
chr2	51253997	51254090	E069	6340
chr2	51255773	51255891	E069	8116
chr2	51256078	51256142	E069	8421
chr2	51256146	51256214	E069	8489
chr2	51257511	51257649	E069	9854
chr2	51258098	51258162	E069	10441
chr2	51258220	51258274	E069	10563
chr2	51258632	51260408	E069	10975
chr2	51252834	51252886	E070	5177
chr2	51252923	51252976	E070	5266
chr2	51253059	51253296	E070	5402
chr2	51253370	51253432	E070	5713
chr2	51253491	51253614	E070	5834
chr2	51253649	51253711	E070	5992
chr2	51253894	51253959	E070	6237
chr2	51253997	51254090	E070	6340
chr2	51257511	51257649	E070	9854
chr2	51258098	51258162	E070	10441
chr2	51258220	51258274	E070	10563
chr2	51258632	51260408	E070	10975
chr2	51253059	51253296	E071	5402
chr2	51253370	51253432	E071	5713
chr2	51253491	51253614	E071	5834
chr2	51253649	51253711	E071	5992
chr2	51253894	51253959	E071	6237
chr2	51253997	51254090	E071	6340
chr2	51255773	51255891	E071	8116
chr2	51256078	51256142	E071	8421
chr2	51256146	51256214	E071	8489
chr2	51257511	51257649	E071	9854
chr2	51258098	51258162	E071	10441
chr2	51258220	51258274	E071	10563
chr2	51258632	51260408	E071	10975
chr2	51252834	51252886	E072	5177
chr2	51252923	51252976	E072	5266
chr2	51253059	51253296	E072	5402
chr2	51253370	51253432	E072	5713
chr2	51253491	51253614	E072	5834
chr2	51253649	51253711	E072	5992
chr2	51253894	51253959	E072	6237
chr2	51253997	51254090	E072	6340
chr2	51255773	51255891	E072	8116
chr2	51256078	51256142	E072	8421
chr2	51256146	51256214	E072	8489
chr2	51257511	51257649	E072	9854
chr2	51258098	51258162	E072	10441
chr2	51258220	51258274	E072	10563
chr2	51258632	51260408	E072	10975
chr2	51252834	51252886	E073	5177
chr2	51252923	51252976	E073	5266
chr2	51253059	51253296	E073	5402
chr2	51253370	51253432	E073	5713
chr2	51253491	51253614	E073	5834
chr2	51253649	51253711	E073	5992
chr2	51253894	51253959	E073	6237
chr2	51253997	51254090	E073	6340
chr2	51255773	51255891	E073	8116
chr2	51256078	51256142	E073	8421
chr2	51256146	51256214	E073	8489
chr2	51257511	51257649	E073	9854
chr2	51258098	51258162	E073	10441
chr2	51258220	51258274	E073	10563
chr2	51258632	51260408	E073	10975
chr2	51253491	51253614	E074	5834
chr2	51253649	51253711	E074	5992
chr2	51253894	51253959	E074	6237
chr2	51253997	51254090	E074	6340
chr2	51257511	51257649	E074	9854
chr2	51258098	51258162	E074	10441
chr2	51258220	51258274	E074	10563
chr2	51258632	51260408	E074	10975
chr2	51252834	51252886	E081	5177
chr2	51252923	51252976	E081	5266
chr2	51253059	51253296	E081	5402
chr2	51253370	51253432	E081	5713
chr2	51253491	51253614	E081	5834
chr2	51253649	51253711	E081	5992
chr2	51253894	51253959	E081	6237
chr2	51253997	51254090	E081	6340
chr2	51257511	51257649	E081	9854
chr2	51258098	51258162	E081	10441
chr2	51258220	51258274	E081	10563
chr2	51258632	51260408	E081	10975
chr2	51252834	51252886	E082	5177
chr2	51252923	51252976	E082	5266
chr2	51253059	51253296	E082	5402
chr2	51253370	51253432	E082	5713
chr2	51253491	51253614	E082	5834
chr2	51253649	51253711	E082	5992
chr2	51253894	51253959	E082	6237
chr2	51253997	51254090	E082	6340
chr2	51257511	51257649	E082	9854
chr2	51258098	51258162	E082	10441
chr2	51258220	51258274	E082	10563
chr2	51258632	51260408	E082	10975