SNP Detail Info-rs2193225

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.50852344T>C
GRCh37.p13 chr 2	NC_000002.11:g.51079482T>C
NRXN1 RefSeqGene	NG_011878.1:g.185193A>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=0.844	C=0.156
1000Genomes	American	Sub	694	T=0.670	C=0.330
1000Genomes	East Asian	Sub	1008	T=0.832	C=0.168
1000Genomes	Europe	Sub	1006	T=0.468	C=0.532
1000Genomes	Global	Study-wide	5008	T=0.705	C=0.295
1000Genomes	South Asian	Sub	978	T=0.650	C=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.448	C=0.552
The Genome Aggregation Database	African	Sub	8722	T=0.773	C=0.227
The Genome Aggregation Database	American	Sub	834	T=0.640	C=0.360
The Genome Aggregation Database	East Asian	Sub	1612	T=0.833	C=0.167
The Genome Aggregation Database	Europe	Sub	18470	T=0.472	C=0.528
The Genome Aggregation Database	Global	Study-wide	29940	T=0.583	C=0.416
The Genome Aggregation Database	Other	Sub	302	T=0.450	C=0.550
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.628	C=0.371
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.456	C=0.544

PMID	Title	Author	Journal
18270208	Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers.	Nussbaum J	Hum Mol Genet
27166759	Converging findings from linkage and association analyses on susceptibility genes for smoking and other addictions.	Yang J	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2193225	0.001	Drug response to nicotine	18270208

eQTL of rs2193225 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 rs2193225 in Fetal Brain

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	51086414	51086474	E067	6932
chr2	51058808	51059417	E069	-20065
chr2	51059490	51059625	E069	-19857
chr2	51085437	51085624	E069	5955
chr2	51048187	51048237	E070	-31245
chr2	51057065	51057315	E070	-22167
chr2	51057720	51057774	E070	-21708
chr2	51058808	51059417	E070	-20065
chr2	51059490	51059625	E070	-19857
chr2	51085026	51085112	E070	5544
chr2	51085437	51085624	E070	5955
chr2	51085790	51085834	E070	6308
chr2	51086414	51086474	E070	6932
chr2	51089596	51089661	E070	10114
chr2	51090910	51091289	E070	11428
chr2	51058808	51059417	E071	-20065
chr2	51058808	51059417	E072	-20065
chr2	51059490	51059625	E072	-19857
chr2	51090910	51091289	E072	11428
chr2	51058808	51059417	E073	-20065
chr2	51065589	51065750	E074	-13732
chr2	51065874	51066011	E074	-13471
chr2	51090910	51091289	E074	11428
chr2	51057065	51057315	E081	-22167
chr2	51058808	51059417	E081	-20065
chr2	51059490	51059625	E081	-19857
chr2	51059973	51060124	E081	-19358
chr2	51077872	51077975	E081	-1507
chr2	51083195	51083314	E081	3713
chr2	51083431	51083593	E081	3949
chr2	51083888	51084235	E081	4406
chr2	51085026	51085112	E081	5544
chr2	51102821	51102924	E081	23339
chr2	51104587	51104828	E081	25105
chr2	51057065	51057315	E082	-22167
chr2	51057720	51057774	E082	-21708
chr2	51058808	51059417	E082	-20065
chr2	51059490	51059625	E082	-19857
chr2	51081469	51081623	E082	1987
chr2	51081736	51081861	E082	2254
chr2	51083195	51083314	E082	3713

rs2193225

Genomic Coordinates

Gene: NRXN1, neurexin 1(minus strand)

Population Frequency

P-Value

eQTL of rs2193225 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2193225 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)