SNP Detail Info-rs6721498

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.50485874G>A
GRCh37.p13 chr 2	NC_000002.11:g.50713012G>A
NRXN1 RefSeqGene	NG_011878.1:g.551663C>T

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 X44	XM_011533183.1: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 X45	XM_017005334.1:c.	N/A	Intron 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	G=0.478	A=0.522
1000Genomes	American	Sub	694	G=0.640	A=0.360
1000Genomes	East Asian	Sub	1008	G=0.526	A=0.474
1000Genomes	Europe	Sub	1006	G=0.475	A=0.525
1000Genomes	Global	Study-wide	5008	G=0.518	A=0.482
1000Genomes	South Asian	Sub	978	G=0.530	A=0.470
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.485	A=0.515
The Genome Aggregation Database	African	Sub	8704	G=0.500	A=0.500
The Genome Aggregation Database	American	Sub	838	G=0.690	A=0.310
The Genome Aggregation Database	East Asian	Sub	1616	G=0.519	A=0.481
The Genome Aggregation Database	Europe	Sub	18456	G=0.478	A=0.521
The Genome Aggregation Database	Global	Study-wide	29916	G=0.491	A=0.508
The Genome Aggregation Database	Other	Sub	302	G=0.370	A=0.630
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.471	A=0.528
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.482	A=0.518

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
rs6721498	0.001	Drug response to nicotine	18270208

eQTL of rs6721498 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 rs6721498 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	50718734	50718928	E068	5722
chr2	50756335	50756484	E068	43323
chr2	50718734	50718928	E069	5722
chr2	50665423	50665766	E070	-47246
chr2	50666027	50666140	E070	-46872
chr2	50671506	50671724	E070	-41288
chr2	50676095	50676184	E070	-36828
chr2	50676579	50676708	E070	-36304
chr2	50692522	50692603	E070	-20409
chr2	50693872	50694159	E070	-18853
chr2	50695501	50695592	E070	-17420
chr2	50718734	50718928	E070	5722
chr2	50750482	50750532	E070	37470
chr2	50752743	50752802	E070	39731
chr2	50752909	50753076	E070	39897
chr2	50760642	50760732	E070	47630
chr2	50762201	50762351	E070	49189
chr2	50762410	50762700	E070	49398
chr2	50762892	50762988	E070	49880
chr2	50718136	50718692	E071	5124
chr2	50718734	50718928	E071	5722
chr2	50718734	50718928	E072	5722
chr2	50718734	50718928	E073	5722
chr2	50665423	50665766	E081	-47246
chr2	50666027	50666140	E081	-46872
chr2	50684304	50684376	E081	-28636
chr2	50718734	50718928	E081	5722
chr2	50759321	50759416	E081	46309
chr2	50759760	50760013	E081	46748
chr2	50762201	50762351	E081	49189
chr2	50762410	50762700	E081	49398
chr2	50762892	50762988	E081	49880
chr2	50665423	50665766	E082	-47246
chr2	50666027	50666140	E082	-46872
chr2	50675558	50675608	E082	-37404
chr2	50675812	50675973	E082	-37039
chr2	50676095	50676184	E082	-36828
chr2	50676579	50676708	E082	-36304
chr2	50759760	50760013	E082	46748
chr2	50762201	50762351	E082	49189
chr2	50762410	50762700	E082	49398
chr2	50762892	50762988	E082	49880

rs6721498

Genomic Coordinates

Gene: NRXN1, neurexin 1(minus strand)

Population Frequency

P-Value

eQTL of rs6721498 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6721498 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)