rs17754467

Homo sapiens
A>G
NRXN3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0172 (5166/29910,GnomAD)
G=0159 (4657/29118,TOPMED)
G=0132 (663/5008,1000G)
G=0231 (892/3854,ALSPAC)
G=0218 (807/3708,TWINSUK)
chr14:78156180 (GRCh38.p7) (14q24.3)
AD
GWASdb2
2   publication(s)
See rs on genome
73 Enhancers around
94 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.78156180A>G
GRCh37.p13 chr 14NC_000014.8:g.78622523A>G

Gene: NRXN3, neurexin 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NRXN3 transcript variant 3NM_001105250.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant 4NM_001272020.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant 1NM_004796.5:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant 2NM_138970.4:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant 5NR_073546.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant 6NR_073547.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X2XM_011537364.2:c.N/AIntron Variant
NRXN3 transcript variant X3XM_017021790.1:c.N/AIntron Variant
NRXN3 transcript variant X4XM_017021791.1:c.N/AIntron Variant
NRXN3 transcript variant X6XM_005268218.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X7XM_006720322.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X21XM_006720323.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X1XM_011537363.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X5XM_011537365.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X9XM_011537366.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X15XM_011537367.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X19XM_011537368.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X20XM_011537369.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X21XM_011537370.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X25XM_011537371.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X26XM_011537372.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X31XM_011537373.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X44XM_011537377.2:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X8XM_017021792.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X10XM_017021793.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X11XM_017021794.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X12XM_017021795.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X13XM_017021796.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X13XM_017021797.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X14XM_017021798.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X17XM_017021799.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X22XM_017021800.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X23XM_017021801.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X24XM_017021802.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X27XM_017021803.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X28XM_017021804.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X29XM_017021805.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X30XM_017021806.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X30XM_017021807.1:c.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X32XR_001750599.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X33XR_001750600.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X34XR_001750601.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X35XR_001750602.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X36XR_001750603.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X37XR_001750604.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X38XR_001750605.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X39XR_001750606.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X40XR_001750607.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X41XR_001750608.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X42XR_001750609.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X44XR_001750610.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X45XR_943561.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X47XR_943562.1:n.N/AGenic Upstream Transcript Variant
NRXN3 transcript variant X46XR_943563.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.909G=0.091
1000GenomesAmericanSub694A=0.840G=0.160
1000GenomesEast AsianSub1008A=0.994G=0.006
1000GenomesEuropeSub1006A=0.776G=0.224
1000GenomesGlobalStudy-wide5008A=0.868G=0.132
1000GenomesSouth AsianSub978A=0.800G=0.200
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.769G=0.231
The Genome Aggregation DatabaseAfricanSub8706A=0.902G=0.098
The Genome Aggregation DatabaseAmericanSub838A=0.830G=0.170
The Genome Aggregation DatabaseEast AsianSub1620A=0.994G=0.006
The Genome Aggregation DatabaseEuropeSub18446A=0.778G=0.222
The Genome Aggregation DatabaseGlobalStudy-wide29910A=0.827G=0.172
The Genome Aggregation DatabaseOtherSub300A=0.760G=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.840G=0.159
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.782G=0.218
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
23691058Dosage transmission disequilibrium test (dTDT) for linkage and association detection.Zhang ZPLoS One

P-Value

SNP ID p-value Traits Study
rs177544670.000000554alcohol dependence23691058
rs177544670.000015Alcohol dependence (early age of onset)20201924
rs177544670.0000155alcoholismpha002892
rs177544670.000027alcohol dependence20201924
rs177544670.0000271alcoholismpha002893

eQTL of rs17754467 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 rs17754467 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 )
chr147859771678597815E067-24708
chr147859808978598345E067-24178
chr147859855078598647E067-23876
chr147863602878636078E06713505
chr147863612678636179E06713603
chr147864417578644711E06721652
chr147864482778644918E06722304
chr147866777678667826E06745253
chr147866800978668120E06745486
chr147859808978598345E068-24178
chr147859855078598647E068-23876
chr147859771678597815E069-24708
chr147859808978598345E069-24178
chr147861859478619202E069-3321
chr147858894478589309E070-33214
chr147858935778589425E070-33098
chr147861925178619349E070-3174
chr147861942178619559E070-2964
chr147861964378619835E070-2688
chr147862372578623775E0701202
chr147862394878623998E0701425
chr147862402278624090E0701499
chr147862432978624389E0701806
chr147862443278624724E0701909
chr147864232578642389E07019802
chr147864248178642554E07019958
chr147864417578644711E07021652
chr147864482778644918E07022304
chr147864769478647744E07025171
chr147864780678647856E07025283
chr147865020478650254E07027681
chr147865038178650441E07027858
chr147865057178650847E07028048
chr147865116078651210E07028637
chr147866056578660615E07038042
chr147866113178661285E07038608
chr147866148778661541E07038964
chr147866231078662364E07039787
chr147866248778662614E07039964
chr147866279378662899E07040270
chr147866380378663909E07041280
chr147866464178664912E07042118
chr147866607578666217E07043552
chr147866632378666373E07043800
chr147866638778666718E07043864
chr147866732078667373E07044797
chr147866746178667511E07044938
chr147866891278669052E07046389
chr147859808978598345E071-24178
chr147859855078598647E071-23876
chr147861859478619202E071-3321
chr147862394878623998E0711425
chr147862402278624090E0711499
chr147862432978624389E0711806
chr147859771678597815E072-24708
chr147859808978598345E072-24178
chr147863602878636078E07213505
chr147863612678636179E07213603
chr147864482778644918E07222304
chr147859808978598345E073-24178
chr147859855078598647E073-23876
chr147865579478655844E07333271
chr147859771678597815E074-24708
chr147859808978598345E074-24178
chr147859855078598647E074-23876
chr147858846078588514E081-34009
chr147858894478589309E081-33214
chr147858935778589425E081-33098
chr147858955178589601E081-32922
chr147858968778589764E081-32759
chr147864780678647856E08125283
chr147866248778662614E08239964
chr147866279378662899E08240270










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr147863637978637216E06713856
chr147863765378637712E06715130
chr147863777678637853E06715253
chr147863795778638049E06715434
chr147863851378638607E06715990
chr147863888578638994E06716362
chr147863911278639185E06716589
chr147863928278639342E06716759
chr147863637978637216E06813856
chr147863765378637712E06815130
chr147863777678637853E06815253
chr147863795778638049E06815434
chr147863851378638607E06815990
chr147863888578638994E06816362
chr147863911278639185E06816589
chr147863928278639342E06816759
chr147863964678639987E06817123
chr147864008078640230E06817557
chr147864029178640341E06817768
chr147864058678640697E06818063
chr147863765378637712E06915130
chr147863777678637853E06915253
chr147863795778638049E06915434
chr147863851378638607E06915990
chr147863888578638994E06916362
chr147863911278639185E06916589
chr147863928278639342E06916759
chr147863964678639987E06917123
chr147863637978637216E07013856
chr147863765378637712E07015130
chr147863777678637853E07015253
chr147863795778638049E07015434
chr147863851378638607E07015990
chr147863888578638994E07016362
chr147863911278639185E07016589
chr147863928278639342E07016759
chr147863964678639987E07017123
chr147864008078640230E07017557
chr147864029178640341E07017768
chr147864058678640697E07018063
chr147864109778641177E07018574
chr147864173778641828E07019214
chr147864216578642229E07019642
chr147863637978637216E07113856
chr147863765378637712E07115130
chr147863777678637853E07115253
chr147863795778638049E07115434
chr147863851378638607E07115990
chr147863637978637216E07213856
chr147863765378637712E07215130
chr147863777678637853E07215253
chr147863795778638049E07215434
chr147863851378638607E07215990
chr147863888578638994E07216362
chr147863911278639185E07216589
chr147863928278639342E07216759
chr147863964678639987E07217123
chr147864008078640230E07217557
chr147864029178640341E07217768
chr147864058678640697E07218063
chr147864109778641177E07218574
chr147863637978637216E07313856
chr147863765378637712E07315130
chr147863777678637853E07315253
chr147863795778638049E07315434
chr147863851378638607E07315990
chr147863888578638994E07316362
chr147863911278639185E07316589
chr147863928278639342E07316759
chr147863765378637712E08115130
chr147863777678637853E08115253
chr147863795778638049E08115434
chr147863851378638607E08115990
chr147863888578638994E08116362
chr147863911278639185E08116589
chr147863928278639342E08116759
chr147863964678639987E08117123
chr147864008078640230E08117557
chr147864029178640341E08117768
chr147864058678640697E08118063
chr147863637978637216E08213856
chr147863765378637712E08215130
chr147863777678637853E08215253
chr147863795778638049E08215434
chr147863851378638607E08215990
chr147863888578638994E08216362
chr147863911278639185E08216589
chr147863928278639342E08216759
chr147863964678639987E08217123
chr147864008078640230E08217557
chr147864029178640341E08217768
chr147864058678640697E08218063
chr147864109778641177E08218574
chr147864173778641828E08219214