rs17101003

Homo sapiens
G>A
NPAS3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0169 (5072/29862,GnomAD)
A=0183 (5351/29118,TOPMED)
A=0152 (760/5008,1000G)
A=0181 (697/3854,ALSPAC)
A=0184 (683/3708,TWINSUK)
chr14:33399174 (GRCh38.p7) (14q13.1)
AD
GWASdb2
1   publication(s)
See rs on genome
211 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.33399174G>A
GRCh37.p13 chr 14NC_000014.8:g.33868380G>A
NPAS3 RefSeqGeneNG_013036.1:g.464922G>A

Gene: NPAS3, neuronal PAS domain protein 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NPAS3 transcript variant 1NM_001164749.1:c.N/AIntron Variant
NPAS3 transcript variant 4NM_001165893.1:c.N/AIntron Variant
NPAS3 transcript variant 2NM_022123.2:c.N/AIntron Variant
NPAS3 transcript variant 3NM_173159.2:c.N/AIntron Variant
NPAS3 transcript variant X3XM_005267991.3:c.N/AIntron Variant
NPAS3 transcript variant X4XM_005267992.3:c.N/AIntron Variant
NPAS3 transcript variant X7XM_011537067.2:c.N/AIntron Variant
NPAS3 transcript variant X5XM_011537069.2:c.N/AIntron Variant
NPAS3 transcript variant X10XM_011537070.2:c.N/AIntron Variant
NPAS3 transcript variant X9XM_011537071.2:c.N/AIntron Variant
NPAS3 transcript variant X11XM_011537072.2:c.N/AIntron Variant
NPAS3 transcript variant X1XM_017021582.1:c.N/AIntron Variant
NPAS3 transcript variant X2XM_017021583.1:c.N/AIntron Variant
NPAS3 transcript variant X6XM_017021584.1:c.N/AIntron Variant
NPAS3 transcript variant X8XM_017021585.1:c.N/AIntron Variant
NPAS3 transcript variant X12XM_017021586.1:c.N/AIntron Variant
NPAS3 transcript variant X13XM_017021587.1:c.N/AIntron Variant
NPAS3 transcript variant X14XM_017021588.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.790A=0.210
1000GenomesAmericanSub694G=0.730A=0.270
1000GenomesEast AsianSub1008G=0.974A=0.026
1000GenomesEuropeSub1006G=0.840A=0.160
1000GenomesGlobalStudy-wide5008G=0.848A=0.152
1000GenomesSouth AsianSub978G=0.890A=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.819A=0.181
The Genome Aggregation DatabaseAfricanSub8702G=0.809A=0.191
The Genome Aggregation DatabaseAmericanSub834G=0.720A=0.280
The Genome Aggregation DatabaseEast AsianSub1594G=0.960A=0.040
The Genome Aggregation DatabaseEuropeSub18432G=0.833A=0.166
The Genome Aggregation DatabaseGlobalStudy-wide29862G=0.830A=0.169
The Genome Aggregation DatabaseOtherSub300G=0.850A=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.816A=0.183
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.816A=0.184
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs171010030.000685alcohol dependence21314694

eQTL of rs17101003 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 rs17101003 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 )
chr143382394333824019E067-44361
chr143382511633825213E067-43167
chr143382536833825744E067-42636
chr143382578333825880E067-42500
chr143382604933826391E067-41989
chr143382650933826665E067-41715
chr143382679733826888E067-41492
chr143382692333827060E067-41320
chr143382725833827386E067-40994
chr143382837033828420E067-39960
chr143382865033828783E067-39597
chr143383367733833791E067-34589
chr143383386733834071E067-34309
chr143383407833834162E067-34218
chr143388897333890269E06720593
chr143390142533901508E06733045
chr143381860533818655E068-49725
chr143381905733819271E068-49109
chr143381959133819957E068-48423
chr143382005633820172E068-48208
chr143382511633825213E068-43167
chr143382536833825744E068-42636
chr143382578333825880E068-42500
chr143382604933826391E068-41989
chr143382650933826665E068-41715
chr143382679733826888E068-41492
chr143382692333827060E068-41320
chr143382725833827386E068-40994
chr143382753133827633E068-40747
chr143382768033828304E068-40076
chr143382837033828420E068-39960
chr143382865033828783E068-39597
chr143382895533829047E068-39333
chr143382915533829369E068-39011
chr143382995033830000E068-38380
chr143383014733830221E068-38159
chr143383022333830323E068-38057
chr143383162533832005E068-36375
chr143383347233833562E068-34818
chr143383367733833791E068-34589
chr143383386733834071E068-34309
chr143383407833834162E068-34218
chr143385553333855633E068-12747
chr143385597833856065E068-12315
chr143385613833856242E068-12138
chr143388897333890269E06820593
chr143390513133905482E06836751
chr143391274233912802E06844362
chr143391283833912888E06844458
chr143391294233913015E06844562
chr143391337933913471E06844999
chr143391348033913596E06845100
chr143391763433917684E06849254
chr143382511633825213E069-43167
chr143382536833825744E069-42636
chr143382578333825880E069-42500
chr143382604933826391E069-41989
chr143382650933826665E069-41715
chr143382679733826888E069-41492
chr143382692333827060E069-41320
chr143382837033828420E069-39960
chr143382865033828783E069-39597
chr143382895533829047E069-39333
chr143382915533829369E069-39011
chr143383203333832129E069-36251
chr143383215933832447E069-35933
chr143383367733833791E069-34589
chr143383386733834071E069-34309
chr143383407833834162E069-34218
chr143385480033854868E069-13512
chr143385492533855036E069-13344
chr143385511633855176E069-13204
chr143385553333855633E069-12747
chr143386290633863084E069-5296
chr143386313133863232E069-5148
chr143390513133905482E06936751
chr143381860533818655E070-49725
chr143382005633820172E070-48208
chr143382060033820656E070-47724
chr143382076333820803E070-47577
chr143382370333823754E070-44626
chr143382375633823806E070-44574
chr143382394333824019E070-44361
chr143382511633825213E070-43167
chr143382536833825744E070-42636
chr143382578333825880E070-42500
chr143382604933826391E070-41989
chr143382650933826665E070-41715
chr143382679733826888E070-41492
chr143382692333827060E070-41320
chr143382725833827386E070-40994
chr143382753133827633E070-40747
chr143382768033828304E070-40076
chr143382837033828420E070-39960
chr143382865033828783E070-39597
chr143383014733830221E070-38159
chr143383317633833359E070-35021
chr143383347233833562E070-34818
chr143383367733833791E070-34589
chr143383386733834071E070-34309
chr143383407833834162E070-34218
chr143383429533834562E070-33818
chr143383473433834788E070-33592
chr143383483533834967E070-33413
chr143383501633835066E070-33314
chr143383564233835692E070-32688
chr143383573033835861E070-32519
chr143384447433844665E070-23715
chr143384517933845302E070-23078
chr143386265333862894E070-5486
chr143386290633863084E070-5296
chr143386313133863232E070-5148
chr143382214733822305E071-46075
chr143382252333822717E071-45663
chr143382511633825213E071-43167
chr143382536833825744E071-42636
chr143382578333825880E071-42500
chr143382604933826391E071-41989
chr143382650933826665E071-41715
chr143382679733826888E071-41492
chr143382692333827060E071-41320
chr143383162533832005E071-36375
chr143383203333832129E071-36251
chr143383215933832447E071-35933
chr143383317633833359E071-35021
chr143383347233833562E071-34818
chr143383367733833791E071-34589
chr143383386733834071E071-34309
chr143383407833834162E071-34218
chr143385480033854868E071-13512
chr143385492533855036E071-13344
chr143385511633855176E071-13204
chr143385553333855633E071-12747
chr143389544133895594E07127061
chr143389568933895792E07127309
chr143382511633825213E072-43167
chr143382536833825744E072-42636
chr143382578333825880E072-42500
chr143382604933826391E072-41989
chr143382650933826665E072-41715
chr143382679733826888E072-41492
chr143382692333827060E072-41320
chr143382725833827386E072-40994
chr143382753133827633E072-40747
chr143382768033828304E072-40076
chr143382837033828420E072-39960
chr143382865033828783E072-39597
chr143382895533829047E072-39333
chr143382915533829369E072-39011
chr143383162533832005E072-36375
chr143383203333832129E072-36251
chr143383215933832447E072-35933
chr143383367733833791E072-34589
chr143383386733834071E072-34309
chr143383407833834162E072-34218
chr143389911233899173E07230732
chr143389929533899336E07230915
chr143389959333899669E07231213
chr143391763433917684E07249254
chr143391804733918175E07249667
chr143382370333823754E073-44626
chr143382375633823806E073-44574
chr143382394333824019E073-44361
chr143382511633825213E073-43167
chr143382536833825744E073-42636
chr143382578333825880E073-42500
chr143382604933826391E073-41989
chr143382650933826665E073-41715
chr143383564233835692E073-32688
chr143385480033854868E073-13512
chr143385492533855036E073-13344
chr143385511633855176E073-13204
chr143391804733918175E07349667
chr143382511633825213E074-43167
chr143382536833825744E074-42636
chr143382578333825880E074-42500
chr143382604933826391E074-41989
chr143382650933826665E074-41715
chr143382679733826888E074-41492
chr143382692333827060E074-41320
chr143382837033828420E074-39960
chr143382865033828783E074-39597
chr143382895533829047E074-39333
chr143382915533829369E074-39011
chr143382995033830000E074-38380
chr143383014733830221E074-38159
chr143383022333830323E074-38057
chr143383347233833562E074-34818
chr143383367733833791E074-34589
chr143383386733834071E074-34309
chr143385480033854868E074-13512
chr143385492533855036E074-13344
chr143385511633855176E074-13204
chr143385553333855633E074-12747
chr143388897333890269E07420593
chr143390513133905482E07436751
chr143390754133907591E07439161
chr143391804733918175E07449667
chr143382060033820656E081-47724
chr143382076333820803E081-47577
chr143382084133820891E081-47489
chr143382536833825744E081-42636
chr143382578333825880E081-42500
chr143382604933826391E081-41989
chr143382650933826665E081-41715
chr143383367733833791E081-34589
chr143383386733834071E081-34309
chr143383407833834162E081-34218
chr143383429533834562E081-33818
chr143388897333890269E08120593
chr143388897333890269E08220593