rs17780175

Homo sapiens
G>A
PDE4D : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0284 (8489/29894,GnomAD)
A=0291 (8486/29118,TOPMED)
A=0231 (1156/5008,1000G)
A=0299 (1153/3854,ALSPAC)
A=0297 (1101/3708,TWINSUK)
chr5:59293960 (GRCh38.p7) (5q11.2)
ND
GWASdb2
1   publication(s)
See rs on genome
124 Enhancers around
31 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.59293960G>A
GRCh37.p13 chr 5NC_000005.9:g.58589786G>A
PDE4D RefSeqGeneNG_027957.1:g.1199140C>T

Gene: PDE4D, phosphodiesterase 4D(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PDE4D transcript variant 1NM_001104631.1:c.N/AIntron Variant
PDE4D transcript variant 3NM_001165899.1:c.N/AIntron Variant
PDE4D transcript variant 4NM_001197218.1:c.N/AIntron Variant
PDE4D transcript variant 5NM_001197219.1:c.N/AIntron Variant
PDE4D transcript variant 2NM_006203.4:c.N/AIntron Variant
PDE4D transcript variant 6NM_001197220.1:c.N/AGenic Upstream Transcript Variant
PDE4D transcript variant 7NM_001197221.1:c.N/AGenic Upstream Transcript Variant
PDE4D transcript variant 8NM_001197222.1:c.N/AGenic Upstream Transcript Variant
PDE4D transcript variant 9NM_001197223.1:c.N/AGenic Upstream Transcript Variant
PDE4D transcript variant X9XM_005248537.3:c.N/AIntron Variant
PDE4D transcript variant X11XM_005248538.4:c.N/AIntron Variant
PDE4D transcript variant X1XM_011543469.1:c.N/AIntron Variant
PDE4D transcript variant X3XM_011543470.2:c.N/AIntron Variant
PDE4D transcript variant X4XM_011543471.1:c.N/AIntron Variant
PDE4D transcript variant X9XM_011543473.1:c.N/AIntron Variant
PDE4D transcript variant X12XM_011543477.2:c.N/AIntron Variant
PDE4D transcript variant X2XM_017009565.1:c.N/AIntron Variant
PDE4D transcript variant X8XM_017009566.1:c.N/AIntron Variant
PDE4D transcript variant X10XM_017009567.1:c.N/AIntron Variant
PDE4D transcript variant X8XM_017009568.1:c.N/AIntron Variant
PDE4D transcript variant X10XM_017009569.1:c.N/AIntron Variant
PDE4D transcript variant X13XM_017009570.1:c.N/AIntron Variant
PDE4D transcript variant X14XM_017009571.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.783A=0.217
1000GenomesAmericanSub694G=0.540A=0.460
1000GenomesEast AsianSub1008G=0.945A=0.055
1000GenomesEuropeSub1006G=0.708A=0.292
1000GenomesGlobalStudy-wide5008G=0.769A=0.231
1000GenomesSouth AsianSub978G=0.790A=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.701A=0.299
The Genome Aggregation DatabaseAfricanSub8712G=0.745A=0.255
The Genome Aggregation DatabaseAmericanSub834G=0.500A=0.500
The Genome Aggregation DatabaseEast AsianSub1596G=0.951A=0.049
The Genome Aggregation DatabaseEuropeSub18450G=0.693A=0.306
The Genome Aggregation DatabaseGlobalStudy-wide29894G=0.716A=0.284
The Genome Aggregation DatabaseOtherSub302G=0.610A=0.390
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.708A=0.291
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.703A=0.297
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs177801750.000265nicotine smoking19268276

eQTL of rs17780175 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 rs17780175 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 )
chr55854109658541326E067-48460
chr55854135958541458E067-48328
chr55854151558541573E067-48213
chr55854168258541743E067-48043
chr55854189858541938E067-47848
chr55854208158542160E067-47626
chr55854223458542295E067-47491
chr55854234458542454E067-47332
chr55854247858542729E067-47057
chr55855188358551933E067-37853
chr55855197458552573E067-37213
chr55861277258614013E06722986
chr55861411058614250E06724324
chr55861459858614670E06724812
chr55861471958614855E06724933
chr55861485958615158E06725073
chr55861520058615375E06725414
chr55861550558615617E06725719
chr55861566158615730E06725875
chr55862429458625116E06734508
chr55854109658541326E068-48460
chr55857273858573216E068-16570
chr55859364458593694E0683858
chr55861250558612610E06822719
chr55861277258614013E06822986
chr55861520058615375E06825414
chr55861550558615617E06825719
chr55861566158615730E06825875
chr55854223458542295E069-47491
chr55854234458542454E069-47332
chr55854247858542729E069-47057
chr55855197458552573E069-37213
chr55857273858573216E069-16570
chr55857355158573661E069-16125
chr55861277258614013E06922986
chr55861485958615158E06925073
chr55861520058615375E06925414
chr55861550558615617E06925719
chr55862429458625116E06934508
chr55863145458631593E06941668
chr55863159958632161E06941813
chr55857260758572684E070-17102
chr55857273858573216E070-16570
chr55861277258614013E07022986
chr55861550558615617E07025719
chr55861566158615730E07025875
chr55862429458625116E07034508
chr55854109658541326E071-48460
chr55854135958541458E071-48328
chr55854151558541573E071-48213
chr55854168258541743E071-48043
chr55855188358551933E071-37853
chr55855197458552573E071-37213
chr55857260758572684E071-17102
chr55857273858573216E071-16570
chr55857355158573661E071-16125
chr55858138758581730E071-8056
chr55859364458593694E0713858
chr55861250558612610E07122719
chr55861277258614013E07122986
chr55862429458625116E07134508
chr55862517758625254E07135391
chr55863145458631593E07141668
chr55863159958632161E07141813
chr55857273858573216E072-16570
chr55857355158573661E072-16125
chr55859491058595142E0725124
chr55861277258614013E07222986
chr55861411058614250E07224324
chr55861520058615375E07225414
chr55861550558615617E07225719
chr55861566158615730E07225875
chr55862429458625116E07234508
chr55863145458631593E07241668
chr55863159958632161E07241813
chr55859364458593694E0733858
chr55861277258614013E07322986
chr55861743458617722E07327648
chr55861868458618724E07328898
chr55854109658541326E074-48460
chr55854135958541458E074-48328
chr55854151558541573E074-48213
chr55854295258543056E074-46730
chr55855188358551933E074-37853
chr55855197458552573E074-37213
chr55857260758572684E074-17102
chr55857273858573216E074-16570
chr55857355158573661E074-16125
chr55858138758581730E074-8056
chr55859364458593694E0743858
chr55861277258614013E07422986
chr55861411058614250E07424324
chr55861520058615375E07425414
chr55861550558615617E07425719
chr55861566158615730E07425875
chr55862429458625116E07434508
chr55862517758625254E07435391
chr55863145458631593E07441668
chr55863159958632161E07441813
chr55863228958632586E07442503
chr55863262658632714E07442840
chr55855517258555245E081-34541
chr55857260758572684E081-17102
chr55857273858573216E081-16570
chr55857355158573661E081-16125
chr55861471958614855E08124933
chr55861485958615158E08125073
chr55861520058615375E08125414
chr55861550558615617E08125719
chr55861566158615730E08125875
chr55861892858619026E08129142
chr55862243758622998E08132651
chr55862303858623446E08133252
chr55862348458623728E08133698
chr55862402558624097E08134239
chr55862413558624270E08134349
chr55862429458625116E08134508
chr55862727258627711E08137486
chr55863545858635564E08145672
chr55863812858638248E08148342
chr55863836858638436E08148582
chr55855996058560054E082-29732
chr55861277258614013E08222986
chr55862429458625116E08234508










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55856994258570064E067-19722
chr55857013258570434E067-19352
chr55857043958570610E067-19176
chr55857068358570751E067-19035
chr55857075958572539E067-17247
chr55857013258570434E068-19352
chr55857043958570610E068-19176
chr55857068358570751E068-19035
chr55857075958572539E068-17247
chr55857075958572539E069-17247
chr55857013258570434E071-19352
chr55857043958570610E071-19176
chr55857068358570751E071-19035
chr55857075958572539E071-17247
chr55856924558569416E072-20370
chr55856946058569673E072-20113
chr55856974158569823E072-19963
chr55856994258570064E072-19722
chr55857013258570434E072-19352
chr55857043958570610E072-19176
chr55857068358570751E072-19035
chr55857075958572539E072-17247
chr55856871358569011E073-20775
chr55856904658569129E073-20657
chr55856994258570064E073-19722
chr55857013258570434E073-19352
chr55857043958570610E073-19176
chr55857068358570751E073-19035
chr55857075958572539E073-17247
chr55857075958572539E074-17247
chr55857075958572539E082-17247