rs9824246

Homo sapiens
A>G
PPP4R2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0071 (2147/29960,GnomAD)
G=0093 (2717/29118,TOPMED)
G=0078 (389/5008,1000G)
G=0042 (163/3854,ALSPAC)
G=0043 (158/3708,TWINSUK)
chr3:73053574 (GRCh38.p7) (3p13)
ND
GWASdb2
1   publication(s)
See rs on genome
210 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.73053574A>G
GRCh37.p13 chr 3NC_000003.11:g.73102725A>G

Gene: PPP4R2, protein phosphatase 4 regulatory subunit 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PPP4R2 transcript variant 2NM_001318025.1:c.N/AIntron Variant
PPP4R2 transcript variant 3NM_001318026.1:c.N/AIntron Variant
PPP4R2 transcript variant 4NM_001318027.1:c.N/AIntron Variant
PPP4R2 transcript variant 1NM_174907.3:c.N/AIntron Variant
PPP4R2 transcript variant 5NM_001318028.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.845G=0.155
1000GenomesAmericanSub694A=0.900G=0.100
1000GenomesEast AsianSub1008A=0.975G=0.025
1000GenomesEuropeSub1006A=0.954G=0.046
1000GenomesGlobalStudy-wide5008A=0.922G=0.078
1000GenomesSouth AsianSub978A=0.950G=0.050
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.958G=0.042
The Genome Aggregation DatabaseAfricanSub8706A=0.854G=0.146
The Genome Aggregation DatabaseAmericanSub838A=0.900G=0.100
The Genome Aggregation DatabaseEast AsianSub1620A=0.977G=0.023
The Genome Aggregation DatabaseEuropeSub18494A=0.960G=0.039
The Genome Aggregation DatabaseGlobalStudy-wide29960A=0.928G=0.071
The Genome Aggregation DatabaseOtherSub302A=0.910G=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.906G=0.093
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.957G=0.043
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
rs98242469.95E-05nicotine smoking19268276

eQTL of rs9824246 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 rs9824246 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 )
chr37305763573057713E067-45012
chr37305837373058433E067-44292
chr37305869573058745E067-43980
chr37305905573059164E067-43561
chr37305928473059844E067-42881
chr37306787873067981E067-34744
chr37306809773068177E067-34548
chr37306835773068467E067-34258
chr37307406373074310E067-28415
chr37307470673074800E067-27925
chr37307497473075024E067-27701
chr37307548373075719E067-27006
chr37307603873076088E067-26637
chr37307826073079141E067-23584
chr37307943973079581E067-23144
chr37307969173079735E067-22990
chr37308656073086734E067-15991
chr37308707573087474E067-15251
chr37308775673087911E067-14814
chr37308797173088109E067-14616
chr37309081573090976E067-11749
chr37309552373095631E067-7094
chr37310199473102044E067-681
chr37310214473102303E067-422
chr37310513973105238E0672414
chr37310528873105435E0672563
chr37310548873105777E0672763
chr37310623373106273E0673508
chr37311998773120357E06717262
chr37305763573057713E068-45012
chr37305828873058338E068-44387
chr37305837373058433E068-44292
chr37305869573058745E068-43980
chr37306219873062248E068-40477
chr37306809773068177E068-34548
chr37306835773068467E068-34258
chr37307406373074310E068-28415
chr37307470673074800E068-27925
chr37307497473075024E068-27701
chr37307548373075719E068-27006
chr37307603873076088E068-26637
chr37307784673077896E068-24829
chr37307826073079141E068-23584
chr37307943973079581E068-23144
chr37308093073081058E068-21667
chr37308622173086540E068-16185
chr37308656073086734E068-15991
chr37308707573087474E068-15251
chr37309081573090976E068-11749
chr37310199473102044E068-681
chr37310214473102303E068-422
chr37310513973105238E0682414
chr37310528873105435E0682563
chr37310548873105777E0682763
chr37310623373106273E0683508
chr37311998773120357E06817262
chr37312036873120534E06817643
chr37312061373120775E06817888
chr37314993873150768E06847213
chr37315082173150873E06848096
chr37315094373151362E06848218
chr37305763573057713E069-45012
chr37305828873058338E069-44387
chr37305837373058433E069-44292
chr37305869573058745E069-43980
chr37305905573059164E069-43561
chr37306219873062248E069-40477
chr37306787873067981E069-34744
chr37306809773068177E069-34548
chr37306835773068467E069-34258
chr37307406373074310E069-28415
chr37307470673074800E069-27925
chr37307497473075024E069-27701
chr37307548373075719E069-27006
chr37307603873076088E069-26637
chr37307826073079141E069-23584
chr37307943973079581E069-23144
chr37307969173079735E069-22990
chr37308585873086025E069-16700
chr37308604673086136E069-16589
chr37308622173086540E069-16185
chr37308656073086734E069-15991
chr37308707573087474E069-15251
chr37308775673087911E069-14814
chr37308797173088109E069-14616
chr37309081573090976E069-11749
chr37309372673093806E069-8919
chr37309385873093908E069-8817
chr37309401873094058E069-8667
chr37309437173094486E069-8239
chr37309469573094790E069-7935
chr37309490473094969E069-7756
chr37309552373095631E069-7094
chr37310199473102044E069-681
chr37310214473102303E069-422
chr37311998773120357E06917262
chr37314993873150768E06947213
chr37308585873086025E070-16700
chr37314993873150768E07047213
chr37305763573057713E071-45012
chr37305828873058338E071-44387
chr37305837373058433E071-44292
chr37305869573058745E071-43980
chr37305905573059164E071-43561
chr37305928473059844E071-42881
chr37306787873067981E071-34744
chr37306809773068177E071-34548
chr37306835773068467E071-34258
chr37307406373074310E071-28415
chr37307470673074800E071-27925
chr37307497473075024E071-27701
chr37307548373075719E071-27006
chr37307603873076088E071-26637
chr37307784673077896E071-24829
chr37307826073079141E071-23584
chr37307943973079581E071-23144
chr37308093073081058E071-21667
chr37308311373083167E071-19558
chr37308505873085108E071-17617
chr37308585873086025E071-16700
chr37308604673086136E071-16589
chr37308622173086540E071-16185
chr37308656073086734E071-15991
chr37308707573087474E071-15251
chr37308775673087911E071-14814
chr37308797173088109E071-14616
chr37308942873089485E071-13240
chr37309081573090976E071-11749
chr37309138473091497E071-11228
chr37309174073091822E071-10903
chr37309372673093806E071-8919
chr37310467173104721E0711946
chr37310486973105039E0712144
chr37310513973105238E0712414
chr37310528873105435E0712563
chr37310548873105777E0712763
chr37310623373106273E0713508
chr37305727973057404E072-45321
chr37305763573057713E072-45012
chr37305828873058338E072-44387
chr37305837373058433E072-44292
chr37305869573058745E072-43980
chr37305905573059164E072-43561
chr37307406373074310E072-28415
chr37307470673074800E072-27925
chr37307497473075024E072-27701
chr37307603873076088E072-26637
chr37307784673077896E072-24829
chr37307826073079141E072-23584
chr37308585873086025E072-16700
chr37308604673086136E072-16589
chr37308622173086540E072-16185
chr37308656073086734E072-15991
chr37308707573087474E072-15251
chr37310486973105039E0722144
chr37310513973105238E0722414
chr37310528873105435E0722563
chr37310548873105777E0722763
chr37314993873150768E07247213
chr37307406373074310E073-28415
chr37308656073086734E073-15991
chr37310513973105238E0732414
chr37310528873105435E0732563
chr37310548873105777E0732763
chr37310595873106011E0733233
chr37313499573135945E07332270
chr37305727973057404E074-45321
chr37305763573057713E074-45012
chr37305828873058338E074-44387
chr37305837373058433E074-44292
chr37305869573058745E074-43980
chr37305905573059164E074-43561
chr37305928473059844E074-42881
chr37306787873067981E074-34744
chr37306809773068177E074-34548
chr37306835773068467E074-34258
chr37307406373074310E074-28415
chr37307470673074800E074-27925
chr37307497473075024E074-27701
chr37307548373075719E074-27006
chr37307603873076088E074-26637
chr37307826073079141E074-23584
chr37307943973079581E074-23144
chr37307969173079735E074-22990
chr37308093073081058E074-21667
chr37308311373083167E074-19558
chr37308585873086025E074-16700
chr37308604673086136E074-16589
chr37308622173086540E074-16185
chr37308656073086734E074-15991
chr37308707573087474E074-15251
chr37308775673087911E074-14814
chr37308797173088109E074-14616
chr37309081573090976E074-11749
chr37309372673093806E074-8919
chr37309385873093908E074-8817
chr37309401873094058E074-8667
chr37309437173094486E074-8239
chr37309469573094790E074-7935
chr37309490473094969E074-7756
chr37309552373095631E074-7094
chr37310486973105039E0742144
chr37310513973105238E0742414
chr37310528873105435E0742563
chr37310548873105777E0742763
chr37312036873120534E07417643
chr37314993873150768E08147213
chr37305828873058338E082-44387
chr37305837373058433E082-44292
chr37309138473091497E082-11228