rs3742179

Homo sapiens
T>C
TEX29 : 2KB Upstream Variant
ARHGEF7 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0160 (4798/29986,GnomAD)
C=0116 (3396/29118,TOPMED)
C=0244 (1221/5008,1000G)
C=0159 (611/3854,ALSPAC)
C=0153 (569/3708,TWINSUK)
chr13:111305738 (GRCh38.p7) (13q34)
ND
GWASdb2
1   publication(s)
See rs on genome
230 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.111305738T>C
GRCh37.p13 chr 13NC_000013.10:g.111958085T>C

Gene: ARHGEF7, Rho guanine nucleotide exchange factor 7(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
ARHGEF7 transcript variant 5NM_001113513.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant 6NM_001320851.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant 7NM_001320852.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant 8NM_001320853.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant 1NM_003899.3:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant 3NM_001113511.2:c.N/AN/A
ARHGEF7 transcript variant 4NM_001113512.2:c.N/AN/A
ARHGEF7 transcript variant 9NM_001320854.1:c.N/AN/A
ARHGEF7 transcript variant 2NM_145735.3:c.N/AN/A
ARHGEF7 transcript variant X1XM_006719956.3:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X3XM_017020815.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X4XM_017020816.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X6XM_017020818.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X7XM_017020819.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X6XM_017020820.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X9XM_017020821.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X9XM_017020822.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X11XM_017020823.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X12XM_017020824.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X13XM_017020825.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X11XM_017020828.1:c.N/ADownstream Transcript Variant
ARHGEF7 transcript variant X13XM_011521133.2:c.N/AN/A
ARHGEF7 transcript variant X2XM_017020814.1:c.N/AN/A
ARHGEF7 transcript variant X5XM_017020817.1:c.N/AN/A
ARHGEF7 transcript variant X14XM_017020826.1:c.N/AN/A
ARHGEF7 transcript variant X15XM_017020827.1:c.N/AN/A
ARHGEF7 transcript variant X19XM_017020829.1:c.N/AN/A
ARHGEF7 transcript variant X14XR_001749712.1:n.N/AN/A

Gene: TEX29, testis expressed 29(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
TEX29 transcript variant 1NM_001303133.1:c.N/AN/A
TEX29 transcript variant 2NM_152324.2:c.N/AN/A
TEX29 transcript variant X2XM_017020388.1:c.N/AUpstream Transcript Variant
TEX29 transcript variant X1XM_017020387.1:c.N/AN/A
TEX29 transcript variant X3XR_001749478.1:n.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.961C=0.039
1000GenomesAmericanSub694T=0.910C=0.090
1000GenomesEast AsianSub1008T=0.316C=0.684
1000GenomesEuropeSub1006T=0.836C=0.164
1000GenomesGlobalStudy-wide5008T=0.756C=0.244
1000GenomesSouth AsianSub978T=0.740C=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.841C=0.159
The Genome Aggregation DatabaseAfricanSub8732T=0.945C=0.055
The Genome Aggregation DatabaseAmericanSub836T=0.830C=0.170
The Genome Aggregation DatabaseEast AsianSub1620T=0.268C=0.732
The Genome Aggregation DatabaseEuropeSub18496T=0.840C=0.159
The Genome Aggregation DatabaseGlobalStudy-wide29986T=0.840C=0.160
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.883C=0.116
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.847C=0.153
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
rs37421790.0002nicotine smoking19268276

eQTL of rs3742179 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr13:111958085ARHGEF7ENSG00000102606.13T>C1.3191e-16190819Cerebellum

meQTL of rs3742179 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 )
chr13111918686111918748E067-39337
chr13111918938111918995E067-39090
chr13111919133111919183E067-38902
chr13111921309111921433E067-36652
chr13111922005111922155E067-35930
chr13111922160111922265E067-35820
chr13111922418111922844E067-35241
chr13111922995111923055E067-35030
chr13111923173111923436E067-34649
chr13111923640111923739E067-34346
chr13111923780111923870E067-34215
chr13111924720111924816E067-33269
chr13111925207111925267E067-32818
chr13111925359111925465E067-32620
chr13111931724111931783E067-26302
chr13111932959111935073E067-23012
chr13111936041111936112E067-21973
chr13111936460111936664E067-21421
chr13111939024111939095E067-18990
chr13111908834111908897E068-49188
chr13111908995111909038E068-49047
chr13111914720111914829E068-43256
chr13111914870111914997E068-43088
chr13111915114111915342E068-42743
chr13111915436111915541E068-42544
chr13111915852111915902E068-42183
chr13111915967111916107E068-41978
chr13111916468111916650E068-41435
chr13111916786111916848E068-41237
chr13111919133111919183E068-38902
chr13111919259111919319E068-38766
chr13111919564111919627E068-38458
chr13111922160111922265E068-35820
chr13111922418111922844E068-35241
chr13111922995111923055E068-35030
chr13111923173111923436E068-34649
chr13111924720111924816E068-33269
chr13111925207111925267E068-32818
chr13111925359111925465E068-32620
chr13111925834111925878E068-32207
chr13111932959111935073E068-23012
chr13111950867111950917E068-7168
chr13111915114111915342E069-42743
chr13111915436111915541E069-42544
chr13111915852111915902E069-42183
chr13111915967111916107E069-41978
chr13111917835111917957E069-40128
chr13111919259111919319E069-38766
chr13111919564111919627E069-38458
chr13111919668111919797E069-38288
chr13111922005111922155E069-35930
chr13111922160111922265E069-35820
chr13111922418111922844E069-35241
chr13111922995111923055E069-35030
chr13111923173111923436E069-34649
chr13111923640111923739E069-34346
chr13111923780111923870E069-34215
chr13111923998111924073E069-34012
chr13111924720111924816E069-33269
chr13111925207111925267E069-32818
chr13111925359111925465E069-32620
chr13111925834111925878E069-32207
chr13111926088111926219E069-31866
chr13111931003111931161E069-26924
chr13111931168111931673E069-26412
chr13111931724111931783E069-26302
chr13111932739111932953E069-25132
chr13111932959111935073E069-23012
chr13111936460111936664E069-21421
chr13111979363111979413E07021278
chr13111980819111980882E07022734
chr13111981020111981090E07022935
chr13111987397111987447E07029312
chr13111987473111987557E07029388
chr13111987628111988023E07029543
chr13111988119111988169E07030034
chr13111988214111988264E07030129
chr13111914720111914829E071-43256
chr13111914870111914997E071-43088
chr13111915114111915342E071-42743
chr13111915436111915541E071-42544
chr13111915852111915902E071-42183
chr13111915967111916107E071-41978
chr13111916468111916650E071-41435
chr13111916786111916848E071-41237
chr13111917961111918426E071-39659
chr13111918459111918642E071-39443
chr13111918686111918748E071-39337
chr13111918938111918995E071-39090
chr13111919133111919183E071-38902
chr13111919259111919319E071-38766
chr13111919564111919627E071-38458
chr13111919668111919797E071-38288
chr13111922005111922155E071-35930
chr13111922160111922265E071-35820
chr13111922418111922844E071-35241
chr13111922995111923055E071-35030
chr13111923173111923436E071-34649
chr13111923640111923739E071-34346
chr13111923780111923870E071-34215
chr13111923998111924073E071-34012
chr13111924720111924816E071-33269
chr13111925207111925267E071-32818
chr13111925359111925465E071-32620
chr13111925834111925878E071-32207
chr13111926088111926219E071-31866
chr13111926240111926365E071-31720
chr13111926751111926824E071-31261
chr13111935403111935606E071-22479
chr13111936041111936112E071-21973
chr13111936460111936664E071-21421
chr13111936809111936873E071-21212
chr13111936910111936960E071-21125
chr13111937021111937114E071-20971
chr13111908834111908897E072-49188
chr13111908995111909038E072-49047
chr13111914720111914829E072-43256
chr13111914870111914997E072-43088
chr13111915114111915342E072-42743
chr13111915436111915541E072-42544
chr13111915852111915902E072-42183
chr13111915967111916107E072-41978
chr13111916468111916650E072-41435
chr13111916786111916848E072-41237
chr13111917835111917957E072-40128
chr13111917961111918426E072-39659
chr13111918459111918642E072-39443
chr13111918686111918748E072-39337
chr13111918938111918995E072-39090
chr13111919133111919183E072-38902
chr13111919259111919319E072-38766
chr13111919564111919627E072-38458
chr13111919668111919797E072-38288
chr13111922005111922155E072-35930
chr13111922160111922265E072-35820
chr13111922418111922844E072-35241
chr13111922995111923055E072-35030
chr13111923173111923436E072-34649
chr13111923640111923739E072-34346
chr13111923780111923870E072-34215
chr13111923998111924073E072-34012
chr13111924720111924816E072-33269
chr13111925207111925267E072-32818
chr13111925359111925465E072-32620
chr13111925834111925878E072-32207
chr13111926088111926219E072-31866
chr13111926240111926365E072-31720
chr13111931724111931783E072-26302
chr13111931815111932468E072-25617
chr13111932545111932620E072-25465
chr13111932739111932953E072-25132
chr13111932959111935073E072-23012
chr13111936460111936664E072-21421
chr13111936809111936873E072-21212
chr13111936910111936960E072-21125
chr13111937021111937114E072-20971
chr13111945563111945750E072-12335
chr13111914720111914829E073-43256
chr13111914870111914997E073-43088
chr13111915114111915342E073-42743
chr13111915436111915541E073-42544
chr13111915852111915902E073-42183
chr13111915967111916107E073-41978
chr13111917961111918426E073-39659
chr13111918459111918642E073-39443
chr13111918686111918748E073-39337
chr13111918938111918995E073-39090
chr13111919133111919183E073-38902
chr13111919259111919319E073-38766
chr13111919564111919627E073-38458
chr13111922005111922155E073-35930
chr13111922160111922265E073-35820
chr13111922418111922844E073-35241
chr13111924720111924816E073-33269
chr13111925207111925267E073-32818
chr13111925359111925465E073-32620
chr13111936041111936112E073-21973
chr13111938624111938790E073-19295
chr13111939024111939095E073-18990
chr13111939206111939256E073-18829
chr13111914720111914829E074-43256
chr13111914870111914997E074-43088
chr13111915114111915342E074-42743
chr13111915436111915541E074-42544
chr13111915852111915902E074-42183
chr13111915967111916107E074-41978
chr13111916468111916650E074-41435
chr13111916786111916848E074-41237
chr13111917835111917957E074-40128
chr13111917961111918426E074-39659
chr13111918459111918642E074-39443
chr13111918686111918748E074-39337
chr13111918938111918995E074-39090
chr13111919133111919183E074-38902
chr13111919259111919319E074-38766
chr13111919564111919627E074-38458
chr13111919668111919797E074-38288
chr13111920213111920564E074-37521
chr13111920677111920767E074-37318
chr13111920851111920916E074-37169
chr13111920982111921036E074-37049
chr13111921309111921433E074-36652
chr13111922005111922155E074-35930
chr13111922160111922265E074-35820
chr13111922418111922844E074-35241
chr13111922995111923055E074-35030
chr13111923173111923436E074-34649
chr13111923640111923739E074-34346
chr13111923780111923870E074-34215
chr13111923998111924073E074-34012
chr13111924720111924816E074-33269
chr13111925207111925267E074-32818
chr13111925359111925465E074-32620
chr13111925834111925878E074-32207
chr13111926088111926219E074-31866
chr13111926240111926365E074-31720
chr13111987628111988023E07429543
chr13111980819111980882E08122734
chr13111987151111987208E08129066
chr13111987397111987447E08129312
chr13111987473111987557E08129388
chr13111987628111988023E08129543
chr13111988119111988169E08130034
chr13111988214111988264E08130129
chr13111996676111997619E08138591
chr13111914720111914829E082-43256
chr13111914870111914997E082-43088
chr13111987628111988023E08229543
chr13111988119111988169E08230034
chr13111988214111988264E08230129