rs16952906

Homo sapiens
T>C
FTO : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0075 (2269/29988,GnomAD)
C=0113 (565/5008,1000G)
C=0098 (376/3854,ALSPAC)
C=0095 (354/3708,TWINSUK)
chr16:54049255 (GRCh38.p7) (16q12.2)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.54049255T>C
GRCh37.p13 chr 16NC_000016.9:g.54083167T>C
FTO RefSeqGeneNG_012969.1:g.350293T>C

Gene: FTO, fat mass and obesity associated(plus strand)

Molecule type Change Amino acid[Codon] SO Term
FTO transcriptNM_001080432.2:c.N/AIntron Variant
FTO transcript variant X1XM_011523313.2:c.N/AIntron Variant
FTO transcript variant X4XM_011523314.2:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X5XM_011523315.2:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X6XM_011523316.2:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X2XM_017023654.1:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X3XM_017023655.1:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X7XM_017023656.1:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X8XM_017023657.1:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X9XM_017023658.1:c.N/AGenic Downstream Transcript Variant
FTO transcript variant X10XR_001751980.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.918C=0.082
1000GenomesAmericanSub694T=0.930C=0.070
1000GenomesEast AsianSub1008T=0.969C=0.031
1000GenomesEuropeSub1006T=0.893C=0.107
1000GenomesGlobalStudy-wide5008T=0.887C=0.113
1000GenomesSouth AsianSub978T=0.730C=0.270
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.902C=0.098
The Genome Aggregation DatabaseAfricanSub8728T=0.912C=0.088
The Genome Aggregation DatabaseAmericanSub838T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1620T=0.981C=0.019
The Genome Aggregation DatabaseEuropeSub18500T=0.925C=0.074
The Genome Aggregation DatabaseGlobalStudy-wide29988T=0.924C=0.075
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.905C=0.095
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs169529060.000979nicotine dependence17158188

eQTL of rs16952906 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 rs16952906 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 )
chr165404155654041632E067-41535
chr165404167854041732E067-41435
chr165404175054041902E067-41265
chr165408800954088210E0674842
chr165408825254088668E0675085
chr165408879854088960E0675631
chr165409629254096695E06713125
chr165406015454060211E068-22956
chr165406050754060605E068-22562
chr165406093754060991E068-22176
chr165406112854061333E068-21834
chr165407229354072376E068-10791
chr165407238154072473E068-10694
chr165408781454087913E0684647
chr165408800954088210E0684842
chr165408825254088668E0685085
chr165408879854088960E0685631
chr165409671854097712E06813551
chr165412733854127921E06844171
chr165406050754060605E069-22562
chr165406093754060991E069-22176
chr165408800954088210E0694842
chr165408825254088668E0695085
chr165412718254127281E06944015
chr165408305954084087E0700
chr165408716254087257E0703995
chr165408736654087765E0704199
chr165408781454087913E0704647
chr165408800954088210E0704842
chr165408825254088668E0705085
chr165408879854088960E0705631
chr165404155654041632E071-41535
chr165404167854041732E071-41435
chr165404175054041902E071-41265
chr165406050754060605E071-22562
chr165406093754060991E071-22176
chr165406112854061333E071-21834
chr165406136054061470E071-21697
chr165406149154061678E071-21489
chr165408305954084087E0710
chr165408825254088668E0715085
chr165408879854088960E0715631
chr165408904254089406E0715875
chr165408985354090053E0716686
chr165409019954090243E0717032
chr165409024454090324E0717077
chr165409318854093553E07110021
chr165409671854097712E07113551
chr165409775554097830E07114588
chr165408825254088668E0725085
chr165408879854088960E0725631
chr165409671854097712E07213551
chr165412681354126853E07243646
chr165412718254127281E07244015
chr165412733854127921E07244171
chr165412799454128056E07244827
chr165403363254033714E074-49453
chr165404155654041632E074-41535
chr165404167854041732E074-41435
chr165404175054041902E074-41265
chr165406136054061470E074-21697
chr165406149154061678E074-21489
chr165408305954084087E0740
chr165408800954088210E0744842
chr165408825254088668E0745085
chr165408879854088960E0745631
chr165408904254089406E0745875
chr165409671854097712E07413551
chr165409775554097830E07414588
chr165410456354104994E07421396
chr165412681354126853E07443646
chr165412718254127281E07444015
chr165412733854127921E07444171
chr165412799454128056E07444827
chr165408800954088210E0814842
chr165406050754060605E082-22562
chr165406379454063844E082-19323
chr165408781454087913E0824647
chr165408879854088960E0825631
chr165410622254106519E08223055
chr165410656754106687E08223400