rs10254402

Homo sapiens
T>C / T>G
LHFPL3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0162 (4861/29922,GnomAD)
C=0179 (895/5008,1000G)
C=0053 (205/3854,ALSPAC)
C=0047 (173/3708,TWINSUK)
chr7:104551951 (GRCh38.p7) (7q22.2)
ND
GWASdb2
1   publication(s)
See rs on genome
119 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.104551951T>C
GRCh38.p7 chr 7NC_000007.14:g.104551951T>G
GRCh37.p13 chr 7NC_000007.13:g.104192398T>C
GRCh37.p13 chr 7NC_000007.13:g.104192398T>G

Gene: LHFPL3, lipoma HMGIC fusion partner-like 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LHFPL3 transcriptNM_199000.2:c.N/AIntron Variant
LHFPL3 transcript variant X1XM_005250327.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.547C=0.453
1000GenomesAmericanSub694T=0.950C=0.050
1000GenomesEast AsianSub1008T=0.853C=0.147
1000GenomesEuropeSub1006T=0.937C=0.063
1000GenomesGlobalStudy-wide5008T=0.821C=0.179
1000GenomesSouth AsianSub978T=0.950C=0.050
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.947C=0.053
The Genome Aggregation DatabaseAfricanSub8686T=0.574C=0.426
The Genome Aggregation DatabaseAmericanSub836T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1600T=0.875C=0.125
The Genome Aggregation DatabaseEuropeSub18500T=0.952C=0.047
The Genome Aggregation DatabaseGlobalStudy-wide29922T=0.837C=0.162
The Genome Aggregation DatabaseOtherSub300T=0.880C=0.120
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.953C=0.047
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
rs102544020.000667nicotine smoking19268276

eQTL of rs10254402 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 rs10254402 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 )
chr73660363536603816E067-38207
chr73660385436603923E067-38100
chr73660399236604490E067-37533
chr73664063636641358E068-665
chr73664414936644199E0682126
chr73664421436644264E0682191
chr73664426636644316E0682243
chr73664436636644453E0682343
chr73664451536645185E0682492
chr73664519636645620E0683173
chr73664567136645722E0683648
chr73664575636646593E0683733
chr73664669836646877E0684675
chr73664690236646969E0684879
chr73664700736647081E0684984
chr73664714236647192E0685119
chr73664733536647696E0685312
chr73666348836663544E06821465
chr73666369536663745E06821672
chr73666406136664125E06822038
chr73666824736668297E06826224
chr73660296036603015E069-39008
chr73660312136603264E069-38759
chr73660331436603358E069-38665
chr73660346136603536E069-38487
chr73660363536603816E069-38207
chr73660385436603923E069-38100
chr73660399236604490E069-37533
chr73664037736640469E069-1554
chr73664063636641358E069-665
chr73664436636644453E0692343
chr73664451536645185E0692492
chr73664519636645620E0693173
chr73664567136645722E0693648
chr73664575636646593E0693733
chr73664669836646877E0694675
chr73664690236646969E0694879
chr73664700736647081E0694984
chr73664714236647192E0695119
chr73666276236663174E06920739
chr73666348836663544E06921465
chr73666369536663745E06921672
chr73664575636646593E0703733
chr73664669836646877E0704675
chr73664690236646969E0704879
chr73664700736647081E0704984
chr73664714236647192E0705119
chr73664733536647696E0705312
chr73666066736660863E07018644
chr73666104136661177E07019018
chr73666118236661389E07019159
chr73667185636671914E07029833
chr73667215436672270E07030131
chr73667227236672360E07030249
chr73667240536672569E07030382
chr73667259536672645E07030572
chr73667269036672828E07030667
chr73667565336676598E07033630
chr73660363536603816E071-38207
chr73660385436603923E071-38100
chr73660399236604490E071-37533
chr73664037736640469E071-1554
chr73664063636641358E071-665
chr73664137536641602E071-421
chr73664451536645185E0712492
chr73664519636645620E0713173
chr73664567136645722E0713648
chr73664575636646593E0713733
chr73664669836646877E0714675
chr73664690236646969E0714879
chr73664700736647081E0714984
chr73664714236647192E0715119
chr73664733536647696E0715312
chr73666276236663174E07120739
chr73664063636641358E072-665
chr73664519636645620E0723173
chr73664567136645722E0723648
chr73664575636646593E0723733
chr73664669836646877E0724675
chr73664690236646969E0724879
chr73664700736647081E0724984
chr73664714236647192E0725119
chr73664733536647696E0725312
chr73660363536603816E074-38207
chr73660385436603923E074-38100
chr73660399236604490E074-37533
chr73664063636641358E074-665
chr73664575636646593E0743733
chr73664669836646877E0744675
chr73664733536647696E0745312
chr73666276236663174E07420739
chr73666348836663544E07421465
chr73666369536663745E07421672
chr73666530036665354E07423277
chr73664519636645620E0813173
chr73664567136645722E0813648
chr73664575636646593E0813733
chr73664669836646877E0814675
chr73664690236646969E0814879
chr73664700736647081E0814984
chr73664714236647192E0815119
chr73664733536647696E0815312
chr73665383436653884E08111811
chr73665399236654065E08111969
chr73665408436654143E08112061
chr73666140036661484E08119377
chr73666157936661680E08119556
chr73666178136661831E08119758
chr73667681736676977E08134794
chr73667702636677076E08135003
chr73667713036677457E08135107
chr73668991036689962E08147887
chr73669018836690270E08148165
chr73669054336690700E08148520
chr73669071436690963E08148691
chr73664575636646593E0823733
chr73664669836646877E0824675
chr73667565336676598E08233630
chr73667665036676722E08234627