rs938413

Homo sapiens
C>T
LPP : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0080 (2427/29986,GnomAD)
C==0122 (3564/29118,TOPMED)
C==0092 (460/5008,1000G)
C==0008 (32/3854,ALSPAC)
C==0010 (37/3708,TWINSUK)
chr3:188646825 (GRCh38.p7) (3q28)
AD
GWASdb2
1   publication(s)
See rs on genome
63 Enhancers around
5 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.188646825C>T
GRCh37.p13 chr 3NC_000003.11:g.188364613C>T
LPP RefSeqGeneNG_016932.2:g.497951C>T

Gene: LPP, LIM domain containing preferred translocation partner in lipoma(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LPP transcript variant 2NM_001167671.2:c.N/AIntron Variant
LPP transcript variant 3NM_001167672.2:c.N/AIntron Variant
LPP transcript variant 1NM_005578.4:c.N/AIntron Variant
LPP transcript variant X4XM_005247446.4:c.N/AIntron Variant
LPP transcript variant X13XM_005247450.4:c.N/AIntron Variant
LPP transcript variant X8XM_005247451.4:c.N/AIntron Variant
LPP transcript variant X13XM_005247453.2:c.N/AIntron Variant
LPP transcript variant X4XM_011512820.2:c.N/AIntron Variant
LPP transcript variant X1XM_011512823.2:c.N/AIntron Variant
LPP transcript variant X11XM_011512827.2:c.N/AIntron Variant
LPP transcript variant X14XM_011512828.2:c.N/AIntron Variant
LPP transcript variant X15XM_011512831.2:c.N/AIntron Variant
LPP transcript variant X3XM_011512833.2:c.N/AIntron Variant
LPP transcript variant X2XM_011512834.2:c.N/AIntron Variant
LPP transcript variant X19XM_011512836.2:c.N/AIntron Variant
LPP transcript variant X6XM_017006377.1:c.N/AIntron Variant
LPP transcript variant X7XM_017006378.1:c.N/AIntron Variant
LPP transcript variant X9XM_017006379.1:c.N/AIntron Variant
LPP transcript variant X11XM_017006380.1:c.N/AIntron Variant
LPP transcript variant X18XM_017006381.1:c.N/AIntron Variant
LPP transcript variant X19XM_017006382.1:c.N/AIntron Variant
LPP transcript variant X17XR_001740144.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.315T=0.685
1000GenomesAmericanSub694C=0.040T=0.960
1000GenomesEast AsianSub1008C=0.000T=1.000
1000GenomesEuropeSub1006C=0.014T=0.986
1000GenomesGlobalStudy-wide5008C=0.092T=0.908
1000GenomesSouth AsianSub978C=0.000T=1.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.008T=0.992
The Genome Aggregation DatabaseAfricanSub8720C=0.259T=0.741
The Genome Aggregation DatabaseAmericanSub838C=0.040T=0.960
The Genome Aggregation DatabaseEast AsianSub1622C=0.000T=1.000
The Genome Aggregation DatabaseEuropeSub18504C=0.006T=0.993
The Genome Aggregation DatabaseGlobalStudy-wide29986C=0.080T=0.919
The Genome Aggregation DatabaseOtherSub302C=0.050T=0.950
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.122T=0.877
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.010T=0.990
PMID Title Author Journal

P-Value

SNP ID p-value Traits Study
rs9384131.27E-11alcohol consumptionpha001402

eQTL of rs938413 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 rs938413 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 )
chr3188341588188341642E067-22971
chr3188364450188364750E0670
chr3188341588188341642E068-22971
chr3188341885188341945E068-22668
chr3188364450188364750E0680
chr3188374016188374776E0689403
chr3188400216188400383E06835603
chr3188400549188400723E06835936
chr3188400775188401307E06836162
chr3188364450188364750E0690
chr3188341588188341642E071-22971
chr3188341885188341945E071-22668
chr3188364450188364750E0710
chr3188397766188397849E07133153
chr3188397954188398272E07133341
chr3188400011188400199E07135398
chr3188400216188400383E07135603
chr3188400549188400723E07135936
chr3188400775188401307E07136162
chr3188406815188407506E07142202
chr3188323709188324188E072-40425
chr3188364450188364750E0720
chr3188397954188398272E07233341
chr3188400216188400383E07235603
chr3188323709188324188E073-40425
chr3188341588188341642E073-22971
chr3188353124188353463E073-11150
chr3188353536188353712E073-10901
chr3188364450188364750E0730
chr3188390385188390550E07325772
chr3188323709188324188E074-40425
chr3188324555188325025E074-39588
chr3188341588188341642E074-22971
chr3188364450188364750E0740
chr3188396942188397022E07432329
chr3188397585188397712E07432972
chr3188397766188397849E07433153
chr3188397954188398272E07433341
chr3188398502188398552E07433889
chr3188398590188398640E07433977
chr3188400549188400723E07435936
chr3188400775188401307E07436162
chr3188342154188342432E081-22181
chr3188377331188377782E08112718
chr3188396942188397022E08132329
chr3188397585188397712E08132972
chr3188397766188397849E08133153
chr3188397954188398272E08133341
chr3188398502188398552E08133889
chr3188398590188398640E08133977
chr3188399690188399744E08135077
chr3188400011188400199E08135398
chr3188400216188400383E08135603
chr3188400549188400723E08135936
chr3188400775188401307E08136162
chr3188385543188386196E08220930
chr3188386372188386477E08221759
chr3188397585188397712E08232972
chr3188397766188397849E08233153
chr3188397954188398272E08233341
chr3188398502188398552E08233889
chr3188398590188398640E08233977
chr3188400216188400383E08235603









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3188411442188411588E07146829
chr3188411442188411588E07246829
chr3188411643188411708E07247030
chr3188411442188411588E07446829
chr3188411643188411708E07447030