rs576434

Homo sapiens
T>C
SMAD9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0427 (12766/29858,GnomAD)
C=0427 (12436/29116,TOPMED)
C=0425 (2127/5008,1000G)
C=0434 (1671/3854,ALSPAC)
C=0460 (1707/3708,TWINSUK)
chr13:36884002 (GRCh38.p7) (13q13.3)
AD
GWASdb2
2   publication(s)
See rs on genome
41 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.36884002T>C
GRCh37.p13 chr 13NC_000013.10:g.37458139T>C
SMAD9 RefSeqGene LRG_703

Gene: SMAD9, SMAD family member 9(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SMAD9 transcript variant aNM_001127217.2:c.N/AIntron Variant
SMAD9 transcript variant bNM_005905.5:c.N/AIntron Variant
SMAD9 transcript variant X3XM_005266403.3:c.N/AIntron Variant
SMAD9 transcript variant X4XM_005266404.3:c.N/AIntron Variant
SMAD9 transcript variant X1XM_006719827.3:c.N/AIntron Variant
SMAD9 transcript variant X2XM_005266401.3:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.570C=0.430
1000GenomesAmericanSub694T=0.620C=0.380
1000GenomesEast AsianSub1008T=0.583C=0.417
1000GenomesEuropeSub1006T=0.549C=0.451
1000GenomesGlobalStudy-wide5008T=0.575C=0.425
1000GenomesSouth AsianSub978T=0.570C=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.566C=0.434
The Genome Aggregation DatabaseAfricanSub8688T=0.551C=0.449
The Genome Aggregation DatabaseAmericanSub834T=0.610C=0.390
The Genome Aggregation DatabaseEast AsianSub1616T=0.588C=0.412
The Genome Aggregation DatabaseEuropeSub18418T=0.580C=0.419
The Genome Aggregation DatabaseGlobalStudy-wide29858T=0.572C=0.427
The Genome Aggregation DatabaseOtherSub302T=0.500C=0.500
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.572C=0.427
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.540C=0.460
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
21984931Genetic variants in TGF-beta pathway are associated with ovarian cancer risk.Yin JPLoS One

P-Value

SNP ID p-value Traits Study
rs5764340.00061alcohol dependence20201924

eQTL of rs576434 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr13:37458139SMAD9ENSG00000120693.9T>C8.4286e-5-36763Cerebellum

meQTL of rs576434 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 )
chr133745847737458539E067338
chr133748676337486857E06728624
chr133748727137487336E06729132
chr133748761137487665E06729472
chr133748771437487796E06729575
chr133745520837455422E068-2717
chr133749047437490601E06832335
chr133749143937491998E06833300
chr133742281837423047E069-35092
chr133742305737423349E069-34790
chr133744649937446628E069-11511
chr133749016237490339E06932023
chr133749047437490601E06932335
chr133749115137491249E06933012
chr133745520837455422E070-2717
chr133749016237490339E07032023
chr133749143937491998E07033300
chr133749234737492419E07034208
chr133745874237458912E071603
chr133749047437490601E07132335
chr133749115137491249E07133012
chr133749143937491998E07133300
chr133748873637489524E07230597
chr133749016237490339E07232023
chr133749047437490601E07232335
chr133745802937458144E0730
chr133748873637489524E07330597
chr133745802937458144E0740
chr133745874237458912E074603
chr133749047437490601E07432335
chr133749115137491249E07433012
chr133749143937491998E07433300
chr133749234737492419E07434208
chr133749016237490339E08132023
chr133749047437490601E08132335
chr133747815537478779E08220016
chr133747892137478971E08220782
chr133749016237490339E08232023
chr133749047437490601E08232335
chr133749115137491249E08233012
chr133749143937491998E08233300










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr133749243137495665E06734292
chr133749243137495665E06834292
chr133749243137495665E06934292
chr133749243137495665E07034292
chr133749243137495665E07134292
chr133749243137495665E07234292
chr133749243137495665E07334292
chr133749243137495665E07434292
chr133749243137495665E08234292