rs13169783

Homo sapiens
T>C
SIMC1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0466 (13956/29922,GnomAD)
T==0476 (13885/29118,TOPMED)
C=0488 (2446/5008,1000G)
T==0420 (1619/3854,ALSPAC)
T==0426 (1578/3708,TWINSUK)
chr5:176337365 (GRCh38.p7) (5q35.2)
AD
GWASdb2
1   publication(s)
See rs on genome
24 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.176337365T>C
GRCh37.p13 chr 5NC_000005.9:g.175764368T>C

Gene: SIMC1, SUMO interacting motifs containing 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SIMC1 transcript variant 1NM_001308195.1:c.N/AIntron Variant
SIMC1 transcript variant 3NM_001308196.1:c.N/AIntron Variant
SIMC1 transcript variant 4NM_001308200.1:c.N/AIntron Variant
SIMC1 transcript variant 2NM_198567.5:c.N/AIntron Variant
SIMC1 transcript variant 5NR_131772.1:n.N/AIntron Variant
SIMC1 transcript variant X1XM_011534553.2:c.N/AIntron Variant
SIMC1 transcript variant X2XM_011534554.2:c.N/AIntron Variant
SIMC1 transcript variant X4XM_011534556.2:c.N/AIntron Variant
SIMC1 transcript variant X3XM_017009454.1:c.N/AIntron Variant
SIMC1 transcript variant X5XM_017009455.1:c.N/AIntron Variant
SIMC1 transcript variant X6XM_017009456.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.532C=0.468
1000GenomesAmericanSub694T=0.550C=0.450
1000GenomesEast AsianSub1008T=0.469C=0.531
1000GenomesEuropeSub1006T=0.421C=0.579
1000GenomesGlobalStudy-wide5008T=0.512C=0.488
1000GenomesSouth AsianSub978T=0.600C=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.420C=0.580
The Genome Aggregation DatabaseAfricanSub8704T=0.529C=0.471
The Genome Aggregation DatabaseAmericanSub834T=0.520C=0.480
The Genome Aggregation DatabaseEast AsianSub1610T=0.458C=0.542
The Genome Aggregation DatabaseEuropeSub18474T=0.436C=0.563
The Genome Aggregation DatabaseGlobalStudy-wide29922T=0.466C=0.533
The Genome Aggregation DatabaseOtherSub300T=0.400C=0.600
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.476C=0.523
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.426C=0.574
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs131697830.0000354alcoholismpha002891
rs131697830.0000354alcohol dependence20201924

eQTL of rs13169783 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr5:175764368RP11-844P9.3ENSG00000251667.1T>C2.0263e-429302Cerebellum
Chr5:175764368RP11-826N14.4ENSG00000251623.1T>C1.0592e-8200208Cortex
Chr5:175764368RP11-826N14.4ENSG00000251623.1T>C5.3199e-8200208Cerebellar_Hemisphere
Chr5:175764368SIMC1ENSG00000170085.13T>C4.3720e-699003Nucleus_accumbens_basal_ganglia

meQTL of rs13169783 in Fetal Brain

Probe ID Position Gene beta p-value
cg26620356chr5:175789238KIAA1191-0.06187523786135853.1735e-12
cg05970307chr5:175789566KIAA1191-0.04172232107758822.9242e-10

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 )
chr5175789718175789874E06725350
chr5175813882175813929E06749514
chr5175782512175782653E06818144
chr5175782705175782798E06818337
chr5175782846175782955E06818478
chr5175783053175783244E06818685
chr5175783053175783244E06918685
chr5175783053175783244E07018685
chr5175786741175787026E07022373
chr5175813882175813929E07049514
chr5175786741175787026E07122373
chr5175787427175787467E07123059
chr5175786741175787026E07222373
chr5175784607175784666E07320239
chr5175782846175782955E07418478
chr5175783053175783244E07418685
chr5175786741175787026E07422373
chr5175786741175787026E08122373
chr5175787427175787467E08123059
chr5175789718175789874E08125350
chr5175813882175813929E08149514
chr5175784607175784666E08220239
chr5175794869175794940E08230501
chr5175813882175813929E08249514










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5175787898175789634E06723530
chr5175791943175793683E06727575
chr5175787898175789634E06823530
chr5175791943175793683E06827575
chr5175787898175789634E06923530
chr5175791943175793683E06927575
chr5175787898175789634E07023530
chr5175791943175793683E07027575
chr5175787898175789634E07123530
chr5175791943175793683E07127575
chr5175787898175789634E07223530
chr5175791943175793683E07227575
chr5175787898175789634E07323530
chr5175791943175793683E07327575
chr5175787898175789634E07423530
chr5175791943175793683E07427575
chr5175787898175789634E08123530
chr5175787898175789634E08223530
chr5175791943175793683E08227575