rs11134972

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SIMC1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0475 (14121/29720,GnomAD)
G==0480 (13984/29118,TOPMED)
A=0484 (2425/5008,1000G)
G==0432 (1664/3854,ALSPAC)
G==0436 (1617/3708,TWINSUK)

Position: chr5:176343418 (GRCh38.p7) (5q35.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 24 Enhancers around

Promoter: 39 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.176343418G>A
GRCh37.p13 chr 5	NC_000005.9:g.175770421G>A

Molecule type	Change	Amino acid[Codon]	SO Term
SIMC1 transcript variant 1	NM_001308195.1:c.	N/A	Intron Variant
SIMC1 transcript variant 3	NM_001308196.1:c.	N/A	Intron Variant
SIMC1 transcript variant 4	NM_001308200.1:c.	N/A	Intron Variant
SIMC1 transcript variant 2	NM_198567.5:c.	N/A	Intron Variant
SIMC1 transcript variant 5	NR_131772.1:n.	N/A	Intron Variant
SIMC1 transcript variant X1	XM_011534553.2:c.	N/A	Intron Variant
SIMC1 transcript variant X2	XM_011534554.2:c.	N/A	Intron Variant
SIMC1 transcript variant X4	XM_011534556.2:c.	N/A	Intron Variant
SIMC1 transcript variant X3	XM_017009454.1:c.	N/A	Intron Variant
SIMC1 transcript variant X5	XM_017009455.1:c.	N/A	Intron Variant
SIMC1 transcript variant X6	XM_017009456.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.542	A=0.458
1000Genomes	American	Sub	694	G=0.550	A=0.450
1000Genomes	East Asian	Sub	1008	G=0.468	A=0.532
1000Genomes	Europe	Sub	1006	G=0.426	A=0.574
1000Genomes	Global	Study-wide	5008	G=0.516	A=0.484
1000Genomes	South Asian	Sub	978	G=0.600	A=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.432	A=0.568
The Genome Aggregation Database	African	Sub	8634	G=0.539	A=0.461
The Genome Aggregation Database	American	Sub	836	G=0.530	A=0.470
The Genome Aggregation Database	East Asian	Sub	1592	G=0.465	A=0.535
The Genome Aggregation Database	Europe	Sub	18356	G=0.444	A=0.555
The Genome Aggregation Database	Global	Study-wide	29720	G=0.475	A=0.524
The Genome Aggregation Database	Other	Sub	302	G=0.420	A=0.580
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.480	A=0.519
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.436	A=0.564

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs11134972	0.0000163	alcoholism	pha002891
rs11134972	0.0000163	alcohol dependence	20201924

eQTL of rs11134972 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr5:175770421	RP11-844P9.3	ENSG00000251667.1	G>A	2.0263e-4	35355	Cerebellum
Chr5:175770421	RP11-826N14.4	ENSG00000251623.1	G>A	5.3199e-8	206261	Cerebellar_Hemisphere
Chr5:175770421	SIMC1	ENSG00000170085.13	G>A	4.3720e-6	105056	Nucleus_accumbens_basal_ganglia

Probe ID	Position	Gene	beta	p-value
cg26620356	chr5:175789238	KIAA1191	-0.0634948881432513	1.0428e-12
cg05970307	chr5:175789566	KIAA1191	-0.0428748653809301	1.1255e-10

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr5	175789718	175789874	E067	19297
chr5	175813882	175813929	E067	43461
chr5	175782512	175782653	E068	12091
chr5	175782705	175782798	E068	12284
chr5	175782846	175782955	E068	12425
chr5	175783053	175783244	E068	12632
chr5	175783053	175783244	E069	12632
chr5	175783053	175783244	E070	12632
chr5	175786741	175787026	E070	16320
chr5	175813882	175813929	E070	43461
chr5	175786741	175787026	E071	16320
chr5	175787427	175787467	E071	17006
chr5	175786741	175787026	E072	16320
chr5	175784607	175784666	E073	14186
chr5	175782846	175782955	E074	12425
chr5	175783053	175783244	E074	12632
chr5	175786741	175787026	E074	16320
chr5	175786741	175787026	E081	16320
chr5	175787427	175787467	E081	17006
chr5	175789718	175789874	E081	19297
chr5	175813882	175813929	E081	43461
chr5	175784607	175784666	E082	14186
chr5	175794869	175794940	E082	24448
chr5	175813882	175813929	E082	43461

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	175787898	175789634	E067	17477
chr5	175791943	175793683	E067	21522
chr5	175814655	175814868	E067	44234
chr5	175814935	175816695	E067	44514
chr5	175787898	175789634	E068	17477
chr5	175791943	175793683	E068	21522
chr5	175814655	175814868	E068	44234
chr5	175814935	175816695	E068	44514
chr5	175787898	175789634	E069	17477
chr5	175791943	175793683	E069	21522
chr5	175814655	175814868	E069	44234
chr5	175814935	175816695	E069	44514
chr5	175787898	175789634	E070	17477
chr5	175791943	175793683	E070	21522
chr5	175814655	175814868	E070	44234
chr5	175814935	175816695	E070	44514
chr5	175787898	175789634	E071	17477
chr5	175791943	175793683	E071	21522
chr5	175814655	175814868	E071	44234
chr5	175814935	175816695	E071	44514
chr5	175787898	175789634	E072	17477
chr5	175791943	175793683	E072	21522
chr5	175814655	175814868	E072	44234
chr5	175814935	175816695	E072	44514
chr5	175787898	175789634	E073	17477
chr5	175791943	175793683	E073	21522
chr5	175814655	175814868	E073	44234
chr5	175814935	175816695	E073	44514
chr5	175787898	175789634	E074	17477
chr5	175791943	175793683	E074	21522
chr5	175814655	175814868	E074	44234
chr5	175814935	175816695	E074	44514
chr5	175787898	175789634	E081	17477
chr5	175814655	175814868	E081	44234
chr5	175814935	175816695	E081	44514
chr5	175787898	175789634	E082	17477
chr5	175791943	175793683	E082	21522
chr5	175814655	175814868	E082	44234
chr5	175814935	175816695	E082	44514