rs406598

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CARS : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0310 (9306/29942,GnomAD)
A=0283 (8256/29118,TOPMED)
A=0386 (1933/5008,1000G)
A=0400 (1543/3854,ALSPAC)
A=0391 (1448/3708,TWINSUK)

Position: chr11:3055055 (GRCh38.p7) (11p15.4)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 247 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.3055055G>A
GRCh37.p13 chr 11	NC_000011.9:g.3076285G>A
GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7	NT_187585.1:g.286087A>G

Gene: CARS, cysteinyl-tRNA synthetase(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CARS transcript variant 3	NM_001014437.2:c.	N/A	Intron Variant
CARS transcript variant 5	NM_001194997.1:c.	N/A	Intron Variant
CARS transcript variant 2	NM_001751.5:c.	N/A	Intron Variant
CARS transcript variant 1	NM_139273.3:c.	N/A	Intron Variant
CARS transcript variant 4	NR_036542.1:n.	N/A	Intron Variant
CARS transcript variant X8	XM_006718341.3:c.	N/A	Intron Variant
CARS transcript variant X9	XM_017018389.1:c.	N/A	Intron Variant
CARS transcript variant X10	XM_017018390.1:c.	N/A	Intron Variant
CARS transcript variant X12	XM_017018392.1:c.	N/A	5 Prime UTR Variant
CARS transcript variant X15	XM_017018391.1:c.	N/A	Genic Upstream Transcript Variant
CARS transcript variant X6	XR_001747995.1:n.	N/A	Intron Variant
CARS transcript variant X7	XR_001747996.1:n.	N/A	Intron Variant
CARS transcript variant X14	XR_001747997.1:n.	N/A	Intron Variant
CARS transcript variant X17	XR_001747998.1:n.	N/A	Intron Variant
CARS transcript variant X1	XR_428857.1:n.	N/A	Intron Variant
CARS transcript variant X7	XR_930913.1:n.	N/A	Intron Variant
CARS transcript variant X16	XR_930914.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.967	A=0.033
1000Genomes	American	Sub	694	G=0.470	A=0.530
1000Genomes	East Asian	Sub	1008	G=0.313	A=0.687
1000Genomes	Europe	Sub	1006	G=0.603	A=0.397
1000Genomes	Global	Study-wide	5008	G=0.614	A=0.386
1000Genomes	South Asian	Sub	978	G=0.560	A=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.600	A=0.400
The Genome Aggregation Database	African	Sub	8724	G=0.917	A=0.083
The Genome Aggregation Database	American	Sub	838	G=0.450	A=0.550
The Genome Aggregation Database	East Asian	Sub	1620	G=0.345	A=0.655
The Genome Aggregation Database	Europe	Sub	18458	G=0.624	A=0.375
The Genome Aggregation Database	Global	Study-wide	29942	G=0.689	A=0.310
The Genome Aggregation Database	Other	Sub	302	G=0.570	A=0.430
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.716	A=0.283
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.609	A=0.391

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
21911749	CPVL/CHN2 genetic variant is associated with diabetic retinopathy in Chinese type 2 diabetic patients.	Hu C	Diabetes

P-Value

SNP ID	p-value	Traits	Study
rs406598	0.00048	alcohol dependence	20201924
rs406598	0.00052	Alcohol dependence (early age of onset)	20201924

eQTL of rs406598 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 rs406598 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg25174290	chr11:3078921	CARS	-0.010088949477001	7.9261e-11

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 )
chr11	3042022	3042072	E067	-34213
chr11	3042262	3042740	E067	-33545
chr11	3051179	3051219	E067	-25066
chr11	3051380	3051434	E067	-24851
chr11	3051514	3051804	E067	-24481
chr11	3056446	3056535	E067	-19750
chr11	3056618	3056925	E067	-19360
chr11	3057609	3058080	E067	-18205
chr11	3062966	3063295	E067	-12990
chr11	3063320	3063649	E067	-12636
chr11	3063724	3064341	E067	-11944
chr11	3064352	3064467	E067	-11818
chr11	3064472	3064738	E067	-11547
chr11	3064790	3065068	E067	-11217
chr11	3065189	3065537	E067	-10748
chr11	3066948	3067262	E067	-9023
chr11	3067533	3067642	E067	-8643
chr11	3070143	3070222	E067	-6063
chr11	3070525	3070657	E067	-5628
chr11	3071953	3072606	E067	-3679
chr11	3072631	3072772	E067	-3513
chr11	3072796	3072945	E067	-3340
chr11	3073012	3073201	E067	-3084
chr11	3073296	3073612	E067	-2673
chr11	3073694	3073734	E067	-2551
chr11	3073811	3073861	E067	-2424
chr11	3073883	3074165	E067	-2120
chr11	3074170	3074250	E067	-2035
chr11	3074337	3074387	E067	-1898
chr11	3076789	3076854	E067	504
chr11	3077156	3077285	E067	871
chr11	3116711	3117692	E067	40426
chr11	3027101	3027156	E068	-49129
chr11	3042022	3042072	E068	-34213
chr11	3042262	3042740	E068	-33545
chr11	3042989	3043063	E068	-33222
chr11	3043250	3043327	E068	-32958
chr11	3043470	3044622	E068	-31663
chr11	3058301	3059394	E068	-16891
chr11	3062966	3063295	E068	-12990
chr11	3063320	3063649	E068	-12636
chr11	3063724	3064341	E068	-11944
chr11	3064352	3064467	E068	-11818
chr11	3064472	3064738	E068	-11547
chr11	3064790	3065068	E068	-11217
chr11	3065189	3065537	E068	-10748
chr11	3070525	3070657	E068	-5628
chr11	3071953	3072606	E068	-3679
chr11	3072631	3072772	E068	-3513
chr11	3072796	3072945	E068	-3340
chr11	3073012	3073201	E068	-3084
chr11	3073296	3073612	E068	-2673
chr11	3077156	3077285	E068	871
chr11	3116247	3116461	E068	39962
chr11	3116630	3116675	E068	40345
chr11	3031065	3031130	E069	-45155
chr11	3031201	3031261	E069	-45024
chr11	3041850	3041909	E069	-34376
chr11	3042022	3042072	E069	-34213
chr11	3042262	3042740	E069	-33545
chr11	3043470	3044622	E069	-31663
chr11	3044667	3044748	E069	-31537
chr11	3050174	3050295	E069	-25990
chr11	3050337	3050432	E069	-25853
chr11	3050556	3050763	E069	-25522
chr11	3051179	3051219	E069	-25066
chr11	3051380	3051434	E069	-24851
chr11	3051514	3051804	E069	-24481
chr11	3058301	3059394	E069	-16891
chr11	3062966	3063295	E069	-12990
chr11	3063320	3063649	E069	-12636
chr11	3063724	3064341	E069	-11944
chr11	3064352	3064467	E069	-11818
chr11	3064472	3064738	E069	-11547
chr11	3064790	3065068	E069	-11217
chr11	3065189	3065537	E069	-10748
chr11	3069088	3069175	E069	-7110
chr11	3069697	3069741	E069	-6544
chr11	3070143	3070222	E069	-6063
chr11	3071953	3072606	E069	-3679
chr11	3072631	3072772	E069	-3513
chr11	3072796	3072945	E069	-3340
chr11	3073012	3073201	E069	-3084
chr11	3073296	3073612	E069	-2673
chr11	3073694	3073734	E069	-2551
chr11	3073811	3073861	E069	-2424
chr11	3073883	3074165	E069	-2120
chr11	3074170	3074250	E069	-2035
chr11	3070525	3070657	E070	-5628
chr11	3073811	3073861	E070	-2424
chr11	3076789	3076854	E070	504
chr11	3077156	3077285	E070	871
chr11	3030921	3030975	E071	-45310
chr11	3031065	3031130	E071	-45155
chr11	3031201	3031261	E071	-45024
chr11	3034658	3034866	E071	-41419
chr11	3035063	3035174	E071	-41111
chr11	3036512	3036578	E071	-39707
chr11	3036655	3036836	E071	-39449
chr11	3041850	3041909	E071	-34376
chr11	3042022	3042072	E071	-34213
chr11	3042262	3042740	E071	-33545
chr11	3050337	3050432	E071	-25853
chr11	3050556	3050763	E071	-25522
chr11	3051179	3051219	E071	-25066
chr11	3051380	3051434	E071	-24851
chr11	3051514	3051804	E071	-24481
chr11	3051865	3052209	E071	-24076
chr11	3057609	3058080	E071	-18205
chr11	3058301	3059394	E071	-16891
chr11	3062966	3063295	E071	-12990
chr11	3063320	3063649	E071	-12636
chr11	3063724	3064341	E071	-11944
chr11	3064352	3064467	E071	-11818
chr11	3064472	3064738	E071	-11547
chr11	3064790	3065068	E071	-11217
chr11	3065189	3065537	E071	-10748
chr11	3065970	3066020	E071	-10265
chr11	3067533	3067642	E071	-8643
chr11	3069576	3069626	E071	-6659
chr11	3069697	3069741	E071	-6544
chr11	3070143	3070222	E071	-6063
chr11	3071953	3072606	E071	-3679
chr11	3072631	3072772	E071	-3513
chr11	3072796	3072945	E071	-3340
chr11	3073012	3073201	E071	-3084
chr11	3073296	3073612	E071	-2673
chr11	3073694	3073734	E071	-2551
chr11	3073811	3073861	E071	-2424
chr11	3073883	3074165	E071	-2120
chr11	3074786	3074867	E071	-1418
chr11	3074905	3074959	E071	-1326
chr11	3075108	3075172	E071	-1113
chr11	3075519	3075651	E071	-634
chr11	3075809	3075895	E071	-390
chr11	3075926	3076058	E071	-227
chr11	3076092	3076146	E071	-139
chr11	3076789	3076854	E071	504
chr11	3116630	3116675	E071	40345
chr11	3116711	3117692	E071	40426
chr11	3030921	3030975	E072	-45310
chr11	3031065	3031130	E072	-45155
chr11	3031201	3031261	E072	-45024
chr11	3031751	3031801	E072	-44484
chr11	3031963	3032013	E072	-44272
chr11	3032182	3032490	E072	-43795
chr11	3036655	3036836	E072	-39449
chr11	3036851	3036917	E072	-39368
chr11	3041850	3041909	E072	-34376
chr11	3042022	3042072	E072	-34213
chr11	3042262	3042740	E072	-33545
chr11	3051179	3051219	E072	-25066
chr11	3051380	3051434	E072	-24851
chr11	3051514	3051804	E072	-24481
chr11	3057609	3058080	E072	-18205
chr11	3058301	3059394	E072	-16891
chr11	3062966	3063295	E072	-12990
chr11	3063320	3063649	E072	-12636
chr11	3063724	3064341	E072	-11944
chr11	3064352	3064467	E072	-11818
chr11	3064472	3064738	E072	-11547
chr11	3064790	3065068	E072	-11217
chr11	3065189	3065537	E072	-10748
chr11	3065970	3066020	E072	-10265
chr11	3066028	3066093	E072	-10192
chr11	3066126	3066207	E072	-10078
chr11	3066948	3067262	E072	-9023
chr11	3067533	3067642	E072	-8643
chr11	3070143	3070222	E072	-6063
chr11	3071953	3072606	E072	-3679
chr11	3072631	3072772	E072	-3513
chr11	3072796	3072945	E072	-3340
chr11	3073012	3073201	E072	-3084
chr11	3073296	3073612	E072	-2673
chr11	3073694	3073734	E072	-2551
chr11	3073811	3073861	E072	-2424
chr11	3073883	3074165	E072	-2120
chr11	3076789	3076854	E072	504
chr11	3030921	3030975	E073	-45310
chr11	3031065	3031130	E073	-45155
chr11	3031201	3031261	E073	-45024
chr11	3042022	3042072	E073	-34213
chr11	3042262	3042740	E073	-33545
chr11	3051179	3051219	E073	-25066
chr11	3051380	3051434	E073	-24851
chr11	3051514	3051804	E073	-24481
chr11	3057609	3058080	E073	-18205
chr11	3058301	3059394	E073	-16891
chr11	3062966	3063295	E073	-12990
chr11	3063320	3063649	E073	-12636
chr11	3063724	3064341	E073	-11944
chr11	3064352	3064467	E073	-11818
chr11	3064472	3064738	E073	-11547
chr11	3064790	3065068	E073	-11217
chr11	3065189	3065537	E073	-10748
chr11	3070143	3070222	E073	-6063
chr11	3071953	3072606	E073	-3679
chr11	3072631	3072772	E073	-3513
chr11	3072796	3072945	E073	-3340
chr11	3073012	3073201	E073	-3084
chr11	3073296	3073612	E073	-2673
chr11	3073694	3073734	E073	-2551
chr11	3073811	3073861	E073	-2424
chr11	3073883	3074165	E073	-2120
chr11	3074170	3074250	E073	-2035
chr11	3075519	3075651	E073	-634
chr11	3075809	3075895	E073	-390
chr11	3077156	3077285	E073	871
chr11	3026636	3026866	E074	-49419
chr11	3026937	3026988	E074	-49297
chr11	3027101	3027156	E074	-49129
chr11	3031065	3031130	E074	-45155
chr11	3031201	3031261	E074	-45024
chr11	3031751	3031801	E074	-44484
chr11	3035063	3035174	E074	-41111
chr11	3041850	3041909	E074	-34376
chr11	3042022	3042072	E074	-34213
chr11	3042262	3042740	E074	-33545
chr11	3051179	3051219	E074	-25066
chr11	3051380	3051434	E074	-24851
chr11	3051514	3051804	E074	-24481
chr11	3051865	3052209	E074	-24076
chr11	3058301	3059394	E074	-16891
chr11	3062966	3063295	E074	-12990
chr11	3063320	3063649	E074	-12636
chr11	3063724	3064341	E074	-11944
chr11	3064352	3064467	E074	-11818
chr11	3064472	3064738	E074	-11547
chr11	3064790	3065068	E074	-11217
chr11	3065189	3065537	E074	-10748
chr11	3067533	3067642	E074	-8643
chr11	3070143	3070222	E074	-6063
chr11	3071953	3072606	E074	-3679
chr11	3072631	3072772	E074	-3513
chr11	3072796	3072945	E074	-3340
chr11	3073012	3073201	E074	-3084
chr11	3073296	3073612	E074	-2673
chr11	3073694	3073734	E074	-2551
chr11	3073811	3073861	E074	-2424
chr11	3073883	3074165	E074	-2120
chr11	3077156	3077285	E074	871
chr11	3070781	3071702	E081	-4583
chr11	3076495	3076545	E081	210
chr11	3077156	3077285	E081	871
chr11	3112832	3113487	E081	36547
chr11	3076789	3076854	E082	504
chr11	3077156	3077285	E082	871

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	3077559	3079427	E067	1274
chr11	3077559	3079427	E068	1274
chr11	3077559	3079427	E069	1274
chr11	3077559	3079427	E070	1274
chr11	3077559	3079427	E071	1274
chr11	3077559	3079427	E072	1274
chr11	3077559	3079427	E073	1274
chr11	3077559	3079427	E074	1274
chr11	3077559	3079427	E081	1274
chr11	3077559	3079427	E082	1274