rs10413635

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC105372242 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0027 (832/29906,GnomAD)
C==0032 (935/29118,TOPMED)
C==0020 (101/5008,1000G)
C==0047 (181/3854,ALSPAC)
C==0044 (163/3708,TWINSUK)

Position: chr19:3068452 (GRCh38.p7) (19p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 165 Enhancers around

Promoter: 48 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.3068452C>T
GRCh37.p13 chr 19	NC_000019.9:g.3068450C>T

Gene: LOC105372242, uncharacterized LOC105372242(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372242 transcript variant X1	XR_001754026.1:n.	N/A	Intron Variant
LOC105372242 transcript variant X2	XR_001754027.1:n.	N/A	Intron Variant
LOC105372242 transcript variant X3	XR_936250.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.002	T=0.998
1000Genomes	American	Sub	694	C=0.030	T=0.970
1000Genomes	East Asian	Sub	1008	C=0.000	T=1.000
1000Genomes	Europe	Sub	1006	C=0.056	T=0.944
1000Genomes	Global	Study-wide	5008	C=0.020	T=0.980
1000Genomes	South Asian	Sub	978	C=0.020	T=0.980
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.047	T=0.953
The Genome Aggregation Database	African	Sub	8694	C=0.009	T=0.991
The Genome Aggregation Database	American	Sub	836	C=0.020	T=0.980
The Genome Aggregation Database	East Asian	Sub	1620	C=0.001	T=0.999
The Genome Aggregation Database	Europe	Sub	18454	C=0.039	T=0.961
The Genome Aggregation Database	Global	Study-wide	29906	C=0.027	T=0.972
The Genome Aggregation Database	Other	Sub	302	C=0.040	T=0.960
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.032	T=0.967
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.044	T=0.956

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

P-Value

SNP ID	p-value	Traits	Study
rs10413635	0.00097	alcohol dependence	20201924

eQTL of rs10413635 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 rs10413635 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 )
chr19	3033877	3034016	E067	-34434
chr19	3057932	3058032	E067	-10418
chr19	3058070	3058216	E067	-10234
chr19	3058261	3058346	E067	-10104
chr19	3058384	3058457	E067	-9993
chr19	3058541	3058980	E067	-9470
chr19	3059034	3059084	E067	-9366
chr19	3059090	3059140	E067	-9310
chr19	3075556	3076402	E067	7106
chr19	3076431	3076582	E067	7981
chr19	3099422	3099488	E067	30972
chr19	3099555	3099688	E067	31105
chr19	3099784	3099849	E067	31334
chr19	3099870	3099969	E067	31420
chr19	3033877	3034016	E068	-34434
chr19	3057932	3058032	E068	-10418
chr19	3058070	3058216	E068	-10234
chr19	3058261	3058346	E068	-10104
chr19	3058384	3058457	E068	-9993
chr19	3058541	3058980	E068	-9470
chr19	3059034	3059084	E068	-9366
chr19	3059090	3059140	E068	-9310
chr19	3060360	3060514	E068	-7936
chr19	3099422	3099488	E068	30972
chr19	3099555	3099688	E068	31105
chr19	3099784	3099849	E068	31334
chr19	3099870	3099969	E068	31420
chr19	3100032	3100112	E068	31582
chr19	3100170	3100220	E068	31720
chr19	3100236	3100338	E068	31786
chr19	3100435	3100533	E068	31985
chr19	3020275	3020325	E069	-48125
chr19	3033877	3034016	E069	-34434
chr19	3057932	3058032	E069	-10418
chr19	3058070	3058216	E069	-10234
chr19	3058261	3058346	E069	-10104
chr19	3058384	3058457	E069	-9993
chr19	3058541	3058980	E069	-9470
chr19	3099422	3099488	E069	30972
chr19	3099555	3099688	E069	31105
chr19	3099784	3099849	E069	31334
chr19	3099870	3099969	E069	31420
chr19	3100032	3100112	E069	31582
chr19	3100170	3100220	E069	31720
chr19	3100236	3100338	E069	31786
chr19	3100435	3100533	E069	31985
chr19	3104046	3104916	E069	35596
chr19	3027816	3027980	E070	-40470
chr19	3033520	3033608	E070	-34842
chr19	3033637	3033769	E070	-34681
chr19	3033877	3034016	E070	-34434
chr19	3037857	3037958	E070	-30492
chr19	3039361	3039961	E070	-28489
chr19	3040064	3040142	E070	-28308
chr19	3040171	3040243	E070	-28207
chr19	3043018	3043150	E070	-25300
chr19	3043156	3043356	E070	-25094
chr19	3051011	3051558	E070	-16892
chr19	3053150	3053649	E070	-14801
chr19	3059034	3059084	E070	-9366
chr19	3059090	3059140	E070	-9310
chr19	3059579	3059632	E070	-8818
chr19	3059638	3060321	E070	-8129
chr19	3060360	3060514	E070	-7936
chr19	3073174	3073577	E070	4724
chr19	3099422	3099488	E070	30972
chr19	3099555	3099688	E070	31105
chr19	3099784	3099849	E070	31334
chr19	3099870	3099969	E070	31420
chr19	3100032	3100112	E070	31582
chr19	3045809	3048010	E071	-20440
chr19	3057932	3058032	E071	-10418
chr19	3058070	3058216	E071	-10234
chr19	3058261	3058346	E071	-10104
chr19	3058384	3058457	E071	-9993
chr19	3058541	3058980	E071	-9470
chr19	3060360	3060514	E071	-7936
chr19	3076431	3076582	E071	7981
chr19	3076622	3076672	E071	8172
chr19	3076854	3076900	E071	8404
chr19	3099422	3099488	E071	30972
chr19	3099555	3099688	E071	31105
chr19	3099784	3099849	E071	31334
chr19	3099870	3099969	E071	31420
chr19	3100032	3100112	E071	31582
chr19	3100170	3100220	E071	31720
chr19	3033877	3034016	E072	-34434
chr19	3057932	3058032	E072	-10418
chr19	3058070	3058216	E072	-10234
chr19	3058261	3058346	E072	-10104
chr19	3058384	3058457	E072	-9993
chr19	3058541	3058980	E072	-9470
chr19	3059034	3059084	E072	-9366
chr19	3059090	3059140	E072	-9310
chr19	3059579	3059632	E072	-8818
chr19	3059638	3060321	E072	-8129
chr19	3060360	3060514	E072	-7936
chr19	3076431	3076582	E072	7981
chr19	3099422	3099488	E072	30972
chr19	3099555	3099688	E072	31105
chr19	3099784	3099849	E072	31334
chr19	3099870	3099969	E072	31420
chr19	3100032	3100112	E072	31582
chr19	3100170	3100220	E072	31720
chr19	3100236	3100338	E072	31786
chr19	3100435	3100533	E072	31985
chr19	3057932	3058032	E073	-10418
chr19	3058070	3058216	E073	-10234
chr19	3058261	3058346	E073	-10104
chr19	3058384	3058457	E073	-9993
chr19	3058541	3058980	E073	-9470
chr19	3059579	3059632	E073	-8818
chr19	3059638	3060321	E073	-8129
chr19	3060360	3060514	E073	-7936
chr19	3075556	3076402	E073	7106
chr19	3099422	3099488	E073	30972
chr19	3099555	3099688	E073	31105
chr19	3099784	3099849	E073	31334
chr19	3099870	3099969	E073	31420
chr19	3100032	3100112	E073	31582
chr19	3100170	3100220	E073	31720
chr19	3100236	3100338	E073	31786
chr19	3100435	3100533	E073	31985
chr19	3100624	3100872	E073	32174
chr19	3101234	3101336	E073	32784
chr19	3104046	3104916	E073	35596
chr19	3104946	3105065	E073	36496
chr19	3020275	3020325	E074	-48125
chr19	3020620	3020670	E074	-47780
chr19	3033877	3034016	E074	-34434
chr19	3057932	3058032	E074	-10418
chr19	3058070	3058216	E074	-10234
chr19	3058261	3058346	E074	-10104
chr19	3058384	3058457	E074	-9993
chr19	3075556	3076402	E074	7106
chr19	3076431	3076582	E074	7981
chr19	3099422	3099488	E074	30972
chr19	3099555	3099688	E074	31105
chr19	3099784	3099849	E074	31334
chr19	3099870	3099969	E074	31420
chr19	3025788	3025834	E081	-42616
chr19	3041976	3042886	E081	-25564
chr19	3043018	3043150	E081	-25300
chr19	3043156	3043356	E081	-25094
chr19	3045809	3048010	E081	-20440
chr19	3053959	3057875	E081	-10575
chr19	3057932	3058032	E081	-10418
chr19	3058070	3058216	E081	-10234
chr19	3058261	3058346	E081	-10104
chr19	3058384	3058457	E081	-9993
chr19	3058541	3058980	E081	-9470
chr19	3059034	3059084	E081	-9366
chr19	3059090	3059140	E081	-9310
chr19	3059579	3059632	E081	-8818
chr19	3059638	3060321	E081	-8129
chr19	3060360	3060514	E081	-7936
chr19	3075556	3076402	E081	7106
chr19	3076431	3076582	E081	7981
chr19	3076622	3076672	E081	8172
chr19	3048115	3048483	E082	-19967
chr19	3058261	3058346	E082	-10104
chr19	3058384	3058457	E082	-9993
chr19	3058541	3058980	E082	-9470
chr19	3099422	3099488	E082	30972
chr19	3099555	3099688	E082	31105

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	3028097	3029810	E067	-38640
chr19	3034187	3037044	E067	-31406
chr19	3060602	3062100	E067	-6350
chr19	3062104	3063756	E067	-4694
chr19	3093757	3093827	E067	25307
chr19	3093878	3094535	E067	25428
chr19	3034187	3037044	E068	-31406
chr19	3060602	3062100	E068	-6350
chr19	3062104	3063756	E068	-4694
chr19	3093757	3093827	E068	25307
chr19	3093878	3094535	E068	25428
chr19	3028097	3029810	E069	-38640
chr19	3034187	3037044	E069	-31406
chr19	3060602	3062100	E069	-6350
chr19	3062104	3063756	E069	-4694
chr19	3093757	3093827	E069	25307
chr19	3093878	3094535	E069	25428
chr19	3034187	3037044	E070	-31406
chr19	3060602	3062100	E070	-6350
chr19	3062104	3063756	E070	-4694
chr19	3093757	3093827	E070	25307
chr19	3093878	3094535	E070	25428
chr19	3028097	3029810	E071	-38640
chr19	3034187	3037044	E071	-31406
chr19	3060602	3062100	E071	-6350
chr19	3062104	3063756	E071	-4694
chr19	3093757	3093827	E071	25307
chr19	3093878	3094535	E071	25428
chr19	3028097	3029810	E072	-38640
chr19	3034187	3037044	E072	-31406
chr19	3060602	3062100	E072	-6350
chr19	3062104	3063756	E072	-4694
chr19	3093757	3093827	E072	25307
chr19	3093878	3094535	E072	25428
chr19	3028097	3029810	E073	-38640
chr19	3034187	3037044	E073	-31406
chr19	3060602	3062100	E073	-6350
chr19	3062104	3063756	E073	-4694
chr19	3093757	3093827	E073	25307
chr19	3093878	3094535	E073	25428
chr19	3034187	3037044	E074	-31406
chr19	3060602	3062100	E074	-6350
chr19	3028097	3029810	E082	-38640
chr19	3034187	3037044	E082	-31406
chr19	3060602	3062100	E082	-6350
chr19	3062104	3063756	E082	-4694
chr19	3093757	3093827	E082	25307
chr19	3093878	3094535	E082	25428