rs17156580

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RAB3IL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0061 (1827/29940,GnomAD)
T=0051 (1493/29118,TOPMED)
T=0054 (268/5008,1000G)
T=0073 (283/3854,ALSPAC)
T=0077 (287/3708,TWINSUK)

Position: chr11:61924869 (GRCh38.p7) (11q12.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 190 Enhancers around

Promoter: 58 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.61924869C>T
GRCh37.p13 chr 11	NC_000011.9:g.61692341C>T

Gene: RAB3IL1, RAB3A interacting protein like 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RAB3IL1 transcript variant 2	NM_001271686.1:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant 1	NM_013401.3:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X2	XM_011545197.2:c.	N/A	Intron Variant
RAB3IL1 transcript variant X4	XM_005274140.4:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X5	XM_006718647.3:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X1	XM_011545196.2:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X3	XM_011545198.2:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X6	XM_011545199.2:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X7	XM_011545200.2:c.	N/A	Genic Upstream Transcript Variant
RAB3IL1 transcript variant X8	XM_011545201.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.958	T=0.042
1000Genomes	American	Sub	694	C=0.960	T=0.040
1000Genomes	East Asian	Sub	1008	C=0.895	T=0.105
1000Genomes	Europe	Sub	1006	C=0.936	T=0.064
1000Genomes	Global	Study-wide	5008	C=0.946	T=0.054
1000Genomes	South Asian	Sub	978	C=0.980	T=0.020
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.927	T=0.073
The Genome Aggregation Database	African	Sub	8710	C=0.958	T=0.042
The Genome Aggregation Database	American	Sub	838	C=0.960	T=0.040
The Genome Aggregation Database	East Asian	Sub	1616	C=0.916	T=0.084
The Genome Aggregation Database	Europe	Sub	18474	C=0.930	T=0.069
The Genome Aggregation Database	Global	Study-wide	29940	C=0.939	T=0.061
The Genome Aggregation Database	Other	Sub	302	C=0.950	T=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.948	T=0.051
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.923	T=0.077

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs17156580	0.000852	alcohol dependence	21314694

eQTL of rs17156580 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 rs17156580 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 )
chr11	61657357	61657583	E067	-34758
chr11	61664983	61667285	E067	-25056
chr11	61678249	61678332	E067	-14009
chr11	61678333	61678393	E067	-13948
chr11	61678398	61678623	E067	-13718
chr11	61678687	61678869	E067	-13472
chr11	61714576	61714645	E067	22235
chr11	61714859	61715716	E067	22518
chr11	61715876	61716379	E067	23535
chr11	61716474	61717833	E067	24133
chr11	61719015	61719131	E067	26674
chr11	61719141	61719308	E067	26800
chr11	61722038	61722097	E067	29697
chr11	61728256	61728507	E067	35915
chr11	61728825	61732039	E067	36484
chr11	61736920	61737302	E067	44579
chr11	61737420	61738175	E067	45079
chr11	61738230	61738321	E067	45889
chr11	61738430	61741763	E067	46089
chr11	61646959	61647009	E068	-45332
chr11	61647226	61647354	E068	-44987
chr11	61655300	61656156	E068	-36185
chr11	61656168	61656366	E068	-35975
chr11	61664983	61667285	E068	-25056
chr11	61679409	61679721	E068	-12620
chr11	61679812	61679887	E068	-12454
chr11	61679950	61680011	E068	-12330
chr11	61687274	61687389	E068	-4952
chr11	61714859	61715716	E068	22518
chr11	61715876	61716379	E068	23535
chr11	61722038	61722097	E068	29697
chr11	61726459	61727213	E068	34118
chr11	61727218	61727390	E068	34877
chr11	61727423	61727606	E068	35082
chr11	61727724	61727807	E068	35383
chr11	61728046	61728132	E068	35705
chr11	61728256	61728507	E068	35915
chr11	61728825	61732039	E068	36484
chr11	61736920	61737302	E068	44579
chr11	61737420	61738175	E068	45079
chr11	61738230	61738321	E068	45889
chr11	61738430	61741763	E068	46089
chr11	61655300	61656156	E069	-36185
chr11	61656168	61656366	E069	-35975
chr11	61664983	61667285	E069	-25056
chr11	61667345	61667454	E069	-24887
chr11	61667540	61667722	E069	-24619
chr11	61714859	61715716	E069	22518
chr11	61715876	61716379	E069	23535
chr11	61719857	61719913	E069	27516
chr11	61722038	61722097	E069	29697
chr11	61727423	61727606	E069	35082
chr11	61727724	61727807	E069	35383
chr11	61728046	61728132	E069	35705
chr11	61728256	61728507	E069	35915
chr11	61728825	61732039	E069	36484
chr11	61736920	61737302	E069	44579
chr11	61737420	61738175	E069	45079
chr11	61738230	61738321	E069	45889
chr11	61738430	61741763	E069	46089
chr11	61646480	61646609	E070	-45732
chr11	61657357	61657583	E070	-34758
chr11	61714859	61715716	E070	22518
chr11	61716474	61717833	E070	24133
chr11	61732158	61732284	E070	39817
chr11	61738430	61741763	E070	46089
chr11	61655182	61655287	E071	-37054
chr11	61655300	61656156	E071	-36185
chr11	61656168	61656366	E071	-35975
chr11	61664479	61664610	E071	-27731
chr11	61664757	61664938	E071	-27403
chr11	61664983	61667285	E071	-25056
chr11	61667345	61667454	E071	-24887
chr11	61675948	61676040	E071	-16301
chr11	61676158	61677035	E071	-15306
chr11	61677983	61678149	E071	-14192
chr11	61678249	61678332	E071	-14009
chr11	61678333	61678393	E071	-13948
chr11	61678398	61678623	E071	-13718
chr11	61678687	61678869	E071	-13472
chr11	61678916	61679369	E071	-12972
chr11	61679409	61679721	E071	-12620
chr11	61685996	61686050	E071	-6291
chr11	61686105	61686306	E071	-6035
chr11	61713901	61713994	E071	21560
chr11	61714400	61714565	E071	22059
chr11	61714576	61714645	E071	22235
chr11	61714859	61715716	E071	22518
chr11	61715876	61716379	E071	23535
chr11	61721411	61721455	E071	29070
chr11	61721557	61721949	E071	29216
chr11	61727423	61727606	E071	35082
chr11	61727724	61727807	E071	35383
chr11	61728046	61728132	E071	35705
chr11	61728256	61728507	E071	35915
chr11	61728825	61732039	E071	36484
chr11	61736920	61737302	E071	44579
chr11	61737420	61738175	E071	45079
chr11	61738230	61738321	E071	45889
chr11	61738430	61741763	E071	46089
chr11	61650751	61651160	E072	-41181
chr11	61651479	61651564	E072	-40777
chr11	61664983	61667285	E072	-25056
chr11	61682933	61682983	E072	-9358
chr11	61682992	61683060	E072	-9281
chr11	61714859	61715716	E072	22518
chr11	61715876	61716379	E072	23535
chr11	61719015	61719131	E072	26674
chr11	61719141	61719308	E072	26800
chr11	61721557	61721949	E072	29216
chr11	61726459	61727213	E072	34118
chr11	61727218	61727390	E072	34877
chr11	61727423	61727606	E072	35082
chr11	61727724	61727807	E072	35383
chr11	61728046	61728132	E072	35705
chr11	61728256	61728507	E072	35915
chr11	61728825	61732039	E072	36484
chr11	61736920	61737302	E072	44579
chr11	61737420	61738175	E072	45079
chr11	61738230	61738321	E072	45889
chr11	61738430	61741763	E072	46089
chr11	61651479	61651564	E073	-40777
chr11	61651663	61651713	E073	-40628
chr11	61655300	61656156	E073	-36185
chr11	61656168	61656366	E073	-35975
chr11	61677658	61677894	E073	-14447
chr11	61677983	61678149	E073	-14192
chr11	61678249	61678332	E073	-14009
chr11	61678333	61678393	E073	-13948
chr11	61678398	61678623	E073	-13718
chr11	61678687	61678869	E073	-13472
chr11	61678916	61679369	E073	-12972
chr11	61679409	61679721	E073	-12620
chr11	61685996	61686050	E073	-6291
chr11	61686105	61686306	E073	-6035
chr11	61686317	61686911	E073	-5430
chr11	61714859	61715716	E073	22518
chr11	61715876	61716379	E073	23535
chr11	61719141	61719308	E073	26800
chr11	61719857	61719913	E073	27516
chr11	61721557	61721949	E073	29216
chr11	61722038	61722097	E073	29697
chr11	61727423	61727606	E073	35082
chr11	61727724	61727807	E073	35383
chr11	61728046	61728132	E073	35705
chr11	61728256	61728507	E073	35915
chr11	61728825	61732039	E073	36484
chr11	61737420	61738175	E073	45079
chr11	61738230	61738321	E073	45889
chr11	61738430	61741763	E073	46089
chr11	61655182	61655287	E074	-37054
chr11	61655300	61656156	E074	-36185
chr11	61656168	61656366	E074	-35975
chr11	61677496	61677650	E074	-14691
chr11	61677658	61677894	E074	-14447
chr11	61677983	61678149	E074	-14192
chr11	61682663	61682733	E074	-9608
chr11	61682933	61682983	E074	-9358
chr11	61682992	61683060	E074	-9281
chr11	61685996	61686050	E074	-6291
chr11	61686105	61686306	E074	-6035
chr11	61713901	61713994	E074	21560
chr11	61714400	61714565	E074	22059
chr11	61714576	61714645	E074	22235
chr11	61714859	61715716	E074	22518
chr11	61715876	61716379	E074	23535
chr11	61716474	61717833	E074	24133
chr11	61719857	61719913	E074	27516
chr11	61720282	61720503	E074	27941
chr11	61721557	61721949	E074	29216
chr11	61722038	61722097	E074	29697
chr11	61724825	61725056	E074	32484
chr11	61727218	61727390	E074	34877
chr11	61727423	61727606	E074	35082
chr11	61727724	61727807	E074	35383
chr11	61728256	61728507	E074	35915
chr11	61728825	61732039	E074	36484
chr11	61736920	61737302	E074	44579
chr11	61737420	61738175	E074	45079
chr11	61738230	61738321	E074	45889
chr11	61738430	61741763	E074	46089
chr11	61657357	61657583	E081	-34758
chr11	61715876	61716379	E081	23535
chr11	61716474	61717833	E081	24133
chr11	61717894	61717993	E081	25553
chr11	61718171	61718244	E081	25830
chr11	61732560	61732873	E081	40219
chr11	61716474	61717833	E082	24133
chr11	61717894	61717993	E082	25553
chr11	61732158	61732284	E082	39817

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	61657935	61659886	E067	-32455
chr11	61683818	61683954	E067	-8387
chr11	61684004	61684464	E067	-7877
chr11	61684509	61685950	E067	-6391
chr11	61733585	61733673	E067	41244
chr11	61733742	61736773	E067	41401
chr11	61657935	61659886	E068	-32455
chr11	61683818	61683954	E068	-8387
chr11	61684004	61684464	E068	-7877
chr11	61684509	61685950	E068	-6391
chr11	61719653	61719744	E068	27312
chr11	61733742	61736773	E068	41401
chr11	61657935	61659886	E069	-32455
chr11	61683818	61683954	E069	-8387
chr11	61684004	61684464	E069	-7877
chr11	61684509	61685950	E069	-6391
chr11	61733585	61733673	E069	41244
chr11	61733742	61736773	E069	41401
chr11	61659947	61660100	E070	-32241
chr11	61684004	61684464	E070	-7877
chr11	61684509	61685950	E070	-6391
chr11	61733585	61733673	E070	41244
chr11	61733742	61736773	E070	41401
chr11	61657935	61659886	E071	-32455
chr11	61659947	61660100	E071	-32241
chr11	61683145	61683250	E071	-9091
chr11	61683818	61683954	E071	-8387
chr11	61684004	61684464	E071	-7877
chr11	61684509	61685950	E071	-6391
chr11	61719653	61719744	E071	27312
chr11	61733585	61733673	E071	41244
chr11	61733742	61736773	E071	41401
chr11	61657935	61659886	E072	-32455
chr11	61683818	61683954	E072	-8387
chr11	61684004	61684464	E072	-7877
chr11	61684509	61685950	E072	-6391
chr11	61733585	61733673	E072	41244
chr11	61733742	61736773	E072	41401
chr11	61657935	61659886	E073	-32455
chr11	61683818	61683954	E073	-8387
chr11	61684004	61684464	E073	-7877
chr11	61684509	61685950	E073	-6391
chr11	61733585	61733673	E073	41244
chr11	61733742	61736773	E073	41401
chr11	61657935	61659886	E074	-32455
chr11	61683145	61683250	E074	-9091
chr11	61683818	61683954	E074	-8387
chr11	61684004	61684464	E074	-7877
chr11	61684509	61685950	E074	-6391
chr11	61719653	61719744	E074	27312
chr11	61733742	61736773	E074	41401
chr11	61732948	61733466	E081	40607
chr11	61657935	61659886	E082	-32455
chr11	61684004	61684464	E082	-7877
chr11	61684509	61685950	E082	-6391
chr11	61732948	61733466	E082	40607
chr11	61733585	61733673	E082	41244
chr11	61733742	61736773	E082	41401