rs9506528

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

IFT88 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0428 (12828/29910,GnomAD)
A=0411 (11971/29118,TOPMED)
A=0350 (1754/5008,1000G)
G==0473 (1823/3854,ALSPAC)
G==0467 (1730/3708,TWINSUK)

Position: chr13:20614200 (GRCh38.p7) (13q12.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 34 Enhancers around

Promoter: 24 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.20614200G>A
GRCh37.p13 chr 13	NC_000013.10:g.21188339G>A

Gene: IFT88, intraflagellar transport 88(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IFT88 transcript variant 3	NM_001318491.1:c.	N/A	Intron Variant
IFT88 transcript variant 4	NM_001318493.1:c.	N/A	Intron Variant
IFT88 transcript variant 2	NM_006531.4:c.	N/A	Intron Variant
IFT88 transcript variant 1	NM_175605.4:c.	N/A	Intron Variant
IFT88 transcript variant 5	NR_134653.1:n.	N/A	Intron Variant
IFT88 transcript variant X1	XM_005266553.2:c.	N/A	Intron Variant
IFT88 transcript variant X3	XM_006719870.3:c.	N/A	Intron Variant
IFT88 transcript variant X2	XM_011535241.2:c.	N/A	Intron Variant
IFT88 transcript variant X4	XM_011535242.1:c.	N/A	Intron Variant
IFT88 transcript variant X2	XM_011535243.1:c.	N/A	Intron Variant
IFT88 transcript variant X1	XM_017020757.1:c.	N/A	Intron Variant
IFT88 transcript variant X4	XM_017020758.1:c.	N/A	Intron Variant
IFT88 transcript variant X5	XM_017020759.1:c.	N/A	Intron Variant
IFT88 transcript variant X9	XM_017020760.1:c.	N/A	Intron Variant
IFT88 transcript variant X10	XM_017020761.1:c.	N/A	Intron Variant
IFT88 transcript variant X7	XM_017020762.1:c.	N/A	Intron Variant
IFT88 transcript variant X8	XM_017020763.1:c.	N/A	Intron Variant
IFT88 transcript variant X13	XM_017020764.1:c.	N/A	Intron Variant
IFT88 transcript variant X14	XM_017020765.1:c.	N/A	Intron Variant
IFT88 transcript variant X16	XM_017020766.1:c.	N/A	Intron Variant
IFT88 transcript variant X17	XM_017020767.1:c.	N/A	Intron Variant
IFT88 transcript variant X12	XM_017020768.1:c.	N/A	Intron Variant
IFT88 transcript variant X19	XM_017020769.1:c.	N/A	Intron Variant
IFT88 transcript variant X20	XM_017020770.1:c.	N/A	Intron Variant
IFT88 transcript variant X21	XM_017020771.1:c.	N/A	Intron Variant
IFT88 transcript variant X22	XM_017020772.1:c.	N/A	Intron Variant
IFT88 transcript variant X14	XM_017020773.1:c.	N/A	Intron Variant
IFT88 transcript variant X25	XM_017020774.1:c.	N/A	Intron Variant
IFT88 transcript variant X15	XM_017020775.1:c.	N/A	Intron Variant
IFT88 transcript variant X20	XM_017020776.1:c.	N/A	Intron Variant
IFT88 transcript variant X15	XR_001749679.1:n.	N/A	Intron Variant
IFT88 transcript variant X24	XR_001749681.1:n.	N/A	Intron Variant
IFT88 transcript variant X16	XR_001749682.1:n.	N/A	Intron Variant
IFT88 transcript variant X17	XR_001749683.1:n.	N/A	Intron Variant
IFT88 transcript variant X29	XR_001749684.1:n.	N/A	Intron Variant
IFT88 transcript variant X30	XR_001749685.1:n.	N/A	Intron Variant
IFT88 transcript variant X18	XR_001749686.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.738	A=0.262
1000Genomes	American	Sub	694	G=0.700	A=0.300
1000Genomes	East Asian	Sub	1008	G=0.728	A=0.272
1000Genomes	Europe	Sub	1006	G=0.466	A=0.534
1000Genomes	Global	Study-wide	5008	G=0.650	A=0.350
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=0.473	A=0.527
The Genome Aggregation Database	African	Sub	8700	G=0.712	A=0.288
The Genome Aggregation Database	American	Sub	838	G=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1616	G=0.693	A=0.307
The Genome Aggregation Database	Europe	Sub	18454	G=0.488	A=0.511
The Genome Aggregation Database	Global	Study-wide	29910	G=0.571	A=0.428
The Genome Aggregation Database	Other	Sub	302	G=0.530	A=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.588	A=0.411
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.467	A=0.533

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
rs9506528	0.000763	alcohol dependence	20201924

eQTL of rs9506528 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 rs9506528 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 )
chr13	21147236	21147286	E067	-41053
chr13	21211641	21211697	E067	23302
chr13	21211762	21211922	E067	23423
chr13	21147236	21147286	E068	-41053
chr13	21147489	21147583	E068	-40756
chr13	21202440	21202490	E068	14101
chr13	21202497	21202547	E068	14158
chr13	21210779	21210852	E068	22440
chr13	21210974	21211108	E068	22635
chr13	21211500	21211550	E068	23161
chr13	21211641	21211697	E068	23302
chr13	21211762	21211922	E068	23423
chr13	21211641	21211697	E069	23302
chr13	21211762	21211922	E069	23423
chr13	21183255	21183725	E070	-4614
chr13	21210779	21210852	E070	22440
chr13	21210974	21211108	E070	22635
chr13	21211500	21211550	E070	23161
chr13	21211641	21211697	E070	23302
chr13	21211762	21211922	E070	23423
chr13	21237435	21237505	E070	49096
chr13	21184176	21184383	E071	-3956
chr13	21139862	21139949	E072	-48390
chr13	21139981	21140035	E072	-48304
chr13	21184176	21184383	E072	-3956
chr13	21211641	21211697	E072	23302
chr13	21211762	21211922	E072	23423
chr13	21183255	21183725	E074	-4614
chr13	21184176	21184383	E074	-3956
chr13	21210974	21211108	E074	22635
chr13	21211500	21211550	E074	23161
chr13	21211641	21211697	E074	23302
chr13	21211762	21211922	E074	23423
chr13	21210779	21210852	E082	22440

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr13	21140419	21142554	E067	-45785
chr13	21182776	21182828	E067	-5511
chr13	21182862	21183020	E067	-5319
chr13	21140419	21142554	E068	-45785
chr13	21182776	21182828	E068	-5511
chr13	21182862	21183020	E068	-5319
chr13	21140419	21142554	E069	-45785
chr13	21182776	21182828	E069	-5511
chr13	21182862	21183020	E069	-5319
chr13	21140419	21142554	E070	-45785
chr13	21140419	21142554	E071	-45785
chr13	21182776	21182828	E071	-5511
chr13	21182862	21183020	E071	-5319
chr13	21140419	21142554	E072	-45785
chr13	21182776	21182828	E072	-5511
chr13	21182862	21183020	E072	-5319
chr13	21140419	21142554	E073	-45785
chr13	21182776	21182828	E073	-5511
chr13	21182862	21183020	E073	-5319
chr13	21140419	21142554	E074	-45785
chr13	21182776	21182828	E074	-5511
chr13	21182862	21183020	E074	-5319
chr13	21140419	21142554	E081	-45785
chr13	21140419	21142554	E082	-45785