rs7545274

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

CEP104 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0201 (6029/29934,GnomAD)
A=0190 (5559/29118,TOPMED)
A=0125 (624/5008,1000G)
A=0251 (969/3854,ALSPAC)
A=0247 (915/3708,TWINSUK)

Position: chr1:3827697 (GRCh38.p7) (1p36.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 85 Enhancers around

Promoter: 68 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.3827697C>A
GRCh37.p13 chr 1	NC_000001.10:g.3744261C>A
CEP104 RefSeqGene	NG_046726.1:g.34537G>T

Gene: CEP104, centrosomal protein 104(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CEP104 transcript	NM_014704.3:c.	N/A	Intron Variant
CEP104 transcript variant X2	XM_005244815.4:c.	N/A	Intron Variant
CEP104 transcript variant X1	XM_011542473.2:c.	N/A	Intron Variant
CEP104 transcript variant X3	XM_011542474.2:c.	N/A	Intron Variant
CEP104 transcript variant X4	XM_011542475.2:c.	N/A	Intron Variant
CEP104 transcript variant X6	XM_011542476.2:c.	N/A	Intron Variant
CEP104 transcript variant X9	XM_011542477.2:c.	N/A	Intron Variant
CEP104 transcript variant X5	XM_017002917.1:c.	N/A	Intron Variant
CEP104 transcript variant X7	XM_017002918.1:c.	N/A	Intron Variant
CEP104 transcript variant X8	XM_017002919.1:c.	N/A	Intron Variant
CEP104 transcript variant X10	XM_011542478.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.874	A=0.126
1000Genomes	American	Sub	694	C=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	C=0.998	A=0.002
1000Genomes	Europe	Sub	1006	C=0.787	A=0.213
1000Genomes	Global	Study-wide	5008	C=0.875	A=0.125
1000Genomes	South Asian	Sub	978	C=0.860	A=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.749	A=0.251
The Genome Aggregation Database	African	Sub	8728	C=0.875	A=0.125
The Genome Aggregation Database	American	Sub	838	C=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1618	C=0.999	A=0.001
The Genome Aggregation Database	Europe	Sub	18448	C=0.741	A=0.258
The Genome Aggregation Database	Global	Study-wide	29934	C=0.798	A=0.201
The Genome Aggregation Database	Other	Sub	302	C=0.740	A=0.260
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.809	A=0.190
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.753	A=0.247

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
rs7545274	0.000886	alcohol dependence	21314694

eQTL of rs7545274 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 rs7545274 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 )
chr1	3710096	3710526	E067	-33735
chr1	3710547	3710635	E067	-33626
chr1	3710779	3710893	E067	-33368
chr1	3772329	3772379	E067	28068
chr1	3775530	3775580	E067	31269
chr1	3779922	3780360	E067	35661
chr1	3708660	3708740	E068	-35521
chr1	3710096	3710526	E068	-33735
chr1	3710547	3710635	E068	-33626
chr1	3710779	3710893	E068	-33368
chr1	3717289	3717349	E068	-26912
chr1	3772329	3772379	E068	28068
chr1	3710096	3710526	E069	-33735
chr1	3710547	3710635	E069	-33626
chr1	3710779	3710893	E069	-33368
chr1	3779794	3779835	E069	35533
chr1	3779922	3780360	E069	35661
chr1	3710096	3710526	E070	-33735
chr1	3710547	3710635	E070	-33626
chr1	3710779	3710893	E070	-33368
chr1	3737457	3737586	E070	-6675
chr1	3737690	3737974	E070	-6287
chr1	3738073	3738389	E070	-5872
chr1	3763234	3763430	E070	18973
chr1	3763790	3763917	E070	19529
chr1	3772329	3772379	E070	28068
chr1	3775530	3775580	E070	31269
chr1	3695267	3695394	E071	-48867
chr1	3695558	3695687	E071	-48574
chr1	3710096	3710526	E071	-33735
chr1	3710547	3710635	E071	-33626
chr1	3710779	3710893	E071	-33368
chr1	3744401	3744572	E071	140
chr1	3744717	3744892	E071	456
chr1	3745131	3745212	E071	870
chr1	3772329	3772379	E071	28068
chr1	3775530	3775580	E071	31269
chr1	3694554	3694604	E072	-49657
chr1	3694657	3694755	E072	-49506
chr1	3694813	3694886	E072	-49375
chr1	3695267	3695394	E072	-48867
chr1	3695558	3695687	E072	-48574
chr1	3705435	3705485	E072	-38776
chr1	3705564	3705768	E072	-38493
chr1	3710096	3710526	E072	-33735
chr1	3710547	3710635	E072	-33626
chr1	3710779	3710893	E072	-33368
chr1	3717963	3718066	E072	-26195
chr1	3718117	3718194	E072	-26067
chr1	3744717	3744892	E072	456
chr1	3694554	3694604	E073	-49657
chr1	3694657	3694755	E073	-49506
chr1	3694813	3694886	E073	-49375
chr1	3695267	3695394	E073	-48867
chr1	3695558	3695687	E073	-48574
chr1	3706598	3707011	E073	-37250
chr1	3710096	3710526	E073	-33735
chr1	3710547	3710635	E073	-33626
chr1	3710779	3710893	E073	-33368
chr1	3716709	3716889	E073	-27372
chr1	3716929	3717001	E073	-27260
chr1	3772329	3772379	E073	28068
chr1	3710096	3710526	E074	-33735
chr1	3710547	3710635	E074	-33626
chr1	3710779	3710893	E074	-33368
chr1	3744401	3744572	E074	140
chr1	3775530	3775580	E074	31269
chr1	3710096	3710526	E081	-33735
chr1	3710547	3710635	E081	-33626
chr1	3710779	3710893	E081	-33368
chr1	3737457	3737586	E081	-6675
chr1	3737690	3737974	E081	-6287
chr1	3738073	3738389	E081	-5872
chr1	3744401	3744572	E081	140
chr1	3744717	3744892	E081	456
chr1	3772329	3772379	E081	28068
chr1	3775530	3775580	E081	31269
chr1	3710096	3710526	E082	-33735
chr1	3710547	3710635	E082	-33626
chr1	3737457	3737586	E082	-6675
chr1	3737690	3737974	E082	-6287
chr1	3738073	3738389	E082	-5872
chr1	3744401	3744572	E082	140
chr1	3744717	3744892	E082	456
chr1	3772329	3772379	E082	28068

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	3712240	3712353	E067	-31908
chr1	3712411	3712544	E067	-31717
chr1	3712562	3712676	E067	-31585
chr1	3712765	3713736	E067	-30525
chr1	3772942	3773054	E067	28681
chr1	3773091	3773365	E067	28830
chr1	3773429	3774692	E067	29168
chr1	3712240	3712353	E068	-31908
chr1	3712411	3712544	E068	-31717
chr1	3712562	3712676	E068	-31585
chr1	3712765	3713736	E068	-30525
chr1	3772942	3773054	E068	28681
chr1	3773091	3773365	E068	28830
chr1	3773429	3774692	E068	29168
chr1	3712240	3712353	E069	-31908
chr1	3712411	3712544	E069	-31717
chr1	3712562	3712676	E069	-31585
chr1	3712765	3713736	E069	-30525
chr1	3772942	3773054	E069	28681
chr1	3773091	3773365	E069	28830
chr1	3773429	3774692	E069	29168
chr1	3712240	3712353	E070	-31908
chr1	3712411	3712544	E070	-31717
chr1	3712562	3712676	E070	-31585
chr1	3712765	3713736	E070	-30525
chr1	3772942	3773054	E070	28681
chr1	3773091	3773365	E070	28830
chr1	3773429	3774692	E070	29168
chr1	3712240	3712353	E071	-31908
chr1	3712411	3712544	E071	-31717
chr1	3712562	3712676	E071	-31585
chr1	3712765	3713736	E071	-30525
chr1	3772942	3773054	E071	28681
chr1	3773091	3773365	E071	28830
chr1	3773429	3774692	E071	29168
chr1	3712240	3712353	E072	-31908
chr1	3712411	3712544	E072	-31717
chr1	3712562	3712676	E072	-31585
chr1	3712765	3713736	E072	-30525
chr1	3772942	3773054	E072	28681
chr1	3773091	3773365	E072	28830
chr1	3773429	3774692	E072	29168
chr1	3712240	3712353	E073	-31908
chr1	3712411	3712544	E073	-31717
chr1	3712562	3712676	E073	-31585
chr1	3712765	3713736	E073	-30525
chr1	3772942	3773054	E073	28681
chr1	3773091	3773365	E073	28830
chr1	3773429	3774692	E073	29168
chr1	3712240	3712353	E074	-31908
chr1	3712411	3712544	E074	-31717
chr1	3712562	3712676	E074	-31585
chr1	3712765	3713736	E074	-30525
chr1	3772942	3773054	E074	28681
chr1	3773091	3773365	E074	28830
chr1	3773429	3774692	E074	29168
chr1	3712240	3712353	E081	-31908
chr1	3712411	3712544	E081	-31717
chr1	3712562	3712676	E081	-31585
chr1	3712765	3713736	E081	-30525
chr1	3773429	3774692	E081	29168
chr1	3712240	3712353	E082	-31908
chr1	3712411	3712544	E082	-31717
chr1	3712562	3712676	E082	-31585
chr1	3712765	3713736	E082	-30525
chr1	3772942	3773054	E082	28681
chr1	3773091	3773365	E082	28830
chr1	3773429	3774692	E082	29168