rs6661602

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0290 (8617/29634,GnomAD)
C==0271 (7893/29118,TOPMED)
C==0231 (1158/5008,1000G)
C==0372 (1435/3854,ALSPAC)
C==0388 (1438/3708,TWINSUK)

Position: chr1:146006739 (GRCh38.p7) (1q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 66 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.146006739A>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH	NW_003871055.3:g.2822152A>G
GRCh37.p13 chr 1	NC_000001.10:g.145428296C>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.110	A==0.890
1000Genomes	American	Sub	694	G=0.370	A==0.630
1000Genomes	East Asian	Sub	1008	G=0.165	A==0.835
1000Genomes	Europe	Sub	1006	G=0.363	A==0.637
1000Genomes	Global	Study-wide	5008	G=0.231	A==0.769
1000Genomes	South Asian	Sub	978	G=0.230	A==0.770
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.372	A==0.628
The Genome Aggregation Database	African	Sub	8680	G=0.142	A==0.858
The Genome Aggregation Database	American	Sub	834	G=0.350	A==0.650
The Genome Aggregation Database	East Asian	Sub	1618	G=0.201	A==0.799
The Genome Aggregation Database	Europe	Sub	18202	G=0.366	A==0.633
The Genome Aggregation Database	Global	Study-wide	29634	G=0.290	A==0.709
The Genome Aggregation Database	Other	Sub	300	G=0.330	A==0.670
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.271	A==0.728
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.388	A==0.612

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
rs6661602	0.000276	alcohol dependence	21314694

eQTL of rs6661602 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:145428296	NBPF10	ENSG00000163386.16	C>T	3.4331e-5	138524	Caudate_basal_ganglia
Chr1:145428296	NBPF10	ENSG00000163386.16	C>T	1.4690e-4	138524	Amygdala
Chr1:145428296	RP11-458D21.1	ENSG00000233396.3	C>T	5.9981e-5	45862	Amygdala

meQTL of rs6661602 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	2865591	2865653	E067	43439
chr1	2822509	2822559	E068	357
chr1	2822743	2822945	E068	591
chr1	2865591	2865653	E068	43439
chr1	2869245	2869307	E068	47093
chr1	2790932	2791042	E069	-31110
chr1	2791187	2791460	E069	-30692
chr1	2792392	2792476	E069	-29676
chr1	2792593	2792885	E069	-29267
chr1	2792889	2793063	E069	-29089
chr1	2822509	2822559	E069	357
chr1	2822743	2822945	E069	591
chr1	2865591	2865653	E069	43439
chr1	2866679	2866841	E069	44527
chr1	2867429	2867483	E069	45277
chr1	2867775	2867876	E069	45623
chr1	2869245	2869307	E069	47093
chr1	2790932	2791042	E070	-31110
chr1	2791187	2791460	E070	-30692
chr1	2791711	2792291	E070	-29861
chr1	2808713	2808835	E070	-13317
chr1	2829326	2829566	E070	7174
chr1	2772548	2772635	E071	-49517
chr1	2790932	2791042	E071	-31110
chr1	2791187	2791460	E071	-30692
chr1	2792392	2792476	E071	-29676
chr1	2822509	2822559	E071	357
chr1	2822743	2822945	E071	591
chr1	2865591	2865653	E071	43439
chr1	2866679	2866841	E071	44527
chr1	2869245	2869307	E071	47093
chr1	2822509	2822559	E072	357
chr1	2822743	2822945	E072	591
chr1	2831418	2831531	E072	9266
chr1	2865591	2865653	E072	43439
chr1	2866679	2866841	E072	44527
chr1	2867429	2867483	E072	45277
chr1	2869245	2869307	E072	47093
chr1	2869638	2869709	E072	47486
chr1	2822509	2822559	E073	357
chr1	2822743	2822945	E073	591
chr1	2865591	2865653	E073	43439
chr1	2791711	2792291	E074	-29861
chr1	2792392	2792476	E074	-29676
chr1	2822509	2822559	E074	357
chr1	2822743	2822945	E074	591
chr1	2865591	2865653	E074	43439
chr1	2866679	2866841	E074	44527
chr1	2869245	2869307	E074	47093
chr1	2772548	2772635	E081	-49517
chr1	2792392	2792476	E081	-29676
chr1	2792593	2792885	E081	-29267
chr1	2792889	2793063	E081	-29089
chr1	2799612	2800018	E081	-22134
chr1	2800074	2800114	E081	-22038
chr1	2828002	2828361	E081	5850
chr1	2829326	2829566	E081	7174
chr1	2842586	2842691	E081	20434
chr1	2843561	2843615	E081	21409
chr1	2844051	2844250	E081	21899
chr1	2844473	2844798	E081	22321
chr1	2845290	2845484	E081	23138
chr1	2822509	2822559	E082	357
chr1	2828002	2828361	E082	5850
chr1	2844473	2844798	E082	22321
chr1	2845290	2845484	E082	23138