rs6698987

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

DNM3 : Intron Variant
LOC102724528 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0157 (4674/29768,GnomAD)
C=0228 (6661/29118,TOPMED)
C=0203 (1018/5008,1000G)
C=0040 (153/3854,ALSPAC)
C=0047 (176/3708,TWINSUK)

Position: chr1:172399827 (GRCh38.p7) (1q24.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 188 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.172399827T>C
GRCh37.p13 chr 1	NC_000001.10:g.172368967T>C

Gene: DNM3, dynamin 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DNM3 transcript variant 2	NM_001136127.2:c.	N/A	Intron Variant
DNM3 transcript variant 1	NM_015569.4:c.	N/A	Intron Variant
DNM3 transcript variant 3	NM_001278252.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X6	XM_005245079.1:c.	N/A	Intron Variant
DNM3 transcript variant X7	XM_005245080.1:c.	N/A	Intron Variant
DNM3 transcript variant X1	XM_017000976.1:c.	N/A	Intron Variant
DNM3 transcript variant X2	XM_017000977.1:c.	N/A	Intron Variant
DNM3 transcript variant X3	XM_017000978.1:c.	N/A	Intron Variant
DNM3 transcript variant X4	XM_017000979.1:c.	N/A	Intron Variant
DNM3 transcript variant X5	XM_017000980.1:c.	N/A	Intron Variant
DNM3 transcript variant X8	XM_017000981.1:c.	N/A	Intron Variant
DNM3 transcript variant X8	XM_017000983.1:c.	N/A	Intron Variant
DNM3 transcript variant X9	XM_017000984.1:c.	N/A	Intron Variant
DNM3 transcript variant X12	XM_017000987.1:c.	N/A	Intron Variant
DNM3 transcript variant X18	XM_006711268.2:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X9	XM_017000982.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X10	XM_017000985.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X11	XM_017000986.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X13	XM_017000988.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X15	XM_017000989.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X21	XM_017000990.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X18	XM_017000991.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X21	XM_017000992.1:c.	N/A	Genic Downstream Transcript Variant
DNM3 transcript variant X16	XR_001737108.1:n.	N/A	Intron Variant
DNM3 transcript variant X20	XR_001737109.1:n.	N/A	Intron Variant
DNM3 transcript variant X19	XR_001737110.1:n.	N/A	Intron Variant
DNM3 transcript variant X20	XR_001737111.1:n.	N/A	Intron Variant
DNM3 transcript variant X14	XR_001737107.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC102724528, uncharacterized LOC102724528(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724528 transcript variant X2	XR_001738292.1:n....XR_001738292.1:n.1726A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X1	XR_922283.2:n.186A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X3	XR_922284.2:n.186A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X4	XR_001738293.1:n....XR_001738293.1:n.1717A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X5	XR_922285.2:n.105A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X6	XR_001738294.1:n....XR_001738294.1:n.105A>G	A>G	Non Coding Transcript Variant
LOC102724528 transcript variant X7	XR_001738295.1:n....XR_001738295.1:n.937A>G	A>G	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.503	C=0.497
1000Genomes	American	Sub	694	T=0.880	C=0.120
1000Genomes	East Asian	Sub	1008	T=0.874	C=0.126
1000Genomes	Europe	Sub	1006	T=0.960	C=0.040
1000Genomes	Global	Study-wide	5008	T=0.797	C=0.203
1000Genomes	South Asian	Sub	978	T=0.890	C=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.960	C=0.040
The Genome Aggregation Database	African	Sub	8634	T=0.584	C=0.416
The Genome Aggregation Database	American	Sub	830	T=0.910	C=0.090
The Genome Aggregation Database	East Asian	Sub	1608	T=0.889	C=0.111
The Genome Aggregation Database	Europe	Sub	18394	T=0.955	C=0.044
The Genome Aggregation Database	Global	Study-wide	29768	T=0.843	C=0.157
The Genome Aggregation Database	Other	Sub	302	T=0.980	C=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.771	C=0.228
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.953	C=0.047

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
rs6698987	0.000176	alcohol dependence	21314694

eQTL of rs6698987 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 rs6698987 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	172327033	172327253	E067	-41714
chr1	172327261	172329194	E067	-39773
chr1	172329287	172329406	E067	-39561
chr1	172329658	172330481	E067	-38486
chr1	172359779	172361214	E067	-7753
chr1	172361938	172361988	E067	-6979
chr1	172362126	172362413	E067	-6554
chr1	172362615	172362856	E067	-6111
chr1	172363260	172363847	E067	-5120
chr1	172363850	172363957	E067	-5010
chr1	172363959	172364223	E067	-4744
chr1	172366518	172366825	E067	-2142
chr1	172366959	172367027	E067	-1940
chr1	172367240	172369550	E067	0
chr1	172369573	172369772	E067	606
chr1	172372106	172372173	E067	3139
chr1	172372201	172372284	E067	3234
chr1	172372401	172372586	E067	3434
chr1	172372814	172372899	E067	3847
chr1	172320543	172321383	E068	-47584
chr1	172327261	172329194	E068	-39773
chr1	172329287	172329406	E068	-39561
chr1	172329658	172330481	E068	-38486
chr1	172330644	172330694	E068	-38273
chr1	172332073	172332148	E068	-36819
chr1	172344405	172344679	E068	-24288
chr1	172359463	172359654	E068	-9313
chr1	172359664	172359772	E068	-9195
chr1	172359779	172361214	E068	-7753
chr1	172362126	172362413	E068	-6554
chr1	172362615	172362856	E068	-6111
chr1	172363260	172363847	E068	-5120
chr1	172363850	172363957	E068	-5010
chr1	172363959	172364223	E068	-4744
chr1	172366518	172366825	E068	-2142
chr1	172366959	172367027	E068	-1940
chr1	172367240	172369550	E068	0
chr1	172369573	172369772	E068	606
chr1	172371754	172371829	E068	2787
chr1	172371892	172371942	E068	2925
chr1	172372106	172372173	E068	3139
chr1	172372201	172372284	E068	3234
chr1	172372401	172372586	E068	3434
chr1	172390886	172390999	E068	21919
chr1	172391211	172391290	E068	22244
chr1	172391391	172391448	E068	22424
chr1	172411644	172411688	E068	42677
chr1	172413625	172413772	E068	44658
chr1	172320121	172320220	E069	-48747
chr1	172320223	172320539	E069	-48428
chr1	172320543	172321383	E069	-47584
chr1	172326734	172326852	E069	-42115
chr1	172327033	172327253	E069	-41714
chr1	172327261	172329194	E069	-39773
chr1	172329287	172329406	E069	-39561
chr1	172329658	172330481	E069	-38486
chr1	172359463	172359654	E069	-9313
chr1	172359664	172359772	E069	-9195
chr1	172359779	172361214	E069	-7753
chr1	172362615	172362856	E069	-6111
chr1	172363260	172363847	E069	-5120
chr1	172363850	172363957	E069	-5010
chr1	172363959	172364223	E069	-4744
chr1	172364744	172365202	E069	-3765
chr1	172365514	172365581	E069	-3386
chr1	172366518	172366825	E069	-2142
chr1	172366959	172367027	E069	-1940
chr1	172367240	172369550	E069	0
chr1	172369573	172369772	E069	606
chr1	172371754	172371829	E069	2787
chr1	172371892	172371942	E069	2925
chr1	172372106	172372173	E069	3139
chr1	172372201	172372284	E069	3234
chr1	172372401	172372586	E069	3434
chr1	172372814	172372899	E069	3847
chr1	172390886	172390999	E069	21919
chr1	172391211	172391290	E069	22244
chr1	172391391	172391448	E069	22424
chr1	172327033	172327253	E070	-41714
chr1	172327261	172329194	E070	-39773
chr1	172411644	172411688	E070	42677
chr1	172413625	172413772	E070	44658
chr1	172319791	172319860	E071	-49107
chr1	172320121	172320220	E071	-48747
chr1	172320223	172320539	E071	-48428
chr1	172320543	172321383	E071	-47584
chr1	172327033	172327253	E071	-41714
chr1	172329287	172329406	E071	-39561
chr1	172329658	172330481	E071	-38486
chr1	172330644	172330694	E071	-38273
chr1	172330916	172331005	E071	-37962
chr1	172344405	172344679	E071	-24288
chr1	172358058	172358122	E071	-10845
chr1	172359463	172359654	E071	-9313
chr1	172359664	172359772	E071	-9195
chr1	172359779	172361214	E071	-7753
chr1	172361227	172361368	E071	-7599
chr1	172361938	172361988	E071	-6979
chr1	172362126	172362413	E071	-6554
chr1	172362615	172362856	E071	-6111
chr1	172363260	172363847	E071	-5120
chr1	172363850	172363957	E071	-5010
chr1	172363959	172364223	E071	-4744
chr1	172366959	172367027	E071	-1940
chr1	172367240	172369550	E071	0
chr1	172369573	172369772	E071	606
chr1	172372401	172372586	E071	3434
chr1	172372814	172372899	E071	3847
chr1	172390886	172390999	E071	21919
chr1	172391211	172391290	E071	22244
chr1	172391391	172391448	E071	22424
chr1	172411644	172411688	E071	42677
chr1	172413625	172413772	E071	44658
chr1	172320543	172321383	E072	-47584
chr1	172327033	172327253	E072	-41714
chr1	172327261	172329194	E072	-39773
chr1	172329287	172329406	E072	-39561
chr1	172329658	172330481	E072	-38486
chr1	172330644	172330694	E072	-38273
chr1	172330916	172331005	E072	-37962
chr1	172332073	172332148	E072	-36819
chr1	172344405	172344679	E072	-24288
chr1	172359463	172359654	E072	-9313
chr1	172359664	172359772	E072	-9195
chr1	172361938	172361988	E072	-6979
chr1	172362126	172362413	E072	-6554
chr1	172362615	172362856	E072	-6111
chr1	172363850	172363957	E072	-5010
chr1	172363959	172364223	E072	-4744
chr1	172366959	172367027	E072	-1940
chr1	172367240	172369550	E072	0
chr1	172369573	172369772	E072	606
chr1	172372401	172372586	E072	3434
chr1	172390886	172390999	E072	21919
chr1	172391211	172391290	E072	22244
chr1	172391391	172391448	E072	22424
chr1	172326734	172326852	E073	-42115
chr1	172327033	172327253	E073	-41714
chr1	172327261	172329194	E073	-39773
chr1	172329287	172329406	E073	-39561
chr1	172329658	172330481	E073	-38486
chr1	172363260	172363847	E073	-5120
chr1	172363850	172363957	E073	-5010
chr1	172363959	172364223	E073	-4744
chr1	172399027	172399098	E073	30060
chr1	172411644	172411688	E073	42677
chr1	172320121	172320220	E074	-48747
chr1	172320223	172320539	E074	-48428
chr1	172320543	172321383	E074	-47584
chr1	172327033	172327253	E074	-41714
chr1	172327261	172329194	E074	-39773
chr1	172329287	172329406	E074	-39561
chr1	172329658	172330481	E074	-38486
chr1	172330644	172330694	E074	-38273
chr1	172330916	172331005	E074	-37962
chr1	172332073	172332148	E074	-36819
chr1	172344405	172344679	E074	-24288
chr1	172347009	172347105	E074	-21862
chr1	172347156	172347206	E074	-21761
chr1	172358058	172358122	E074	-10845
chr1	172358180	172358230	E074	-10737
chr1	172359463	172359654	E074	-9313
chr1	172359664	172359772	E074	-9195
chr1	172362126	172362413	E074	-6554
chr1	172362615	172362856	E074	-6111
chr1	172363260	172363847	E074	-5120
chr1	172363850	172363957	E074	-5010
chr1	172366518	172366825	E074	-2142
chr1	172366959	172367027	E074	-1940
chr1	172367240	172369550	E074	0
chr1	172372201	172372284	E074	3234
chr1	172372401	172372586	E074	3434
chr1	172372814	172372899	E074	3847
chr1	172390886	172390999	E074	21919
chr1	172391211	172391290	E074	22244
chr1	172391391	172391448	E074	22424
chr1	172398437	172398912	E074	29470
chr1	172398913	172398978	E074	29946
chr1	172399027	172399098	E074	30060
chr1	172413625	172413772	E074	44658
chr1	172327261	172329194	E081	-39773
chr1	172363959	172364223	E081	-4744
chr1	172364744	172365202	E081	-3765
chr1	172365514	172365581	E081	-3386
chr1	172413625	172413772	E081	44658
chr1	172329287	172329406	E082	-39561
chr1	172363959	172364223	E082	-4744
chr1	172364744	172365202	E082	-3765

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	172412379	172412419	E067	43412
chr1	172412635	172413621	E067	43668
chr1	172412379	172412419	E068	43412
chr1	172412635	172413621	E068	43668
chr1	172412379	172412419	E069	43412
chr1	172412635	172413621	E069	43668
chr1	172412379	172412419	E070	43412
chr1	172412635	172413621	E070	43668
chr1	172412379	172412419	E071	43412
chr1	172412635	172413621	E071	43668
chr1	172412379	172412419	E072	43412
chr1	172412635	172413621	E072	43668
chr1	172412379	172412419	E073	43412
chr1	172412635	172413621	E073	43668
chr1	172412379	172412419	E074	43412
chr1	172412635	172413621	E074	43668
chr1	172412379	172412419	E081	43412
chr1	172412635	172413621	E081	43668
chr1	172412379	172412419	E082	43412
chr1	172412635	172413621	E082	43668