rs11676683

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

AFF3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0425 (12706/29894,GnomAD)
A==0399 (11642/29116,TOPMED)
A==0392 (1962/5008,1000G)
A==0498 (1921/3854,ALSPAC)
C=0491 (1821/3708,TWINSUK)

Position: chr2:99659463 (GRCh38.p7) (2q11.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 164 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.99659463A>C
GRCh37.p13 chr 2	NC_000002.11:g.100275925A>C

Gene: AFF3, AF4/FMR2 family member 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AFF3 transcript variant 2	NM_001025108.1:c.	N/A	Intron Variant
AFF3 transcript variant 1	NM_002285.2:c.	N/A	Intron Variant
AFF3 transcript variant X10	XM_005263943.3:c.	N/A	Intron Variant
AFF3 transcript variant X11	XM_005263945.3:c.	N/A	Intron Variant
AFF3 transcript variant X1	XM_011511169.2:c.	N/A	Intron Variant
AFF3 transcript variant X4	XM_011511170.2:c.	N/A	Intron Variant
AFF3 transcript variant X2	XM_011511171.2:c.	N/A	Intron Variant
AFF3 transcript variant X3	XM_011511172.2:c.	N/A	Intron Variant
AFF3 transcript variant X5	XM_011511173.2:c.	N/A	Intron Variant
AFF3 transcript variant X6	XM_011511174.2:c.	N/A	Intron Variant
AFF3 transcript variant X7	XM_011511175.2:c.	N/A	Intron Variant
AFF3 transcript variant X8	XM_011511176.2:c.	N/A	Intron Variant
AFF3 transcript variant X9	XM_011511177.2:c.	N/A	Intron Variant
AFF3 transcript variant X13	XM_011511178.2:c.	N/A	Intron Variant
AFF3 transcript variant X14	XM_011511179.2:c.	N/A	Intron Variant
AFF3 transcript variant X12	XM_017004085.1:c.	N/A	Intron Variant
AFF3 transcript variant X15	XM_017004086.1:c.	N/A	Intron Variant
AFF3 transcript variant X16	XM_017004087.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.263	C=0.737
1000Genomes	American	Sub	694	A=0.460	C=0.540
1000Genomes	East Asian	Sub	1008	A=0.343	C=0.657
1000Genomes	Europe	Sub	1006	A=0.509	C=0.491
1000Genomes	Global	Study-wide	5008	A=0.392	C=0.608
1000Genomes	South Asian	Sub	978	A=0.450	C=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.498	C=0.502
The Genome Aggregation Database	African	Sub	8700	A=0.308	C=0.692
The Genome Aggregation Database	American	Sub	836	A=0.380	C=0.620
The Genome Aggregation Database	East Asian	Sub	1618	A=0.362	C=0.638
The Genome Aggregation Database	Europe	Sub	18438	A=0.486	C=0.513
The Genome Aggregation Database	Global	Study-wide	29894	A=0.425	C=0.575
The Genome Aggregation Database	Other	Sub	302	A=0.530	C=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.399	C=0.600
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.509	C=0.491

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs11676683	0.00058	alcohol dependence	24277619

eQTL of rs11676683 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 rs11676683 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 )
chr2	100260366	100261326	E067	-14599
chr2	100264602	100265344	E067	-10581
chr2	100278933	100279064	E067	3008
chr2	100279081	100279877	E067	3156
chr2	100316940	100317229	E067	41015
chr2	100241001	100241112	E068	-34813
chr2	100241147	100241225	E068	-34700
chr2	100252656	100253534	E068	-22391
chr2	100253546	100253626	E068	-22299
chr2	100260366	100261326	E068	-14599
chr2	100265445	100265933	E068	-9992
chr2	100270905	100271253	E068	-4672
chr2	100278933	100279064	E068	3008
chr2	100279081	100279877	E068	3156
chr2	100280258	100280367	E068	4333
chr2	100294029	100294176	E068	18104
chr2	100294441	100294510	E068	18516
chr2	100232218	100232360	E069	-43565
chr2	100252418	100252535	E069	-23390
chr2	100252656	100253534	E069	-22391
chr2	100253546	100253626	E069	-22299
chr2	100260366	100261326	E069	-14599
chr2	100270905	100271253	E069	-4672
chr2	100278933	100279064	E069	3008
chr2	100279081	100279877	E069	3156
chr2	100294029	100294176	E069	18104
chr2	100294441	100294510	E069	18516
chr2	100316940	100317229	E069	41015
chr2	100241001	100241112	E070	-34813
chr2	100241147	100241225	E070	-34700
chr2	100241278	100241448	E070	-34477
chr2	100252656	100253534	E070	-22391
chr2	100253546	100253626	E070	-22299
chr2	100253709	100254047	E070	-21878
chr2	100260366	100261326	E070	-14599
chr2	100264602	100265344	E070	-10581
chr2	100265445	100265933	E070	-9992
chr2	100266211	100266261	E070	-9664
chr2	100277287	100277514	E070	1362
chr2	100279081	100279877	E070	3156
chr2	100280258	100280367	E070	4333
chr2	100311651	100311820	E070	35726
chr2	100311835	100311898	E070	35910
chr2	100323161	100323787	E070	47236
chr2	100232218	100232360	E071	-43565
chr2	100252418	100252535	E071	-23390
chr2	100252656	100253534	E071	-22391
chr2	100253546	100253626	E071	-22299
chr2	100253709	100254047	E071	-21878
chr2	100260366	100261326	E071	-14599
chr2	100270905	100271253	E071	-4672
chr2	100277287	100277514	E071	1362
chr2	100277517	100277805	E071	1592
chr2	100277886	100277930	E071	1961
chr2	100278933	100279064	E071	3008
chr2	100279081	100279877	E071	3156
chr2	100316940	100317229	E071	41015
chr2	100323161	100323787	E071	47236
chr2	100232218	100232360	E072	-43565
chr2	100252418	100252535	E072	-23390
chr2	100252656	100253534	E072	-22391
chr2	100253546	100253626	E072	-22299
chr2	100260366	100261326	E072	-14599
chr2	100278933	100279064	E072	3008
chr2	100279081	100279877	E072	3156
chr2	100280258	100280367	E072	4333
chr2	100294029	100294176	E072	18104
chr2	100294441	100294510	E072	18516
chr2	100316494	100316583	E072	40569
chr2	100316940	100317229	E072	41015
chr2	100229296	100229397	E073	-46528
chr2	100231592	100232186	E073	-43739
chr2	100260366	100261326	E073	-14599
chr2	100264602	100265344	E073	-10581
chr2	100265445	100265933	E073	-9992
chr2	100278933	100279064	E073	3008
chr2	100279081	100279877	E073	3156
chr2	100280258	100280367	E073	4333
chr2	100252418	100252535	E074	-23390
chr2	100252656	100253534	E074	-22391
chr2	100253546	100253626	E074	-22299
chr2	100260366	100261326	E074	-14599
chr2	100279081	100279877	E074	3156
chr2	100294029	100294176	E074	18104
chr2	100316494	100316583	E074	40569
chr2	100316940	100317229	E074	41015
chr2	100323161	100323787	E074	47236
chr2	100226186	100226765	E081	-49160
chr2	100228399	100228458	E081	-47467
chr2	100229034	100229117	E081	-46808
chr2	100229296	100229397	E081	-46528
chr2	100232218	100232360	E081	-43565
chr2	100234337	100234406	E081	-41519
chr2	100234484	100234569	E081	-41356
chr2	100235541	100236105	E081	-39820
chr2	100237500	100237550	E081	-38375
chr2	100237652	100237855	E081	-38070
chr2	100237972	100238049	E081	-37876
chr2	100238211	100238529	E081	-37396
chr2	100239174	100239250	E081	-36675
chr2	100239253	100239423	E081	-36502
chr2	100241001	100241112	E081	-34813
chr2	100241147	100241225	E081	-34700
chr2	100241278	100241448	E081	-34477
chr2	100241712	100241766	E081	-34159
chr2	100242386	100242511	E081	-33414
chr2	100251107	100251481	E081	-24444
chr2	100252656	100253534	E081	-22391
chr2	100253546	100253626	E081	-22299
chr2	100253709	100254047	E081	-21878
chr2	100254129	100254352	E081	-21573
chr2	100254360	100254650	E081	-21275
chr2	100262494	100262845	E081	-13080
chr2	100264285	100264369	E081	-11556
chr2	100264602	100265344	E081	-10581
chr2	100265445	100265933	E081	-9992
chr2	100266020	100266132	E081	-9793
chr2	100266211	100266261	E081	-9664
chr2	100266351	100266405	E081	-9520
chr2	100270118	100270194	E081	-5731
chr2	100295949	100296005	E081	20024
chr2	100296127	100296220	E081	20202
chr2	100311651	100311820	E081	35726
chr2	100311835	100311898	E081	35910
chr2	100318142	100318437	E081	42217
chr2	100322352	100322418	E081	46427
chr2	100322867	100322952	E081	46942
chr2	100323161	100323787	E081	47236
chr2	100323798	100323957	E081	47873
chr2	100323985	100324406	E081	48060
chr2	100324629	100325025	E081	48704
chr2	100235541	100236105	E082	-39820
chr2	100237500	100237550	E082	-38375
chr2	100239174	100239250	E082	-36675
chr2	100239253	100239423	E082	-36502
chr2	100241001	100241112	E082	-34813
chr2	100241147	100241225	E082	-34700
chr2	100241278	100241448	E082	-34477
chr2	100241712	100241766	E082	-34159
chr2	100242386	100242511	E082	-33414
chr2	100252656	100253534	E082	-22391
chr2	100253546	100253626	E082	-22299
chr2	100253709	100254047	E082	-21878
chr2	100254129	100254352	E082	-21573
chr2	100256973	100257605	E082	-18320
chr2	100260366	100261326	E082	-14599
chr2	100264285	100264369	E082	-11556
chr2	100264602	100265344	E082	-10581
chr2	100265445	100265933	E082	-9992
chr2	100266020	100266132	E082	-9793
chr2	100266211	100266261	E082	-9664
chr2	100266351	100266405	E082	-9520
chr2	100270905	100271253	E082	-4672
chr2	100280258	100280367	E082	4333
chr2	100294029	100294176	E082	18104
chr2	100294441	100294510	E082	18516
chr2	100294758	100294954	E082	18833
chr2	100311651	100311820	E082	35726
chr2	100311835	100311898	E082	35910
chr2	100322867	100322952	E082	46942
chr2	100323161	100323787	E082	47236
chr2	100323798	100323957	E082	47873
chr2	100323985	100324406	E082	48060
chr2	100324629	100325025	E082	48704