rs4851222

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

AFF3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0441 (13190/29890,GnomAD)
G==0414 (12078/29116,TOPMED)
G==0401 (2007/5008,1000G)
A=0453 (2069/4566,GO-ESP)
A=0479 (1845/3854,ALSPAC)
A=0459 (1703/3708,TWINSUK)

Position: chr2:99672469 (GRCh38.p7) (2q11.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 156 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.99672469G>A
GRCh37.p13 chr 2	NC_000002.11:g.100288931G>A

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 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
AFF3 transcript variant X13	XM_011511178.2:c.	N/A	5 Prime UTR Variant
AFF3 transcript variant X14	XM_011511179.2:c.	N/A	5 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.262	A=0.738
1000Genomes	American	Sub	694	G=0.470	A=0.530
1000Genomes	East Asian	Sub	1008	G=0.346	A=0.654
1000Genomes	Europe	Sub	1006	G=0.536	A=0.464
1000Genomes	Global	Study-wide	5008	G=0.401	A=0.599
1000Genomes	South Asian	Sub	978	G=0.460	A=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.521	A=0.479
The Genome Aggregation Database	African	Sub	8688	G=0.309	A=0.691
The Genome Aggregation Database	American	Sub	838	G=0.400	A=0.600
The Genome Aggregation Database	East Asian	Sub	1612	G=0.363	A=0.637
The Genome Aggregation Database	Europe	Sub	18450	G=0.509	A=0.490
The Genome Aggregation Database	Global	Study-wide	29890	G=0.441	A=0.558
The Genome Aggregation Database	Other	Sub	302	G=0.590	A=0.410
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.414	A=0.585
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.541	A=0.459

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
rs4851222	0.00058	alcohol dependence	24277619

eQTL of rs4851222 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 rs4851222 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	-27605
chr2	100264602	100265344	E067	-23587
chr2	100278933	100279064	E067	-9867
chr2	100279081	100279877	E067	-9054
chr2	100316940	100317229	E067	28009
chr2	100241001	100241112	E068	-47819
chr2	100241147	100241225	E068	-47706
chr2	100252656	100253534	E068	-35397
chr2	100253546	100253626	E068	-35305
chr2	100260366	100261326	E068	-27605
chr2	100265445	100265933	E068	-22998
chr2	100270905	100271253	E068	-17678
chr2	100278933	100279064	E068	-9867
chr2	100279081	100279877	E068	-9054
chr2	100280258	100280367	E068	-8564
chr2	100294029	100294176	E068	5098
chr2	100294441	100294510	E068	5510
chr2	100252418	100252535	E069	-36396
chr2	100252656	100253534	E069	-35397
chr2	100253546	100253626	E069	-35305
chr2	100260366	100261326	E069	-27605
chr2	100270905	100271253	E069	-17678
chr2	100278933	100279064	E069	-9867
chr2	100279081	100279877	E069	-9054
chr2	100294029	100294176	E069	5098
chr2	100294441	100294510	E069	5510
chr2	100316940	100317229	E069	28009
chr2	100241001	100241112	E070	-47819
chr2	100241147	100241225	E070	-47706
chr2	100241278	100241448	E070	-47483
chr2	100252656	100253534	E070	-35397
chr2	100253546	100253626	E070	-35305
chr2	100253709	100254047	E070	-34884
chr2	100260366	100261326	E070	-27605
chr2	100264602	100265344	E070	-23587
chr2	100265445	100265933	E070	-22998
chr2	100266211	100266261	E070	-22670
chr2	100277287	100277514	E070	-11417
chr2	100279081	100279877	E070	-9054
chr2	100280258	100280367	E070	-8564
chr2	100311651	100311820	E070	22720
chr2	100311835	100311898	E070	22904
chr2	100323161	100323787	E070	34230
chr2	100252418	100252535	E071	-36396
chr2	100252656	100253534	E071	-35397
chr2	100253546	100253626	E071	-35305
chr2	100253709	100254047	E071	-34884
chr2	100260366	100261326	E071	-27605
chr2	100270905	100271253	E071	-17678
chr2	100277287	100277514	E071	-11417
chr2	100277517	100277805	E071	-11126
chr2	100277886	100277930	E071	-11001
chr2	100278933	100279064	E071	-9867
chr2	100279081	100279877	E071	-9054
chr2	100316940	100317229	E071	28009
chr2	100323161	100323787	E071	34230
chr2	100326410	100326551	E071	37479
chr2	100252418	100252535	E072	-36396
chr2	100252656	100253534	E072	-35397
chr2	100253546	100253626	E072	-35305
chr2	100260366	100261326	E072	-27605
chr2	100278933	100279064	E072	-9867
chr2	100279081	100279877	E072	-9054
chr2	100280258	100280367	E072	-8564
chr2	100294029	100294176	E072	5098
chr2	100294441	100294510	E072	5510
chr2	100316494	100316583	E072	27563
chr2	100316940	100317229	E072	28009
chr2	100260366	100261326	E073	-27605
chr2	100264602	100265344	E073	-23587
chr2	100265445	100265933	E073	-22998
chr2	100278933	100279064	E073	-9867
chr2	100279081	100279877	E073	-9054
chr2	100280258	100280367	E073	-8564
chr2	100252418	100252535	E074	-36396
chr2	100252656	100253534	E074	-35397
chr2	100253546	100253626	E074	-35305
chr2	100260366	100261326	E074	-27605
chr2	100279081	100279877	E074	-9054
chr2	100294029	100294176	E074	5098
chr2	100316494	100316583	E074	27563
chr2	100316940	100317229	E074	28009
chr2	100323161	100323787	E074	34230
chr2	100239174	100239250	E081	-49681
chr2	100239253	100239423	E081	-49508
chr2	100241001	100241112	E081	-47819
chr2	100241147	100241225	E081	-47706
chr2	100241278	100241448	E081	-47483
chr2	100241712	100241766	E081	-47165
chr2	100242386	100242511	E081	-46420
chr2	100251107	100251481	E081	-37450
chr2	100252656	100253534	E081	-35397
chr2	100253546	100253626	E081	-35305
chr2	100253709	100254047	E081	-34884
chr2	100254129	100254352	E081	-34579
chr2	100254360	100254650	E081	-34281
chr2	100262494	100262845	E081	-26086
chr2	100264285	100264369	E081	-24562
chr2	100264602	100265344	E081	-23587
chr2	100265445	100265933	E081	-22998
chr2	100266020	100266132	E081	-22799
chr2	100266211	100266261	E081	-22670
chr2	100266351	100266405	E081	-22526
chr2	100270118	100270194	E081	-18737
chr2	100295949	100296005	E081	7018
chr2	100296127	100296220	E081	7196
chr2	100311651	100311820	E081	22720
chr2	100311835	100311898	E081	22904
chr2	100318142	100318437	E081	29211
chr2	100322352	100322418	E081	33421
chr2	100322867	100322952	E081	33936
chr2	100323161	100323787	E081	34230
chr2	100323798	100323957	E081	34867
chr2	100323985	100324406	E081	35054
chr2	100324629	100325025	E081	35698
chr2	100326410	100326551	E081	37479
chr2	100327134	100327609	E081	38203
chr2	100327611	100327790	E081	38680
chr2	100327791	100328115	E081	38860
chr2	100328442	100328496	E081	39511
chr2	100239174	100239250	E082	-49681
chr2	100239253	100239423	E082	-49508
chr2	100241001	100241112	E082	-47819
chr2	100241147	100241225	E082	-47706
chr2	100241278	100241448	E082	-47483
chr2	100241712	100241766	E082	-47165
chr2	100242386	100242511	E082	-46420
chr2	100252656	100253534	E082	-35397
chr2	100253546	100253626	E082	-35305
chr2	100253709	100254047	E082	-34884
chr2	100254129	100254352	E082	-34579
chr2	100256973	100257605	E082	-31326
chr2	100260366	100261326	E082	-27605
chr2	100264285	100264369	E082	-24562
chr2	100264602	100265344	E082	-23587
chr2	100265445	100265933	E082	-22998
chr2	100266020	100266132	E082	-22799
chr2	100266211	100266261	E082	-22670
chr2	100266351	100266405	E082	-22526
chr2	100270905	100271253	E082	-17678
chr2	100280258	100280367	E082	-8564
chr2	100294029	100294176	E082	5098
chr2	100294441	100294510	E082	5510
chr2	100294758	100294954	E082	5827
chr2	100311651	100311820	E082	22720
chr2	100311835	100311898	E082	22904
chr2	100322867	100322952	E082	33936
chr2	100323161	100323787	E082	34230
chr2	100323798	100323957	E082	34867
chr2	100323985	100324406	E082	35054
chr2	100324629	100325025	E082	35698
chr2	100326410	100326551	E082	37479
chr2	100327134	100327609	E082	38203
chr2	100327611	100327790	E082	38680
chr2	100327791	100328115	E082	38860
chr2	100328442	100328496	E082	39511