rs2255723

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0280 (8387/29866,GnomAD)
G==0267 (7789/29118,TOPMED)
G==0193 (968/5008,1000G)
G==0366 (1410/3854,ALSPAC)
G==0378 (1400/3708,TWINSUK)

Position: chr1:92902752 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 264 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.92902752G>T
GRCh37.p13 chr 1	NC_000001.10:g.93368309G>T
FAM69A RefSeqGene	NG_033051.1:g.63771C>A

Gene: FAM69A, family with sequence similarity 69 member A(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM69A transcript variant 1	NM_001006605.4:c.	N/A	Intron Variant
FAM69A transcript variant 2	NM_001252269.1:c.	N/A	Intron Variant
FAM69A transcript variant 3	NM_001252270.1:c.	N/A	Intron Variant
FAM69A transcript variant 5	NM_001252273.1:c.	N/A	Intron Variant
FAM69A transcript variant 4	NM_001252271.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.157	T=0.843
1000Genomes	American	Sub	694	G=0.270	T=0.730
1000Genomes	East Asian	Sub	1008	G=0.035	T=0.965
1000Genomes	Europe	Sub	1006	G=0.366	T=0.634
1000Genomes	Global	Study-wide	5008	G=0.193	T=0.807
1000Genomes	South Asian	Sub	978	G=0.180	T=0.820
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.366	T=0.634
The Genome Aggregation Database	African	Sub	8686	G=0.170	T=0.830
The Genome Aggregation Database	American	Sub	838	G=0.230	T=0.770
The Genome Aggregation Database	East Asian	Sub	1622	G=0.042	T=0.958
The Genome Aggregation Database	Europe	Sub	18420	G=0.357	T=0.642
The Genome Aggregation Database	Global	Study-wide	29866	G=0.280	T=0.719
The Genome Aggregation Database	Other	Sub	300	G=0.240	T=0.760
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.267	T=0.732
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.378	T=0.622

PMID	Title	Author	Journal
20087403	Tag-SNP analysis of the GFI1-EVI5-RPL5-FAM69 risk locus for multiple sclerosis.	Alcina A	Eur J Hum Genet
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs2255723	7.2E-05	alcohol consumption	23953852

eQTL of rs2255723 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93368309	FAM69A	ENSG00000154511.7	G>T	2.3665e-3	-58748	Cortex
Chr1:93368309	EVI5	ENSG00000067208.10	G>T	1.7380e-4	110348	Caudate_basal_ganglia

meQTL of rs2255723 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.0669262119126827	6.2034e-35

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	93324170	93325314	E067	-42995
chr1	93325436	93325502	E067	-42807
chr1	93325557	93325675	E067	-42634
chr1	93343820	93343872	E067	-24437
chr1	93345115	93345155	E067	-23154
chr1	93345345	93345583	E067	-22726
chr1	93374886	93375287	E067	6577
chr1	93375470	93375946	E067	7161
chr1	93387980	93388181	E067	19671
chr1	93388368	93388425	E067	20059
chr1	93395074	93395126	E067	26765
chr1	93395262	93395469	E067	26953
chr1	93395476	93395638	E067	27167
chr1	93399397	93399563	E067	31088
chr1	93399901	93399999	E067	31592
chr1	93400049	93400806	E067	31740
chr1	93408809	93409073	E067	40500
chr1	93409807	93409924	E067	41498
chr1	93410075	93410197	E067	41766
chr1	93410636	93410715	E067	42327
chr1	93410897	93411007	E067	42588
chr1	93411087	93411201	E067	42778
chr1	93411573	93411731	E067	43264
chr1	93413201	93413363	E067	44892
chr1	93415652	93415926	E067	47343
chr1	93416028	93416280	E067	47719
chr1	93416304	93416406	E067	47995
chr1	93416622	93417201	E067	48313
chr1	93417658	93417790	E067	49349
chr1	93325436	93325502	E068	-42807
chr1	93325557	93325675	E068	-42634
chr1	93341920	93342406	E068	-25903
chr1	93345115	93345155	E068	-23154
chr1	93345345	93345583	E068	-22726
chr1	93348315	93348424	E068	-19885
chr1	93348501	93348646	E068	-19663
chr1	93348862	93349389	E068	-18920
chr1	93375470	93375946	E068	7161
chr1	93387980	93388181	E068	19671
chr1	93388368	93388425	E068	20059
chr1	93393378	93393664	E068	25069
chr1	93395074	93395126	E068	26765
chr1	93395262	93395469	E068	26953
chr1	93395476	93395638	E068	27167
chr1	93397024	93397554	E068	28715
chr1	93399119	93399316	E068	30810
chr1	93399397	93399563	E068	31088
chr1	93399901	93399999	E068	31592
chr1	93406253	93406443	E068	37944
chr1	93407249	93407329	E068	38940
chr1	93407540	93408010	E068	39231
chr1	93408695	93408757	E068	40386
chr1	93408809	93409073	E068	40500
chr1	93409807	93409924	E068	41498
chr1	93410075	93410197	E068	41766
chr1	93410636	93410715	E068	42327
chr1	93410897	93411007	E068	42588
chr1	93411087	93411201	E068	42778
chr1	93411573	93411731	E068	43264
chr1	93413201	93413363	E068	44892
chr1	93413747	93413884	E068	45438
chr1	93415652	93415926	E068	47343
chr1	93416304	93416406	E068	47995
chr1	93416622	93417201	E068	48313
chr1	93417658	93417790	E068	49349
chr1	93325436	93325502	E069	-42807
chr1	93325557	93325675	E069	-42634
chr1	93343820	93343872	E069	-24437
chr1	93345115	93345155	E069	-23154
chr1	93345345	93345583	E069	-22726
chr1	93348315	93348424	E069	-19885
chr1	93348501	93348646	E069	-19663
chr1	93367434	93367557	E069	-752
chr1	93374886	93375287	E069	6577
chr1	93375470	93375946	E069	7161
chr1	93387980	93388181	E069	19671
chr1	93388368	93388425	E069	20059
chr1	93395074	93395126	E069	26765
chr1	93395262	93395469	E069	26953
chr1	93395476	93395638	E069	27167
chr1	93399119	93399316	E069	30810
chr1	93399397	93399563	E069	31088
chr1	93399901	93399999	E069	31592
chr1	93400049	93400806	E069	31740
chr1	93402249	93402344	E069	33940
chr1	93406253	93406443	E069	37944
chr1	93407540	93408010	E069	39231
chr1	93408695	93408757	E069	40386
chr1	93408809	93409073	E069	40500
chr1	93409807	93409924	E069	41498
chr1	93410075	93410197	E069	41766
chr1	93410636	93410715	E069	42327
chr1	93410897	93411007	E069	42588
chr1	93411087	93411201	E069	42778
chr1	93411573	93411731	E069	43264
chr1	93415652	93415926	E069	47343
chr1	93416028	93416280	E069	47719
chr1	93416304	93416406	E069	47995
chr1	93416622	93417201	E069	48313
chr1	93342489	93342613	E070	-25696
chr1	93342703	93342819	E070	-25490
chr1	93342952	93343219	E070	-25090
chr1	93343266	93343741	E070	-24568
chr1	93343820	93343872	E070	-24437
chr1	93345115	93345155	E070	-23154
chr1	93345345	93345583	E070	-22726
chr1	93400049	93400806	E070	31740
chr1	93401684	93401829	E070	33375
chr1	93407249	93407329	E070	38940
chr1	93407540	93408010	E070	39231
chr1	93408809	93409073	E070	40500
chr1	93319620	93320383	E071	-47926
chr1	93325436	93325502	E071	-42807
chr1	93325557	93325675	E071	-42634
chr1	93338384	93338515	E071	-29794
chr1	93343820	93343872	E071	-24437
chr1	93345115	93345155	E071	-23154
chr1	93345345	93345583	E071	-22726
chr1	93346729	93347461	E071	-20848
chr1	93348501	93348646	E071	-19663
chr1	93348862	93349389	E071	-18920
chr1	93374886	93375287	E071	6577
chr1	93375470	93375946	E071	7161
chr1	93388368	93388425	E071	20059
chr1	93395074	93395126	E071	26765
chr1	93395262	93395469	E071	26953
chr1	93395476	93395638	E071	27167
chr1	93399119	93399316	E071	30810
chr1	93399397	93399563	E071	31088
chr1	93399901	93399999	E071	31592
chr1	93400049	93400806	E071	31740
chr1	93401684	93401829	E071	33375
chr1	93402249	93402344	E071	33940
chr1	93406253	93406443	E071	37944
chr1	93408695	93408757	E071	40386
chr1	93409807	93409924	E071	41498
chr1	93410075	93410197	E071	41766
chr1	93410636	93410715	E071	42327
chr1	93410897	93411007	E071	42588
chr1	93411087	93411201	E071	42778
chr1	93411573	93411731	E071	43264
chr1	93413201	93413363	E071	44892
chr1	93413747	93413884	E071	45438
chr1	93415652	93415926	E071	47343
chr1	93416028	93416280	E071	47719
chr1	93416304	93416406	E071	47995
chr1	93416622	93417201	E071	48313
chr1	93417658	93417790	E071	49349
chr1	93417911	93417961	E071	49602
chr1	93318311	93318384	E072	-49925
chr1	93318988	93319144	E072	-49165
chr1	93324170	93325314	E072	-42995
chr1	93338384	93338515	E072	-29794
chr1	93343820	93343872	E072	-24437
chr1	93345115	93345155	E072	-23154
chr1	93345345	93345583	E072	-22726
chr1	93346729	93347461	E072	-20848
chr1	93367434	93367557	E072	-752
chr1	93374886	93375287	E072	6577
chr1	93375470	93375946	E072	7161
chr1	93387980	93388181	E072	19671
chr1	93388368	93388425	E072	20059
chr1	93395074	93395126	E072	26765
chr1	93395262	93395469	E072	26953
chr1	93395476	93395638	E072	27167
chr1	93399397	93399563	E072	31088
chr1	93399901	93399999	E072	31592
chr1	93400049	93400806	E072	31740
chr1	93407249	93407329	E072	38940
chr1	93407540	93408010	E072	39231
chr1	93408695	93408757	E072	40386
chr1	93408809	93409073	E072	40500
chr1	93409807	93409924	E072	41498
chr1	93410075	93410197	E072	41766
chr1	93410636	93410715	E072	42327
chr1	93410897	93411007	E072	42588
chr1	93411087	93411201	E072	42778
chr1	93411573	93411731	E072	43264
chr1	93415652	93415926	E072	47343
chr1	93416028	93416280	E072	47719
chr1	93416304	93416406	E072	47995
chr1	93416622	93417201	E072	48313
chr1	93417658	93417790	E072	49349
chr1	93345115	93345155	E073	-23154
chr1	93345345	93345583	E073	-22726
chr1	93348501	93348646	E073	-19663
chr1	93348862	93349389	E073	-18920
chr1	93374886	93375287	E073	6577
chr1	93395074	93395126	E073	26765
chr1	93395262	93395469	E073	26953
chr1	93395476	93395638	E073	27167
chr1	93399119	93399316	E073	30810
chr1	93399397	93399563	E073	31088
chr1	93400049	93400806	E073	31740
chr1	93407249	93407329	E073	38940
chr1	93408695	93408757	E073	40386
chr1	93409807	93409924	E073	41498
chr1	93410075	93410197	E073	41766
chr1	93410897	93411007	E073	42588
chr1	93411087	93411201	E073	42778
chr1	93411573	93411731	E073	43264
chr1	93415652	93415926	E073	47343
chr1	93416028	93416280	E073	47719
chr1	93416304	93416406	E073	47995
chr1	93416622	93417201	E073	48313
chr1	93417658	93417790	E073	49349
chr1	93417911	93417961	E073	49602
chr1	93324170	93325314	E074	-42995
chr1	93325436	93325502	E074	-42807
chr1	93325557	93325675	E074	-42634
chr1	93336380	93336485	E074	-31824
chr1	93338384	93338515	E074	-29794
chr1	93345115	93345155	E074	-23154
chr1	93345345	93345583	E074	-22726
chr1	93348315	93348424	E074	-19885
chr1	93348501	93348646	E074	-19663
chr1	93348862	93349389	E074	-18920
chr1	93374886	93375287	E074	6577
chr1	93375470	93375946	E074	7161
chr1	93388368	93388425	E074	20059
chr1	93392406	93392469	E074	24097
chr1	93392525	93392598	E074	24216
chr1	93395074	93395126	E074	26765
chr1	93395262	93395469	E074	26953
chr1	93395476	93395638	E074	27167
chr1	93399119	93399316	E074	30810
chr1	93399397	93399563	E074	31088
chr1	93399901	93399999	E074	31592
chr1	93400049	93400806	E074	31740
chr1	93406253	93406443	E074	37944
chr1	93407249	93407329	E074	38940
chr1	93408695	93408757	E074	40386
chr1	93408809	93409073	E074	40500
chr1	93409807	93409924	E074	41498
chr1	93410075	93410197	E074	41766
chr1	93410897	93411007	E074	42588
chr1	93411087	93411201	E074	42778
chr1	93411573	93411731	E074	43264
chr1	93413201	93413363	E074	44892
chr1	93413747	93413884	E074	45438
chr1	93415652	93415926	E074	47343
chr1	93416028	93416280	E074	47719
chr1	93416304	93416406	E074	47995
chr1	93416622	93417201	E074	48313
chr1	93417658	93417790	E074	49349
chr1	93417911	93417961	E074	49602
chr1	93318311	93318384	E081	-49925
chr1	93342952	93343219	E081	-25090
chr1	93343266	93343741	E081	-24568
chr1	93399119	93399316	E081	30810
chr1	93399397	93399563	E081	31088
chr1	93399901	93399999	E081	31592
chr1	93400049	93400806	E081	31740
chr1	93401684	93401829	E081	33375
chr1	93402249	93402344	E081	33940
chr1	93408695	93408757	E081	40386
chr1	93408809	93409073	E081	40500
chr1	93342952	93343219	E082	-25090
chr1	93343266	93343741	E082	-24568
chr1	93343820	93343872	E082	-24437
chr1	93400049	93400806	E082	31740
chr1	93407540	93408010	E082	39231
chr1	93408695	93408757	E082	40386
chr1	93408809	93409073	E082	40500