rs7515257

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0346 (10371/29932,GnomAD)
A=0365 (10652/29118,TOPMED)
A=0261 (1305/5008,1000G)
A=0369 (1423/3854,ALSPAC)
A=0378 (1401/3708,TWINSUK)

Position: chr1:92928161 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 331 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.92928161G>A
GRCh37.p13 chr 1	NC_000001.10:g.93393718G>A
FAM69A RefSeqGene	NG_033051.1:g.38362C>T

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=0.617	A=0.383
1000Genomes	American	Sub	694	G=0.710	A=0.290
1000Genomes	East Asian	Sub	1008	G=0.960	A=0.040
1000Genomes	Europe	Sub	1006	G=0.632	A=0.368
1000Genomes	Global	Study-wide	5008	G=0.739	A=0.261
1000Genomes	South Asian	Sub	978	G=0.810	A=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.631	A=0.369
The Genome Aggregation Database	African	Sub	8714	G=0.612	A=0.388
The Genome Aggregation Database	American	Sub	836	G=0.760	A=0.240
The Genome Aggregation Database	East Asian	Sub	1620	G=0.949	A=0.051
The Genome Aggregation Database	Europe	Sub	18460	G=0.640	A=0.359
The Genome Aggregation Database	Global	Study-wide	29932	G=0.653	A=0.346
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.634	A=0.365
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.622	A=0.378

PMID	Title	Author	Journal
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs7515257	7.86E-05	alcohol consumption	23953852

eQTL of rs7515257 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93393718	FAM69A	ENSG00000154511.7	G>A	2.3665e-3	-33339	Cortex
Chr1:93393718	EVI5	ENSG00000067208.10	G>A	1.7380e-4	135757	Caudate_basal_ganglia

meQTL of rs7515257 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.0579879181406423	1.8777e-29

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	93343820	93343872	E067	-49846
chr1	93345115	93345155	E067	-48563
chr1	93345345	93345583	E067	-48135
chr1	93374886	93375287	E067	-18431
chr1	93375470	93375946	E067	-17772
chr1	93387980	93388181	E067	-5537
chr1	93388368	93388425	E067	-5293
chr1	93395074	93395126	E067	1356
chr1	93395262	93395469	E067	1544
chr1	93395476	93395638	E067	1758
chr1	93399397	93399563	E067	5679
chr1	93399901	93399999	E067	6183
chr1	93400049	93400806	E067	6331
chr1	93408809	93409073	E067	15091
chr1	93409807	93409924	E067	16089
chr1	93410075	93410197	E067	16357
chr1	93410636	93410715	E067	16918
chr1	93410897	93411007	E067	17179
chr1	93411087	93411201	E067	17369
chr1	93411573	93411731	E067	17855
chr1	93413201	93413363	E067	19483
chr1	93415652	93415926	E067	21934
chr1	93416028	93416280	E067	22310
chr1	93416304	93416406	E067	22586
chr1	93416622	93417201	E067	22904
chr1	93417658	93417790	E067	23940
chr1	93421704	93421823	E067	27986
chr1	93421849	93421959	E067	28131
chr1	93422195	93422584	E067	28477
chr1	93422586	93422693	E067	28868
chr1	93422753	93422818	E067	29035
chr1	93422865	93423244	E067	29147
chr1	93423872	93424033	E067	30154
chr1	93424075	93424184	E067	30357
chr1	93424219	93424301	E067	30501
chr1	93424333	93424410	E067	30615
chr1	93425050	93425102	E067	31332
chr1	93438108	93438623	E067	44390
chr1	93345115	93345155	E068	-48563
chr1	93345345	93345583	E068	-48135
chr1	93348315	93348424	E068	-45294
chr1	93348501	93348646	E068	-45072
chr1	93348862	93349389	E068	-44329
chr1	93375470	93375946	E068	-17772
chr1	93387980	93388181	E068	-5537
chr1	93388368	93388425	E068	-5293
chr1	93393378	93393664	E068	-54
chr1	93395074	93395126	E068	1356
chr1	93395262	93395469	E068	1544
chr1	93395476	93395638	E068	1758
chr1	93397024	93397554	E068	3306
chr1	93399119	93399316	E068	5401
chr1	93399397	93399563	E068	5679
chr1	93399901	93399999	E068	6183
chr1	93406253	93406443	E068	12535
chr1	93407249	93407329	E068	13531
chr1	93407540	93408010	E068	13822
chr1	93408695	93408757	E068	14977
chr1	93408809	93409073	E068	15091
chr1	93409807	93409924	E068	16089
chr1	93410075	93410197	E068	16357
chr1	93410636	93410715	E068	16918
chr1	93410897	93411007	E068	17179
chr1	93411087	93411201	E068	17369
chr1	93411573	93411731	E068	17855
chr1	93413201	93413363	E068	19483
chr1	93413747	93413884	E068	20029
chr1	93415652	93415926	E068	21934
chr1	93416304	93416406	E068	22586
chr1	93416622	93417201	E068	22904
chr1	93417658	93417790	E068	23940
chr1	93421704	93421823	E068	27986
chr1	93421849	93421959	E068	28131
chr1	93422195	93422584	E068	28477
chr1	93422586	93422693	E068	28868
chr1	93422753	93422818	E068	29035
chr1	93422865	93423244	E068	29147
chr1	93423690	93423788	E068	29972
chr1	93423872	93424033	E068	30154
chr1	93424075	93424184	E068	30357
chr1	93424219	93424301	E068	30501
chr1	93424333	93424410	E068	30615
chr1	93433605	93433702	E068	39887
chr1	93433803	93434038	E068	40085
chr1	93434090	93434266	E068	40372
chr1	93343820	93343872	E069	-49846
chr1	93345115	93345155	E069	-48563
chr1	93345345	93345583	E069	-48135
chr1	93348315	93348424	E069	-45294
chr1	93348501	93348646	E069	-45072
chr1	93367434	93367557	E069	-26161
chr1	93374886	93375287	E069	-18431
chr1	93375470	93375946	E069	-17772
chr1	93387980	93388181	E069	-5537
chr1	93388368	93388425	E069	-5293
chr1	93395074	93395126	E069	1356
chr1	93395262	93395469	E069	1544
chr1	93395476	93395638	E069	1758
chr1	93399119	93399316	E069	5401
chr1	93399397	93399563	E069	5679
chr1	93399901	93399999	E069	6183
chr1	93400049	93400806	E069	6331
chr1	93402249	93402344	E069	8531
chr1	93406253	93406443	E069	12535
chr1	93407540	93408010	E069	13822
chr1	93408695	93408757	E069	14977
chr1	93408809	93409073	E069	15091
chr1	93409807	93409924	E069	16089
chr1	93410075	93410197	E069	16357
chr1	93410636	93410715	E069	16918
chr1	93410897	93411007	E069	17179
chr1	93411087	93411201	E069	17369
chr1	93411573	93411731	E069	17855
chr1	93415652	93415926	E069	21934
chr1	93416028	93416280	E069	22310
chr1	93416304	93416406	E069	22586
chr1	93416622	93417201	E069	22904
chr1	93421704	93421823	E069	27986
chr1	93421849	93421959	E069	28131
chr1	93422195	93422584	E069	28477
chr1	93422586	93422693	E069	28868
chr1	93422753	93422818	E069	29035
chr1	93422865	93423244	E069	29147
chr1	93423690	93423788	E069	29972
chr1	93423872	93424033	E069	30154
chr1	93424075	93424184	E069	30357
chr1	93428506	93428818	E069	34788
chr1	93428890	93428938	E069	35172
chr1	93438108	93438623	E069	44390
chr1	93343820	93343872	E070	-49846
chr1	93345115	93345155	E070	-48563
chr1	93345345	93345583	E070	-48135
chr1	93400049	93400806	E070	6331
chr1	93401684	93401829	E070	7966
chr1	93407249	93407329	E070	13531
chr1	93407540	93408010	E070	13822
chr1	93408809	93409073	E070	15091
chr1	93421704	93421823	E070	27986
chr1	93421849	93421959	E070	28131
chr1	93343820	93343872	E071	-49846
chr1	93345115	93345155	E071	-48563
chr1	93345345	93345583	E071	-48135
chr1	93346729	93347461	E071	-46257
chr1	93348501	93348646	E071	-45072
chr1	93348862	93349389	E071	-44329
chr1	93374886	93375287	E071	-18431
chr1	93375470	93375946	E071	-17772
chr1	93388368	93388425	E071	-5293
chr1	93395074	93395126	E071	1356
chr1	93395262	93395469	E071	1544
chr1	93395476	93395638	E071	1758
chr1	93399119	93399316	E071	5401
chr1	93399397	93399563	E071	5679
chr1	93399901	93399999	E071	6183
chr1	93400049	93400806	E071	6331
chr1	93401684	93401829	E071	7966
chr1	93402249	93402344	E071	8531
chr1	93406253	93406443	E071	12535
chr1	93408695	93408757	E071	14977
chr1	93409807	93409924	E071	16089
chr1	93410075	93410197	E071	16357
chr1	93410636	93410715	E071	16918
chr1	93410897	93411007	E071	17179
chr1	93411087	93411201	E071	17369
chr1	93411573	93411731	E071	17855
chr1	93413201	93413363	E071	19483
chr1	93413747	93413884	E071	20029
chr1	93415652	93415926	E071	21934
chr1	93416028	93416280	E071	22310
chr1	93416304	93416406	E071	22586
chr1	93416622	93417201	E071	22904
chr1	93417658	93417790	E071	23940
chr1	93417911	93417961	E071	24193
chr1	93421704	93421823	E071	27986
chr1	93421849	93421959	E071	28131
chr1	93422195	93422584	E071	28477
chr1	93422586	93422693	E071	28868
chr1	93422753	93422818	E071	29035
chr1	93422865	93423244	E071	29147
chr1	93423690	93423788	E071	29972
chr1	93423872	93424033	E071	30154
chr1	93424075	93424184	E071	30357
chr1	93424219	93424301	E071	30501
chr1	93424333	93424410	E071	30615
chr1	93433605	93433702	E071	39887
chr1	93433803	93434038	E071	40085
chr1	93434090	93434266	E071	40372
chr1	93438108	93438623	E071	44390
chr1	93438671	93439486	E071	44953
chr1	93343820	93343872	E072	-49846
chr1	93345115	93345155	E072	-48563
chr1	93345345	93345583	E072	-48135
chr1	93346729	93347461	E072	-46257
chr1	93367434	93367557	E072	-26161
chr1	93374886	93375287	E072	-18431
chr1	93375470	93375946	E072	-17772
chr1	93387980	93388181	E072	-5537
chr1	93388368	93388425	E072	-5293
chr1	93395074	93395126	E072	1356
chr1	93395262	93395469	E072	1544
chr1	93395476	93395638	E072	1758
chr1	93399397	93399563	E072	5679
chr1	93399901	93399999	E072	6183
chr1	93400049	93400806	E072	6331
chr1	93407249	93407329	E072	13531
chr1	93407540	93408010	E072	13822
chr1	93408695	93408757	E072	14977
chr1	93408809	93409073	E072	15091
chr1	93409807	93409924	E072	16089
chr1	93410075	93410197	E072	16357
chr1	93410636	93410715	E072	16918
chr1	93410897	93411007	E072	17179
chr1	93411087	93411201	E072	17369
chr1	93411573	93411731	E072	17855
chr1	93415652	93415926	E072	21934
chr1	93416028	93416280	E072	22310
chr1	93416304	93416406	E072	22586
chr1	93416622	93417201	E072	22904
chr1	93417658	93417790	E072	23940
chr1	93421704	93421823	E072	27986
chr1	93421849	93421959	E072	28131
chr1	93422195	93422584	E072	28477
chr1	93422586	93422693	E072	28868
chr1	93422753	93422818	E072	29035
chr1	93422865	93423244	E072	29147
chr1	93423690	93423788	E072	29972
chr1	93423872	93424033	E072	30154
chr1	93424075	93424184	E072	30357
chr1	93424219	93424301	E072	30501
chr1	93424333	93424410	E072	30615
chr1	93438108	93438623	E072	44390
chr1	93345115	93345155	E073	-48563
chr1	93345345	93345583	E073	-48135
chr1	93348501	93348646	E073	-45072
chr1	93348862	93349389	E073	-44329
chr1	93374886	93375287	E073	-18431
chr1	93395074	93395126	E073	1356
chr1	93395262	93395469	E073	1544
chr1	93395476	93395638	E073	1758
chr1	93399119	93399316	E073	5401
chr1	93399397	93399563	E073	5679
chr1	93400049	93400806	E073	6331
chr1	93407249	93407329	E073	13531
chr1	93408695	93408757	E073	14977
chr1	93409807	93409924	E073	16089
chr1	93410075	93410197	E073	16357
chr1	93410897	93411007	E073	17179
chr1	93411087	93411201	E073	17369
chr1	93411573	93411731	E073	17855
chr1	93415652	93415926	E073	21934
chr1	93416028	93416280	E073	22310
chr1	93416304	93416406	E073	22586
chr1	93416622	93417201	E073	22904
chr1	93417658	93417790	E073	23940
chr1	93417911	93417961	E073	24193
chr1	93421704	93421823	E073	27986
chr1	93421849	93421959	E073	28131
chr1	93422195	93422584	E073	28477
chr1	93422586	93422693	E073	28868
chr1	93422753	93422818	E073	29035
chr1	93422865	93423244	E073	29147
chr1	93423690	93423788	E073	29972
chr1	93423872	93424033	E073	30154
chr1	93424075	93424184	E073	30357
chr1	93424219	93424301	E073	30501
chr1	93424333	93424410	E073	30615
chr1	93438108	93438623	E073	44390
chr1	93345115	93345155	E074	-48563
chr1	93345345	93345583	E074	-48135
chr1	93348315	93348424	E074	-45294
chr1	93348501	93348646	E074	-45072
chr1	93348862	93349389	E074	-44329
chr1	93374886	93375287	E074	-18431
chr1	93375470	93375946	E074	-17772
chr1	93388368	93388425	E074	-5293
chr1	93392406	93392469	E074	-1249
chr1	93392525	93392598	E074	-1120
chr1	93395074	93395126	E074	1356
chr1	93395262	93395469	E074	1544
chr1	93395476	93395638	E074	1758
chr1	93399119	93399316	E074	5401
chr1	93399397	93399563	E074	5679
chr1	93399901	93399999	E074	6183
chr1	93400049	93400806	E074	6331
chr1	93406253	93406443	E074	12535
chr1	93407249	93407329	E074	13531
chr1	93408695	93408757	E074	14977
chr1	93408809	93409073	E074	15091
chr1	93409807	93409924	E074	16089
chr1	93410075	93410197	E074	16357
chr1	93410897	93411007	E074	17179
chr1	93411087	93411201	E074	17369
chr1	93411573	93411731	E074	17855
chr1	93413201	93413363	E074	19483
chr1	93413747	93413884	E074	20029
chr1	93415652	93415926	E074	21934
chr1	93416028	93416280	E074	22310
chr1	93416304	93416406	E074	22586
chr1	93416622	93417201	E074	22904
chr1	93417658	93417790	E074	23940
chr1	93417911	93417961	E074	24193
chr1	93418425	93418544	E074	24707
chr1	93419026	93419150	E074	25308
chr1	93419168	93419344	E074	25450
chr1	93421704	93421823	E074	27986
chr1	93421849	93421959	E074	28131
chr1	93422195	93422584	E074	28477
chr1	93422586	93422693	E074	28868
chr1	93422753	93422818	E074	29035
chr1	93422865	93423244	E074	29147
chr1	93423690	93423788	E074	29972
chr1	93423872	93424033	E074	30154
chr1	93424075	93424184	E074	30357
chr1	93424219	93424301	E074	30501
chr1	93424333	93424410	E074	30615
chr1	93433605	93433702	E074	39887
chr1	93433803	93434038	E074	40085
chr1	93438108	93438623	E074	44390
chr1	93399119	93399316	E081	5401
chr1	93399397	93399563	E081	5679
chr1	93399901	93399999	E081	6183
chr1	93400049	93400806	E081	6331
chr1	93401684	93401829	E081	7966
chr1	93402249	93402344	E081	8531
chr1	93408695	93408757	E081	14977
chr1	93408809	93409073	E081	15091
chr1	93343820	93343872	E082	-49846
chr1	93400049	93400806	E082	6331
chr1	93407540	93408010	E082	13822
chr1	93408695	93408757	E082	14977
chr1	93408809	93409073	E082	15091

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93425530	93428497	E067	31812
chr1	93425530	93428497	E068	31812
chr1	93425530	93428497	E069	31812
chr1	93425530	93428497	E070	31812
chr1	93425530	93428497	E071	31812
chr1	93425530	93428497	E072	31812
chr1	93425530	93428497	E073	31812
chr1	93425530	93428497	E074	31812
chr1	93425530	93428497	E082	31812