rs2481713

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 (8406/29936,GnomAD)
G==0267 (7779/29118,TOPMED)
G==0193 (967/5008,1000G)
G==0366 (1412/3854,ALSPAC)
G==0377 (1399/3708,TWINSUK)

Position: chr1:92889332 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 190 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.92889332G>T
GRCh37.p13 chr 1	NC_000001.10:g.93354889G>T
FAM69A RefSeqGene	NG_033051.1:g.77191C>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	8722	G=0.169	T=0.831
The Genome Aggregation Database	American	Sub	838	G=0.230	T=0.770
The Genome Aggregation Database	East Asian	Sub	1622	G=0.043	T=0.957
The Genome Aggregation Database	Europe	Sub	18454	G=0.357	T=0.642
The Genome Aggregation Database	Global	Study-wide	29936	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=0.377	T=0.623

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
rs2481713	6.86E-05	alcohol consumption	23953852

eQTL of rs2481713 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93354889	FAM69A	ENSG00000154511.7	G>T	2.3665e-3	-72168	Cortex
Chr1:93354889	EVI5	ENSG00000067208.10	G>T	1.7380e-4	96928	Caudate_basal_ganglia

meQTL of rs2481713 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	93317337	93317402	E067	-37487
chr1	93317473	93317740	E067	-37149
chr1	93324170	93325314	E067	-29575
chr1	93325436	93325502	E067	-29387
chr1	93325557	93325675	E067	-29214
chr1	93343820	93343872	E067	-11017
chr1	93345115	93345155	E067	-9734
chr1	93345345	93345583	E067	-9306
chr1	93374886	93375287	E067	19997
chr1	93375470	93375946	E067	20581
chr1	93387980	93388181	E067	33091
chr1	93388368	93388425	E067	33479
chr1	93395074	93395126	E067	40185
chr1	93395262	93395469	E067	40373
chr1	93395476	93395638	E067	40587
chr1	93399397	93399563	E067	44508
chr1	93399901	93399999	E067	45012
chr1	93400049	93400806	E067	45160
chr1	93305014	93305105	E068	-49784
chr1	93305123	93305252	E068	-49637
chr1	93305604	93305649	E068	-49240
chr1	93305765	93305832	E068	-49057
chr1	93306031	93306085	E068	-48804
chr1	93308618	93308852	E068	-46037
chr1	93309181	93309247	E068	-45642
chr1	93309346	93309396	E068	-45493
chr1	93309449	93309521	E068	-45368
chr1	93309558	93309608	E068	-45281
chr1	93317337	93317402	E068	-37487
chr1	93317473	93317740	E068	-37149
chr1	93325436	93325502	E068	-29387
chr1	93325557	93325675	E068	-29214
chr1	93341920	93342406	E068	-12483
chr1	93345115	93345155	E068	-9734
chr1	93345345	93345583	E068	-9306
chr1	93348315	93348424	E068	-6465
chr1	93348501	93348646	E068	-6243
chr1	93348862	93349389	E068	-5500
chr1	93375470	93375946	E068	20581
chr1	93387980	93388181	E068	33091
chr1	93388368	93388425	E068	33479
chr1	93393378	93393664	E068	38489
chr1	93395074	93395126	E068	40185
chr1	93395262	93395469	E068	40373
chr1	93395476	93395638	E068	40587
chr1	93397024	93397554	E068	42135
chr1	93399119	93399316	E068	44230
chr1	93399397	93399563	E068	44508
chr1	93399901	93399999	E068	45012
chr1	93305014	93305105	E069	-49784
chr1	93305123	93305252	E069	-49637
chr1	93305604	93305649	E069	-49240
chr1	93305765	93305832	E069	-49057
chr1	93306031	93306085	E069	-48804
chr1	93306247	93306444	E069	-48445
chr1	93308498	93308578	E069	-46311
chr1	93325436	93325502	E069	-29387
chr1	93325557	93325675	E069	-29214
chr1	93343820	93343872	E069	-11017
chr1	93345115	93345155	E069	-9734
chr1	93345345	93345583	E069	-9306
chr1	93348315	93348424	E069	-6465
chr1	93348501	93348646	E069	-6243
chr1	93367434	93367557	E069	12545
chr1	93374886	93375287	E069	19997
chr1	93375470	93375946	E069	20581
chr1	93387980	93388181	E069	33091
chr1	93388368	93388425	E069	33479
chr1	93395074	93395126	E069	40185
chr1	93395262	93395469	E069	40373
chr1	93395476	93395638	E069	40587
chr1	93399119	93399316	E069	44230
chr1	93399397	93399563	E069	44508
chr1	93399901	93399999	E069	45012
chr1	93400049	93400806	E069	45160
chr1	93402249	93402344	E069	47360
chr1	93342489	93342613	E070	-12276
chr1	93342703	93342819	E070	-12070
chr1	93342952	93343219	E070	-11670
chr1	93343266	93343741	E070	-11148
chr1	93343820	93343872	E070	-11017
chr1	93345115	93345155	E070	-9734
chr1	93345345	93345583	E070	-9306
chr1	93400049	93400806	E070	45160
chr1	93401684	93401829	E070	46795
chr1	93305014	93305105	E071	-49784
chr1	93305123	93305252	E071	-49637
chr1	93317337	93317402	E071	-37487
chr1	93317473	93317740	E071	-37149
chr1	93319620	93320383	E071	-34506
chr1	93325436	93325502	E071	-29387
chr1	93325557	93325675	E071	-29214
chr1	93338384	93338515	E071	-16374
chr1	93343820	93343872	E071	-11017
chr1	93345115	93345155	E071	-9734
chr1	93345345	93345583	E071	-9306
chr1	93346729	93347461	E071	-7428
chr1	93348501	93348646	E071	-6243
chr1	93348862	93349389	E071	-5500
chr1	93374886	93375287	E071	19997
chr1	93375470	93375946	E071	20581
chr1	93388368	93388425	E071	33479
chr1	93395074	93395126	E071	40185
chr1	93395262	93395469	E071	40373
chr1	93395476	93395638	E071	40587
chr1	93399119	93399316	E071	44230
chr1	93399397	93399563	E071	44508
chr1	93399901	93399999	E071	45012
chr1	93400049	93400806	E071	45160
chr1	93401684	93401829	E071	46795
chr1	93402249	93402344	E071	47360
chr1	93305123	93305252	E072	-49637
chr1	93305604	93305649	E072	-49240
chr1	93305765	93305832	E072	-49057
chr1	93306031	93306085	E072	-48804
chr1	93306247	93306444	E072	-48445
chr1	93317337	93317402	E072	-37487
chr1	93317473	93317740	E072	-37149
chr1	93318075	93318232	E072	-36657
chr1	93318311	93318384	E072	-36505
chr1	93318988	93319144	E072	-35745
chr1	93324170	93325314	E072	-29575
chr1	93338384	93338515	E072	-16374
chr1	93343820	93343872	E072	-11017
chr1	93345115	93345155	E072	-9734
chr1	93345345	93345583	E072	-9306
chr1	93346729	93347461	E072	-7428
chr1	93367434	93367557	E072	12545
chr1	93374886	93375287	E072	19997
chr1	93375470	93375946	E072	20581
chr1	93387980	93388181	E072	33091
chr1	93388368	93388425	E072	33479
chr1	93395074	93395126	E072	40185
chr1	93395262	93395469	E072	40373
chr1	93395476	93395638	E072	40587
chr1	93399397	93399563	E072	44508
chr1	93399901	93399999	E072	45012
chr1	93400049	93400806	E072	45160
chr1	93305014	93305105	E073	-49784
chr1	93305123	93305252	E073	-49637
chr1	93305604	93305649	E073	-49240
chr1	93305765	93305832	E073	-49057
chr1	93306031	93306085	E073	-48804
chr1	93306247	93306444	E073	-48445
chr1	93345115	93345155	E073	-9734
chr1	93345345	93345583	E073	-9306
chr1	93348501	93348646	E073	-6243
chr1	93348862	93349389	E073	-5500
chr1	93374886	93375287	E073	19997
chr1	93395074	93395126	E073	40185
chr1	93395262	93395469	E073	40373
chr1	93395476	93395638	E073	40587
chr1	93399119	93399316	E073	44230
chr1	93399397	93399563	E073	44508
chr1	93400049	93400806	E073	45160
chr1	93324170	93325314	E074	-29575
chr1	93325436	93325502	E074	-29387
chr1	93325557	93325675	E074	-29214
chr1	93336380	93336485	E074	-18404
chr1	93338384	93338515	E074	-16374
chr1	93345115	93345155	E074	-9734
chr1	93345345	93345583	E074	-9306
chr1	93348315	93348424	E074	-6465
chr1	93348501	93348646	E074	-6243
chr1	93348862	93349389	E074	-5500
chr1	93374886	93375287	E074	19997
chr1	93375470	93375946	E074	20581
chr1	93388368	93388425	E074	33479
chr1	93392406	93392469	E074	37517
chr1	93392525	93392598	E074	37636
chr1	93395074	93395126	E074	40185
chr1	93395262	93395469	E074	40373
chr1	93395476	93395638	E074	40587
chr1	93399119	93399316	E074	44230
chr1	93399397	93399563	E074	44508
chr1	93399901	93399999	E074	45012
chr1	93400049	93400806	E074	45160
chr1	93318311	93318384	E081	-36505
chr1	93342952	93343219	E081	-11670
chr1	93343266	93343741	E081	-11148
chr1	93399119	93399316	E081	44230
chr1	93399397	93399563	E081	44508
chr1	93399901	93399999	E081	45012
chr1	93400049	93400806	E081	45160
chr1	93401684	93401829	E081	46795
chr1	93402249	93402344	E081	47360
chr1	93342952	93343219	E082	-11670
chr1	93343266	93343741	E082	-11148
chr1	93343820	93343872	E082	-11017
chr1	93400049	93400806	E082	45160