rs2391177

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0308 (9234/29940,GnomAD)
G==0310 (9046/29118,TOPMED)
G==0221 (1106/5008,1000G)
G==0366 (1411/3854,ALSPAC)
G==0378 (1402/3708,TWINSUK)

Position: chr1:92888386 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 194 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.92888386G>A
GRCh37.p13 chr 1	NC_000001.10:g.93353943G>A
FAM69A RefSeqGene	NG_033051.1:g.78137C>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=0.258	A=0.742
1000Genomes	American	Sub	694	G=0.280	A=0.720
1000Genomes	East Asian	Sub	1008	G=0.035	A=0.965
1000Genomes	Europe	Sub	1006	G=0.367	A=0.633
1000Genomes	Global	Study-wide	5008	G=0.221	A=0.779
1000Genomes	South Asian	Sub	978	G=0.170	A=0.830
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.366	A=0.634
The Genome Aggregation Database	African	Sub	8720	G=0.264	A=0.736
The Genome Aggregation Database	American	Sub	838	G=0.240	A=0.760
The Genome Aggregation Database	East Asian	Sub	1622	G=0.043	A=0.957
The Genome Aggregation Database	Europe	Sub	18458	G=0.357	A=0.642
The Genome Aggregation Database	Global	Study-wide	29940	G=0.308	A=0.691
The Genome Aggregation Database	Other	Sub	302	G=0.240	A=0.760
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.310	A=0.689
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.378	A=0.622

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
rs2391177	7.81E-05	alcohol consumption	23953852

eQTL of rs2391177 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93353943	FAM69A	ENSG00000154511.7	G>A	2.3665e-3	-73114	Cortex
Chr1:93353943	EVI5	ENSG00000067208.10	G>A	1.7380e-4	95982	Caudate_basal_ganglia

meQTL of rs2391177 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.064550443692387	6.2436e-37

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	93304201	93304337	E067	-49606
chr1	93317337	93317402	E067	-36541
chr1	93317473	93317740	E067	-36203
chr1	93324170	93325314	E067	-28629
chr1	93325436	93325502	E067	-28441
chr1	93325557	93325675	E067	-28268
chr1	93343820	93343872	E067	-10071
chr1	93345115	93345155	E067	-8788
chr1	93345345	93345583	E067	-8360
chr1	93374886	93375287	E067	20943
chr1	93375470	93375946	E067	21527
chr1	93387980	93388181	E067	34037
chr1	93388368	93388425	E067	34425
chr1	93395074	93395126	E067	41131
chr1	93395262	93395469	E067	41319
chr1	93395476	93395638	E067	41533
chr1	93399397	93399563	E067	45454
chr1	93399901	93399999	E067	45958
chr1	93400049	93400806	E067	46106
chr1	93305014	93305105	E068	-48838
chr1	93305123	93305252	E068	-48691
chr1	93305604	93305649	E068	-48294
chr1	93305765	93305832	E068	-48111
chr1	93306031	93306085	E068	-47858
chr1	93308618	93308852	E068	-45091
chr1	93309181	93309247	E068	-44696
chr1	93309346	93309396	E068	-44547
chr1	93309449	93309521	E068	-44422
chr1	93309558	93309608	E068	-44335
chr1	93317337	93317402	E068	-36541
chr1	93317473	93317740	E068	-36203
chr1	93325436	93325502	E068	-28441
chr1	93325557	93325675	E068	-28268
chr1	93341920	93342406	E068	-11537
chr1	93345115	93345155	E068	-8788
chr1	93345345	93345583	E068	-8360
chr1	93348315	93348424	E068	-5519
chr1	93348501	93348646	E068	-5297
chr1	93348862	93349389	E068	-4554
chr1	93375470	93375946	E068	21527
chr1	93387980	93388181	E068	34037
chr1	93388368	93388425	E068	34425
chr1	93393378	93393664	E068	39435
chr1	93395074	93395126	E068	41131
chr1	93395262	93395469	E068	41319
chr1	93395476	93395638	E068	41533
chr1	93397024	93397554	E068	43081
chr1	93399119	93399316	E068	45176
chr1	93399397	93399563	E068	45454
chr1	93399901	93399999	E068	45958
chr1	93304201	93304337	E069	-49606
chr1	93305014	93305105	E069	-48838
chr1	93305123	93305252	E069	-48691
chr1	93305604	93305649	E069	-48294
chr1	93305765	93305832	E069	-48111
chr1	93306031	93306085	E069	-47858
chr1	93306247	93306444	E069	-47499
chr1	93308498	93308578	E069	-45365
chr1	93325436	93325502	E069	-28441
chr1	93325557	93325675	E069	-28268
chr1	93343820	93343872	E069	-10071
chr1	93345115	93345155	E069	-8788
chr1	93345345	93345583	E069	-8360
chr1	93348315	93348424	E069	-5519
chr1	93348501	93348646	E069	-5297
chr1	93367434	93367557	E069	13491
chr1	93374886	93375287	E069	20943
chr1	93375470	93375946	E069	21527
chr1	93387980	93388181	E069	34037
chr1	93388368	93388425	E069	34425
chr1	93395074	93395126	E069	41131
chr1	93395262	93395469	E069	41319
chr1	93395476	93395638	E069	41533
chr1	93399119	93399316	E069	45176
chr1	93399397	93399563	E069	45454
chr1	93399901	93399999	E069	45958
chr1	93400049	93400806	E069	46106
chr1	93402249	93402344	E069	48306
chr1	93342489	93342613	E070	-11330
chr1	93342703	93342819	E070	-11124
chr1	93342952	93343219	E070	-10724
chr1	93343266	93343741	E070	-10202
chr1	93343820	93343872	E070	-10071
chr1	93345115	93345155	E070	-8788
chr1	93345345	93345583	E070	-8360
chr1	93400049	93400806	E070	46106
chr1	93401684	93401829	E070	47741
chr1	93304201	93304337	E071	-49606
chr1	93305014	93305105	E071	-48838
chr1	93305123	93305252	E071	-48691
chr1	93317337	93317402	E071	-36541
chr1	93317473	93317740	E071	-36203
chr1	93319620	93320383	E071	-33560
chr1	93325436	93325502	E071	-28441
chr1	93325557	93325675	E071	-28268
chr1	93338384	93338515	E071	-15428
chr1	93343820	93343872	E071	-10071
chr1	93345115	93345155	E071	-8788
chr1	93345345	93345583	E071	-8360
chr1	93346729	93347461	E071	-6482
chr1	93348501	93348646	E071	-5297
chr1	93348862	93349389	E071	-4554
chr1	93374886	93375287	E071	20943
chr1	93375470	93375946	E071	21527
chr1	93388368	93388425	E071	34425
chr1	93395074	93395126	E071	41131
chr1	93395262	93395469	E071	41319
chr1	93395476	93395638	E071	41533
chr1	93399119	93399316	E071	45176
chr1	93399397	93399563	E071	45454
chr1	93399901	93399999	E071	45958
chr1	93400049	93400806	E071	46106
chr1	93401684	93401829	E071	47741
chr1	93402249	93402344	E071	48306
chr1	93305123	93305252	E072	-48691
chr1	93305604	93305649	E072	-48294
chr1	93305765	93305832	E072	-48111
chr1	93306031	93306085	E072	-47858
chr1	93306247	93306444	E072	-47499
chr1	93317337	93317402	E072	-36541
chr1	93317473	93317740	E072	-36203
chr1	93318075	93318232	E072	-35711
chr1	93318311	93318384	E072	-35559
chr1	93318988	93319144	E072	-34799
chr1	93324170	93325314	E072	-28629
chr1	93338384	93338515	E072	-15428
chr1	93343820	93343872	E072	-10071
chr1	93345115	93345155	E072	-8788
chr1	93345345	93345583	E072	-8360
chr1	93346729	93347461	E072	-6482
chr1	93367434	93367557	E072	13491
chr1	93374886	93375287	E072	20943
chr1	93375470	93375946	E072	21527
chr1	93387980	93388181	E072	34037
chr1	93388368	93388425	E072	34425
chr1	93395074	93395126	E072	41131
chr1	93395262	93395469	E072	41319
chr1	93395476	93395638	E072	41533
chr1	93399397	93399563	E072	45454
chr1	93399901	93399999	E072	45958
chr1	93400049	93400806	E072	46106
chr1	93304201	93304337	E073	-49606
chr1	93305014	93305105	E073	-48838
chr1	93305123	93305252	E073	-48691
chr1	93305604	93305649	E073	-48294
chr1	93305765	93305832	E073	-48111
chr1	93306031	93306085	E073	-47858
chr1	93306247	93306444	E073	-47499
chr1	93345115	93345155	E073	-8788
chr1	93345345	93345583	E073	-8360
chr1	93348501	93348646	E073	-5297
chr1	93348862	93349389	E073	-4554
chr1	93374886	93375287	E073	20943
chr1	93395074	93395126	E073	41131
chr1	93395262	93395469	E073	41319
chr1	93395476	93395638	E073	41533
chr1	93399119	93399316	E073	45176
chr1	93399397	93399563	E073	45454
chr1	93400049	93400806	E073	46106
chr1	93324170	93325314	E074	-28629
chr1	93325436	93325502	E074	-28441
chr1	93325557	93325675	E074	-28268
chr1	93336380	93336485	E074	-17458
chr1	93338384	93338515	E074	-15428
chr1	93345115	93345155	E074	-8788
chr1	93345345	93345583	E074	-8360
chr1	93348315	93348424	E074	-5519
chr1	93348501	93348646	E074	-5297
chr1	93348862	93349389	E074	-4554
chr1	93374886	93375287	E074	20943
chr1	93375470	93375946	E074	21527
chr1	93388368	93388425	E074	34425
chr1	93392406	93392469	E074	38463
chr1	93392525	93392598	E074	38582
chr1	93395074	93395126	E074	41131
chr1	93395262	93395469	E074	41319
chr1	93395476	93395638	E074	41533
chr1	93399119	93399316	E074	45176
chr1	93399397	93399563	E074	45454
chr1	93399901	93399999	E074	45958
chr1	93400049	93400806	E074	46106
chr1	93318311	93318384	E081	-35559
chr1	93342952	93343219	E081	-10724
chr1	93343266	93343741	E081	-10202
chr1	93399119	93399316	E081	45176
chr1	93399397	93399563	E081	45454
chr1	93399901	93399999	E081	45958
chr1	93400049	93400806	E081	46106
chr1	93401684	93401829	E081	47741
chr1	93402249	93402344	E081	48306
chr1	93342952	93343219	E082	-10724
chr1	93343266	93343741	E082	-10202
chr1	93343820	93343872	E082	-10071
chr1	93400049	93400806	E082	46106