rs10782946

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0401 (11941/29756,GnomAD)
G==0453 (13189/29118,TOPMED)
G==0330 (1654/5008,1000G)
G==0379 (1460/3854,ALSPAC)
G==0384 (1424/3708,TWINSUK)

Position: chr1:92887112 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 199 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.92887112G>A
GRCh37.p13 chr 1	NC_000001.10:g.93352669G>A
FAM69A RefSeqGene	NG_033051.1:g.79411C>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=0.580	A=0.420
1000Genomes	American	Sub	694	G=0.330	A=0.670
1000Genomes	East Asian	Sub	1008	G=0.041	A=0.959
1000Genomes	Europe	Sub	1006	G=0.377	A=0.623
1000Genomes	Global	Study-wide	5008	G=0.330	A=0.670
1000Genomes	South Asian	Sub	978	G=0.240	A=0.760
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.379	A=0.621
The Genome Aggregation Database	African	Sub	8658	G=0.566	A=0.434
The Genome Aggregation Database	American	Sub	836	G=0.250	A=0.750
The Genome Aggregation Database	East Asian	Sub	1616	G=0.056	A=0.944
The Genome Aggregation Database	Europe	Sub	18344	G=0.363	A=0.636
The Genome Aggregation Database	Global	Study-wide	29756	G=0.401	A=0.598
The Genome Aggregation Database	Other	Sub	302	G=0.250	A=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.453	A=0.547
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.384	A=0.616

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
rs10782946	8.52E-05	alcohol consumption	23953852

eQTL of rs10782946 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93352669	FAM69A	ENSG00000154511.7	G>A	2.3665e-3	-74388	Cortex

meQTL of rs10782946 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.0569614828510656	9.6110e-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	93304201	93304337	E067	-48332
chr1	93317337	93317402	E067	-35267
chr1	93317473	93317740	E067	-34929
chr1	93324170	93325314	E067	-27355
chr1	93325436	93325502	E067	-27167
chr1	93325557	93325675	E067	-26994
chr1	93343820	93343872	E067	-8797
chr1	93345115	93345155	E067	-7514
chr1	93345345	93345583	E067	-7086
chr1	93374886	93375287	E067	22217
chr1	93375470	93375946	E067	22801
chr1	93387980	93388181	E067	35311
chr1	93388368	93388425	E067	35699
chr1	93395074	93395126	E067	42405
chr1	93395262	93395469	E067	42593
chr1	93395476	93395638	E067	42807
chr1	93399397	93399563	E067	46728
chr1	93399901	93399999	E067	47232
chr1	93400049	93400806	E067	47380
chr1	93305014	93305105	E068	-47564
chr1	93305123	93305252	E068	-47417
chr1	93305604	93305649	E068	-47020
chr1	93305765	93305832	E068	-46837
chr1	93306031	93306085	E068	-46584
chr1	93308618	93308852	E068	-43817
chr1	93309181	93309247	E068	-43422
chr1	93309346	93309396	E068	-43273
chr1	93309449	93309521	E068	-43148
chr1	93309558	93309608	E068	-43061
chr1	93317337	93317402	E068	-35267
chr1	93317473	93317740	E068	-34929
chr1	93325436	93325502	E068	-27167
chr1	93325557	93325675	E068	-26994
chr1	93341920	93342406	E068	-10263
chr1	93345115	93345155	E068	-7514
chr1	93345345	93345583	E068	-7086
chr1	93348315	93348424	E068	-4245
chr1	93348501	93348646	E068	-4023
chr1	93348862	93349389	E068	-3280
chr1	93375470	93375946	E068	22801
chr1	93387980	93388181	E068	35311
chr1	93388368	93388425	E068	35699
chr1	93393378	93393664	E068	40709
chr1	93395074	93395126	E068	42405
chr1	93395262	93395469	E068	42593
chr1	93395476	93395638	E068	42807
chr1	93397024	93397554	E068	44355
chr1	93399119	93399316	E068	46450
chr1	93399397	93399563	E068	46728
chr1	93399901	93399999	E068	47232
chr1	93303481	93303616	E069	-49053
chr1	93304201	93304337	E069	-48332
chr1	93305014	93305105	E069	-47564
chr1	93305123	93305252	E069	-47417
chr1	93305604	93305649	E069	-47020
chr1	93305765	93305832	E069	-46837
chr1	93306031	93306085	E069	-46584
chr1	93306247	93306444	E069	-46225
chr1	93308498	93308578	E069	-44091
chr1	93325436	93325502	E069	-27167
chr1	93325557	93325675	E069	-26994
chr1	93343820	93343872	E069	-8797
chr1	93345115	93345155	E069	-7514
chr1	93345345	93345583	E069	-7086
chr1	93348315	93348424	E069	-4245
chr1	93348501	93348646	E069	-4023
chr1	93367434	93367557	E069	14765
chr1	93374886	93375287	E069	22217
chr1	93375470	93375946	E069	22801
chr1	93387980	93388181	E069	35311
chr1	93388368	93388425	E069	35699
chr1	93395074	93395126	E069	42405
chr1	93395262	93395469	E069	42593
chr1	93395476	93395638	E069	42807
chr1	93399119	93399316	E069	46450
chr1	93399397	93399563	E069	46728
chr1	93399901	93399999	E069	47232
chr1	93400049	93400806	E069	47380
chr1	93402249	93402344	E069	49580
chr1	93342489	93342613	E070	-10056
chr1	93342703	93342819	E070	-9850
chr1	93342952	93343219	E070	-9450
chr1	93343266	93343741	E070	-8928
chr1	93343820	93343872	E070	-8797
chr1	93345115	93345155	E070	-7514
chr1	93345345	93345583	E070	-7086
chr1	93400049	93400806	E070	47380
chr1	93401684	93401829	E070	49015
chr1	93304201	93304337	E071	-48332
chr1	93305014	93305105	E071	-47564
chr1	93305123	93305252	E071	-47417
chr1	93317337	93317402	E071	-35267
chr1	93317473	93317740	E071	-34929
chr1	93319620	93320383	E071	-32286
chr1	93325436	93325502	E071	-27167
chr1	93325557	93325675	E071	-26994
chr1	93338384	93338515	E071	-14154
chr1	93343820	93343872	E071	-8797
chr1	93345115	93345155	E071	-7514
chr1	93345345	93345583	E071	-7086
chr1	93346729	93347461	E071	-5208
chr1	93348501	93348646	E071	-4023
chr1	93348862	93349389	E071	-3280
chr1	93374886	93375287	E071	22217
chr1	93375470	93375946	E071	22801
chr1	93388368	93388425	E071	35699
chr1	93395074	93395126	E071	42405
chr1	93395262	93395469	E071	42593
chr1	93395476	93395638	E071	42807
chr1	93399119	93399316	E071	46450
chr1	93399397	93399563	E071	46728
chr1	93399901	93399999	E071	47232
chr1	93400049	93400806	E071	47380
chr1	93401684	93401829	E071	49015
chr1	93402249	93402344	E071	49580
chr1	93305123	93305252	E072	-47417
chr1	93305604	93305649	E072	-47020
chr1	93305765	93305832	E072	-46837
chr1	93306031	93306085	E072	-46584
chr1	93306247	93306444	E072	-46225
chr1	93317337	93317402	E072	-35267
chr1	93317473	93317740	E072	-34929
chr1	93318075	93318232	E072	-34437
chr1	93318311	93318384	E072	-34285
chr1	93318988	93319144	E072	-33525
chr1	93324170	93325314	E072	-27355
chr1	93338384	93338515	E072	-14154
chr1	93343820	93343872	E072	-8797
chr1	93345115	93345155	E072	-7514
chr1	93345345	93345583	E072	-7086
chr1	93346729	93347461	E072	-5208
chr1	93367434	93367557	E072	14765
chr1	93374886	93375287	E072	22217
chr1	93375470	93375946	E072	22801
chr1	93387980	93388181	E072	35311
chr1	93388368	93388425	E072	35699
chr1	93395074	93395126	E072	42405
chr1	93395262	93395469	E072	42593
chr1	93395476	93395638	E072	42807
chr1	93399397	93399563	E072	46728
chr1	93399901	93399999	E072	47232
chr1	93400049	93400806	E072	47380
chr1	93303481	93303616	E073	-49053
chr1	93304201	93304337	E073	-48332
chr1	93305014	93305105	E073	-47564
chr1	93305123	93305252	E073	-47417
chr1	93305604	93305649	E073	-47020
chr1	93305765	93305832	E073	-46837
chr1	93306031	93306085	E073	-46584
chr1	93306247	93306444	E073	-46225
chr1	93345115	93345155	E073	-7514
chr1	93345345	93345583	E073	-7086
chr1	93348501	93348646	E073	-4023
chr1	93348862	93349389	E073	-3280
chr1	93374886	93375287	E073	22217
chr1	93395074	93395126	E073	42405
chr1	93395262	93395469	E073	42593
chr1	93395476	93395638	E073	42807
chr1	93399119	93399316	E073	46450
chr1	93399397	93399563	E073	46728
chr1	93400049	93400806	E073	47380
chr1	93303481	93303616	E074	-49053
chr1	93324170	93325314	E074	-27355
chr1	93325436	93325502	E074	-27167
chr1	93325557	93325675	E074	-26994
chr1	93336380	93336485	E074	-16184
chr1	93338384	93338515	E074	-14154
chr1	93345115	93345155	E074	-7514
chr1	93345345	93345583	E074	-7086
chr1	93348315	93348424	E074	-4245
chr1	93348501	93348646	E074	-4023
chr1	93348862	93349389	E074	-3280
chr1	93374886	93375287	E074	22217
chr1	93375470	93375946	E074	22801
chr1	93388368	93388425	E074	35699
chr1	93392406	93392469	E074	39737
chr1	93392525	93392598	E074	39856
chr1	93395074	93395126	E074	42405
chr1	93395262	93395469	E074	42593
chr1	93395476	93395638	E074	42807
chr1	93399119	93399316	E074	46450
chr1	93399397	93399563	E074	46728
chr1	93399901	93399999	E074	47232
chr1	93400049	93400806	E074	47380
chr1	93318311	93318384	E081	-34285
chr1	93342952	93343219	E081	-9450
chr1	93343266	93343741	E081	-8928
chr1	93399119	93399316	E081	46450
chr1	93399397	93399563	E081	46728
chr1	93399901	93399999	E081	47232
chr1	93400049	93400806	E081	47380
chr1	93401684	93401829	E081	49015
chr1	93402249	93402344	E081	49580
chr1	93302690	93302834	E082	-49835
chr1	93303481	93303616	E082	-49053
chr1	93342952	93343219	E082	-9450
chr1	93343266	93343741	E082	-8928
chr1	93343820	93343872	E082	-8797
chr1	93400049	93400806	E082	47380