rs10493863

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0345 (10346/29920,GnomAD)
C=0366 (10656/29118,TOPMED)
C=0260 (1303/5008,1000G)
C=0369 (1423/3854,ALSPAC)
C=0376 (1394/3708,TWINSUK)

Position: chr1:92934137 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 295 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.92934137T>C
GRCh37.p13 chr 1	NC_000001.10:g.93399694T>C
FAM69A RefSeqGene	NG_033051.1:g.32386A>G

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	T=0.619	C=0.381
1000Genomes	American	Sub	694	T=0.710	C=0.290
1000Genomes	East Asian	Sub	1008	T=0.960	C=0.040
1000Genomes	Europe	Sub	1006	T=0.632	C=0.368
1000Genomes	Global	Study-wide	5008	T=0.740	C=0.260
1000Genomes	South Asian	Sub	978	T=0.810	C=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.631	C=0.369
The Genome Aggregation Database	African	Sub	8708	T=0.613	C=0.387
The Genome Aggregation Database	American	Sub	838	T=0.760	C=0.240
The Genome Aggregation Database	East Asian	Sub	1618	T=0.948	C=0.052
The Genome Aggregation Database	Europe	Sub	18454	T=0.641	C=0.358
The Genome Aggregation Database	Global	Study-wide	29920	T=0.654	C=0.345
The Genome Aggregation Database	Other	Sub	302	T=0.760	C=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.634	C=0.366
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.624	C=0.376

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
rs10493863	7.95E-05	alcohol consumption	23953852

eQTL of rs10493863 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93399694	FAM69A	ENSG00000154511.7	T>C	2.3665e-3	-27363	Cortex
Chr1:93399694	EVI5	ENSG00000067208.10	T>C	1.7380e-4	141733	Caudate_basal_ganglia

meQTL of rs10493863 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	93374886	93375287	E067	-24407
chr1	93375470	93375946	E067	-23748
chr1	93387980	93388181	E067	-11513
chr1	93388368	93388425	E067	-11269
chr1	93395074	93395126	E067	-4568
chr1	93395262	93395469	E067	-4225
chr1	93395476	93395638	E067	-4056
chr1	93399397	93399563	E067	-131
chr1	93399901	93399999	E067	207
chr1	93400049	93400806	E067	355
chr1	93408809	93409073	E067	9115
chr1	93409807	93409924	E067	10113
chr1	93410075	93410197	E067	10381
chr1	93410636	93410715	E067	10942
chr1	93410897	93411007	E067	11203
chr1	93411087	93411201	E067	11393
chr1	93411573	93411731	E067	11879
chr1	93413201	93413363	E067	13507
chr1	93415652	93415926	E067	15958
chr1	93416028	93416280	E067	16334
chr1	93416304	93416406	E067	16610
chr1	93416622	93417201	E067	16928
chr1	93417658	93417790	E067	17964
chr1	93421704	93421823	E067	22010
chr1	93421849	93421959	E067	22155
chr1	93422195	93422584	E067	22501
chr1	93422586	93422693	E067	22892
chr1	93422753	93422818	E067	23059
chr1	93422865	93423244	E067	23171
chr1	93423872	93424033	E067	24178
chr1	93424075	93424184	E067	24381
chr1	93424219	93424301	E067	24525
chr1	93424333	93424410	E067	24639
chr1	93425050	93425102	E067	25356
chr1	93438108	93438623	E067	38414
chr1	93375470	93375946	E068	-23748
chr1	93387980	93388181	E068	-11513
chr1	93388368	93388425	E068	-11269
chr1	93393378	93393664	E068	-6030
chr1	93395074	93395126	E068	-4568
chr1	93395262	93395469	E068	-4225
chr1	93395476	93395638	E068	-4056
chr1	93397024	93397554	E068	-2140
chr1	93399119	93399316	E068	-378
chr1	93399397	93399563	E068	-131
chr1	93399901	93399999	E068	207
chr1	93406253	93406443	E068	6559
chr1	93407249	93407329	E068	7555
chr1	93407540	93408010	E068	7846
chr1	93408695	93408757	E068	9001
chr1	93408809	93409073	E068	9115
chr1	93409807	93409924	E068	10113
chr1	93410075	93410197	E068	10381
chr1	93410636	93410715	E068	10942
chr1	93410897	93411007	E068	11203
chr1	93411087	93411201	E068	11393
chr1	93411573	93411731	E068	11879
chr1	93413201	93413363	E068	13507
chr1	93413747	93413884	E068	14053
chr1	93415652	93415926	E068	15958
chr1	93416304	93416406	E068	16610
chr1	93416622	93417201	E068	16928
chr1	93417658	93417790	E068	17964
chr1	93421704	93421823	E068	22010
chr1	93421849	93421959	E068	22155
chr1	93422195	93422584	E068	22501
chr1	93422586	93422693	E068	22892
chr1	93422753	93422818	E068	23059
chr1	93422865	93423244	E068	23171
chr1	93423690	93423788	E068	23996
chr1	93423872	93424033	E068	24178
chr1	93424075	93424184	E068	24381
chr1	93424219	93424301	E068	24525
chr1	93424333	93424410	E068	24639
chr1	93433605	93433702	E068	33911
chr1	93433803	93434038	E068	34109
chr1	93434090	93434266	E068	34396
chr1	93367434	93367557	E069	-32137
chr1	93374886	93375287	E069	-24407
chr1	93375470	93375946	E069	-23748
chr1	93387980	93388181	E069	-11513
chr1	93388368	93388425	E069	-11269
chr1	93395074	93395126	E069	-4568
chr1	93395262	93395469	E069	-4225
chr1	93395476	93395638	E069	-4056
chr1	93399119	93399316	E069	-378
chr1	93399397	93399563	E069	-131
chr1	93399901	93399999	E069	207
chr1	93400049	93400806	E069	355
chr1	93402249	93402344	E069	2555
chr1	93406253	93406443	E069	6559
chr1	93407540	93408010	E069	7846
chr1	93408695	93408757	E069	9001
chr1	93408809	93409073	E069	9115
chr1	93409807	93409924	E069	10113
chr1	93410075	93410197	E069	10381
chr1	93410636	93410715	E069	10942
chr1	93410897	93411007	E069	11203
chr1	93411087	93411201	E069	11393
chr1	93411573	93411731	E069	11879
chr1	93415652	93415926	E069	15958
chr1	93416028	93416280	E069	16334
chr1	93416304	93416406	E069	16610
chr1	93416622	93417201	E069	16928
chr1	93421704	93421823	E069	22010
chr1	93421849	93421959	E069	22155
chr1	93422195	93422584	E069	22501
chr1	93422586	93422693	E069	22892
chr1	93422753	93422818	E069	23059
chr1	93422865	93423244	E069	23171
chr1	93423690	93423788	E069	23996
chr1	93423872	93424033	E069	24178
chr1	93424075	93424184	E069	24381
chr1	93428506	93428818	E069	28812
chr1	93428890	93428938	E069	29196
chr1	93438108	93438623	E069	38414
chr1	93400049	93400806	E070	355
chr1	93401684	93401829	E070	1990
chr1	93407249	93407329	E070	7555
chr1	93407540	93408010	E070	7846
chr1	93408809	93409073	E070	9115
chr1	93421704	93421823	E070	22010
chr1	93421849	93421959	E070	22155
chr1	93374886	93375287	E071	-24407
chr1	93375470	93375946	E071	-23748
chr1	93388368	93388425	E071	-11269
chr1	93395074	93395126	E071	-4568
chr1	93395262	93395469	E071	-4225
chr1	93395476	93395638	E071	-4056
chr1	93399119	93399316	E071	-378
chr1	93399397	93399563	E071	-131
chr1	93399901	93399999	E071	207
chr1	93400049	93400806	E071	355
chr1	93401684	93401829	E071	1990
chr1	93402249	93402344	E071	2555
chr1	93406253	93406443	E071	6559
chr1	93408695	93408757	E071	9001
chr1	93409807	93409924	E071	10113
chr1	93410075	93410197	E071	10381
chr1	93410636	93410715	E071	10942
chr1	93410897	93411007	E071	11203
chr1	93411087	93411201	E071	11393
chr1	93411573	93411731	E071	11879
chr1	93413201	93413363	E071	13507
chr1	93413747	93413884	E071	14053
chr1	93415652	93415926	E071	15958
chr1	93416028	93416280	E071	16334
chr1	93416304	93416406	E071	16610
chr1	93416622	93417201	E071	16928
chr1	93417658	93417790	E071	17964
chr1	93417911	93417961	E071	18217
chr1	93421704	93421823	E071	22010
chr1	93421849	93421959	E071	22155
chr1	93422195	93422584	E071	22501
chr1	93422586	93422693	E071	22892
chr1	93422753	93422818	E071	23059
chr1	93422865	93423244	E071	23171
chr1	93423690	93423788	E071	23996
chr1	93423872	93424033	E071	24178
chr1	93424075	93424184	E071	24381
chr1	93424219	93424301	E071	24525
chr1	93424333	93424410	E071	24639
chr1	93433605	93433702	E071	33911
chr1	93433803	93434038	E071	34109
chr1	93434090	93434266	E071	34396
chr1	93438108	93438623	E071	38414
chr1	93438671	93439486	E071	38977
chr1	93367434	93367557	E072	-32137
chr1	93374886	93375287	E072	-24407
chr1	93375470	93375946	E072	-23748
chr1	93387980	93388181	E072	-11513
chr1	93388368	93388425	E072	-11269
chr1	93395074	93395126	E072	-4568
chr1	93395262	93395469	E072	-4225
chr1	93395476	93395638	E072	-4056
chr1	93399397	93399563	E072	-131
chr1	93399901	93399999	E072	207
chr1	93400049	93400806	E072	355
chr1	93407249	93407329	E072	7555
chr1	93407540	93408010	E072	7846
chr1	93408695	93408757	E072	9001
chr1	93408809	93409073	E072	9115
chr1	93409807	93409924	E072	10113
chr1	93410075	93410197	E072	10381
chr1	93410636	93410715	E072	10942
chr1	93410897	93411007	E072	11203
chr1	93411087	93411201	E072	11393
chr1	93411573	93411731	E072	11879
chr1	93415652	93415926	E072	15958
chr1	93416028	93416280	E072	16334
chr1	93416304	93416406	E072	16610
chr1	93416622	93417201	E072	16928
chr1	93417658	93417790	E072	17964
chr1	93421704	93421823	E072	22010
chr1	93421849	93421959	E072	22155
chr1	93422195	93422584	E072	22501
chr1	93422586	93422693	E072	22892
chr1	93422753	93422818	E072	23059
chr1	93422865	93423244	E072	23171
chr1	93423690	93423788	E072	23996
chr1	93423872	93424033	E072	24178
chr1	93424075	93424184	E072	24381
chr1	93424219	93424301	E072	24525
chr1	93424333	93424410	E072	24639
chr1	93438108	93438623	E072	38414
chr1	93374886	93375287	E073	-24407
chr1	93395074	93395126	E073	-4568
chr1	93395262	93395469	E073	-4225
chr1	93395476	93395638	E073	-4056
chr1	93399119	93399316	E073	-378
chr1	93399397	93399563	E073	-131
chr1	93400049	93400806	E073	355
chr1	93407249	93407329	E073	7555
chr1	93408695	93408757	E073	9001
chr1	93409807	93409924	E073	10113
chr1	93410075	93410197	E073	10381
chr1	93410897	93411007	E073	11203
chr1	93411087	93411201	E073	11393
chr1	93411573	93411731	E073	11879
chr1	93415652	93415926	E073	15958
chr1	93416028	93416280	E073	16334
chr1	93416304	93416406	E073	16610
chr1	93416622	93417201	E073	16928
chr1	93417658	93417790	E073	17964
chr1	93417911	93417961	E073	18217
chr1	93421704	93421823	E073	22010
chr1	93421849	93421959	E073	22155
chr1	93422195	93422584	E073	22501
chr1	93422586	93422693	E073	22892
chr1	93422753	93422818	E073	23059
chr1	93422865	93423244	E073	23171
chr1	93423690	93423788	E073	23996
chr1	93423872	93424033	E073	24178
chr1	93424075	93424184	E073	24381
chr1	93424219	93424301	E073	24525
chr1	93424333	93424410	E073	24639
chr1	93438108	93438623	E073	38414
chr1	93374886	93375287	E074	-24407
chr1	93375470	93375946	E074	-23748
chr1	93388368	93388425	E074	-11269
chr1	93392406	93392469	E074	-7225
chr1	93392525	93392598	E074	-7096
chr1	93395074	93395126	E074	-4568
chr1	93395262	93395469	E074	-4225
chr1	93395476	93395638	E074	-4056
chr1	93399119	93399316	E074	-378
chr1	93399397	93399563	E074	-131
chr1	93399901	93399999	E074	207
chr1	93400049	93400806	E074	355
chr1	93406253	93406443	E074	6559
chr1	93407249	93407329	E074	7555
chr1	93408695	93408757	E074	9001
chr1	93408809	93409073	E074	9115
chr1	93409807	93409924	E074	10113
chr1	93410075	93410197	E074	10381
chr1	93410897	93411007	E074	11203
chr1	93411087	93411201	E074	11393
chr1	93411573	93411731	E074	11879
chr1	93413201	93413363	E074	13507
chr1	93413747	93413884	E074	14053
chr1	93415652	93415926	E074	15958
chr1	93416028	93416280	E074	16334
chr1	93416304	93416406	E074	16610
chr1	93416622	93417201	E074	16928
chr1	93417658	93417790	E074	17964
chr1	93417911	93417961	E074	18217
chr1	93418425	93418544	E074	18731
chr1	93419026	93419150	E074	19332
chr1	93419168	93419344	E074	19474
chr1	93421704	93421823	E074	22010
chr1	93421849	93421959	E074	22155
chr1	93422195	93422584	E074	22501
chr1	93422586	93422693	E074	22892
chr1	93422753	93422818	E074	23059
chr1	93422865	93423244	E074	23171
chr1	93423690	93423788	E074	23996
chr1	93423872	93424033	E074	24178
chr1	93424075	93424184	E074	24381
chr1	93424219	93424301	E074	24525
chr1	93424333	93424410	E074	24639
chr1	93433605	93433702	E074	33911
chr1	93433803	93434038	E074	34109
chr1	93438108	93438623	E074	38414
chr1	93399119	93399316	E081	-378
chr1	93399397	93399563	E081	-131
chr1	93399901	93399999	E081	207
chr1	93400049	93400806	E081	355
chr1	93401684	93401829	E081	1990
chr1	93402249	93402344	E081	2555
chr1	93408695	93408757	E081	9001
chr1	93408809	93409073	E081	9115
chr1	93400049	93400806	E082	355
chr1	93407540	93408010	E082	7846
chr1	93408695	93408757	E082	9001
chr1	93408809	93409073	E082	9115

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93425530	93428497	E067	25836
chr1	93425530	93428497	E068	25836
chr1	93425530	93428497	E069	25836
chr1	93425530	93428497	E070	25836
chr1	93425530	93428497	E071	25836
chr1	93425530	93428497	E072	25836
chr1	93425530	93428497	E073	25836
chr1	93425530	93428497	E074	25836
chr1	93425530	93428497	E082	25836