rs6698233

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0307 (9203/29914,GnomAD)
T=0308 (8989/29118,TOPMED)
T=0218 (1093/5008,1000G)
T=0366 (1412/3854,ALSPAC)
T=0378 (1402/3708,TWINSUK)

Position: chr1:92931743 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 307 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.92931743C>T
GRCh37.p13 chr 1	NC_000001.10:g.93397300C>T
FAM69A RefSeqGene	NG_033051.1:g.34780G>A
LOC100127934 pseudogene	NG_022794.1:g.265C>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	C=0.753	T=0.247
1000Genomes	American	Sub	694	C=0.720	T=0.280
1000Genomes	East Asian	Sub	1008	C=0.965	T=0.035
1000Genomes	Europe	Sub	1006	C=0.633	T=0.367
1000Genomes	Global	Study-wide	5008	C=0.782	T=0.218
1000Genomes	South Asian	Sub	978	C=0.820	T=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.634	T=0.366
The Genome Aggregation Database	African	Sub	8700	C=0.740	T=0.260
The Genome Aggregation Database	American	Sub	838	C=0.760	T=0.240
The Genome Aggregation Database	East Asian	Sub	1618	C=0.958	T=0.042
The Genome Aggregation Database	Europe	Sub	18456	C=0.642	T=0.357
The Genome Aggregation Database	Global	Study-wide	29914	C=0.692	T=0.307
The Genome Aggregation Database	Other	Sub	302	C=0.760	T=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.691	T=0.308
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.622	T=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
rs6698233	7.62E-05	alcohol consumption	23953852

eQTL of rs6698233 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93397300	EVI5	ENSG00000067208.10	C>T	1.7380e-4	139339	Caudate_basal_ganglia

meQTL of rs6698233 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	93374886	93375287	E067	-22013
chr1	93375470	93375946	E067	-21354
chr1	93387980	93388181	E067	-9119
chr1	93388368	93388425	E067	-8875
chr1	93395074	93395126	E067	-2174
chr1	93395262	93395469	E067	-1831
chr1	93395476	93395638	E067	-1662
chr1	93399397	93399563	E067	2097
chr1	93399901	93399999	E067	2601
chr1	93400049	93400806	E067	2749
chr1	93408809	93409073	E067	11509
chr1	93409807	93409924	E067	12507
chr1	93410075	93410197	E067	12775
chr1	93410636	93410715	E067	13336
chr1	93410897	93411007	E067	13597
chr1	93411087	93411201	E067	13787
chr1	93411573	93411731	E067	14273
chr1	93413201	93413363	E067	15901
chr1	93415652	93415926	E067	18352
chr1	93416028	93416280	E067	18728
chr1	93416304	93416406	E067	19004
chr1	93416622	93417201	E067	19322
chr1	93417658	93417790	E067	20358
chr1	93421704	93421823	E067	24404
chr1	93421849	93421959	E067	24549
chr1	93422195	93422584	E067	24895
chr1	93422586	93422693	E067	25286
chr1	93422753	93422818	E067	25453
chr1	93422865	93423244	E067	25565
chr1	93423872	93424033	E067	26572
chr1	93424075	93424184	E067	26775
chr1	93424219	93424301	E067	26919
chr1	93424333	93424410	E067	27033
chr1	93425050	93425102	E067	27750
chr1	93438108	93438623	E067	40808
chr1	93348315	93348424	E068	-48876
chr1	93348501	93348646	E068	-48654
chr1	93348862	93349389	E068	-47911
chr1	93375470	93375946	E068	-21354
chr1	93387980	93388181	E068	-9119
chr1	93388368	93388425	E068	-8875
chr1	93393378	93393664	E068	-3636
chr1	93395074	93395126	E068	-2174
chr1	93395262	93395469	E068	-1831
chr1	93395476	93395638	E068	-1662
chr1	93397024	93397554	E068	0
chr1	93399119	93399316	E068	1819
chr1	93399397	93399563	E068	2097
chr1	93399901	93399999	E068	2601
chr1	93406253	93406443	E068	8953
chr1	93407249	93407329	E068	9949
chr1	93407540	93408010	E068	10240
chr1	93408695	93408757	E068	11395
chr1	93408809	93409073	E068	11509
chr1	93409807	93409924	E068	12507
chr1	93410075	93410197	E068	12775
chr1	93410636	93410715	E068	13336
chr1	93410897	93411007	E068	13597
chr1	93411087	93411201	E068	13787
chr1	93411573	93411731	E068	14273
chr1	93413201	93413363	E068	15901
chr1	93413747	93413884	E068	16447
chr1	93415652	93415926	E068	18352
chr1	93416304	93416406	E068	19004
chr1	93416622	93417201	E068	19322
chr1	93417658	93417790	E068	20358
chr1	93421704	93421823	E068	24404
chr1	93421849	93421959	E068	24549
chr1	93422195	93422584	E068	24895
chr1	93422586	93422693	E068	25286
chr1	93422753	93422818	E068	25453
chr1	93422865	93423244	E068	25565
chr1	93423690	93423788	E068	26390
chr1	93423872	93424033	E068	26572
chr1	93424075	93424184	E068	26775
chr1	93424219	93424301	E068	26919
chr1	93424333	93424410	E068	27033
chr1	93433605	93433702	E068	36305
chr1	93433803	93434038	E068	36503
chr1	93434090	93434266	E068	36790
chr1	93348315	93348424	E069	-48876
chr1	93348501	93348646	E069	-48654
chr1	93367434	93367557	E069	-29743
chr1	93374886	93375287	E069	-22013
chr1	93375470	93375946	E069	-21354
chr1	93387980	93388181	E069	-9119
chr1	93388368	93388425	E069	-8875
chr1	93395074	93395126	E069	-2174
chr1	93395262	93395469	E069	-1831
chr1	93395476	93395638	E069	-1662
chr1	93399119	93399316	E069	1819
chr1	93399397	93399563	E069	2097
chr1	93399901	93399999	E069	2601
chr1	93400049	93400806	E069	2749
chr1	93402249	93402344	E069	4949
chr1	93406253	93406443	E069	8953
chr1	93407540	93408010	E069	10240
chr1	93408695	93408757	E069	11395
chr1	93408809	93409073	E069	11509
chr1	93409807	93409924	E069	12507
chr1	93410075	93410197	E069	12775
chr1	93410636	93410715	E069	13336
chr1	93410897	93411007	E069	13597
chr1	93411087	93411201	E069	13787
chr1	93411573	93411731	E069	14273
chr1	93415652	93415926	E069	18352
chr1	93416028	93416280	E069	18728
chr1	93416304	93416406	E069	19004
chr1	93416622	93417201	E069	19322
chr1	93421704	93421823	E069	24404
chr1	93421849	93421959	E069	24549
chr1	93422195	93422584	E069	24895
chr1	93422586	93422693	E069	25286
chr1	93422753	93422818	E069	25453
chr1	93422865	93423244	E069	25565
chr1	93423690	93423788	E069	26390
chr1	93423872	93424033	E069	26572
chr1	93424075	93424184	E069	26775
chr1	93428506	93428818	E069	31206
chr1	93428890	93428938	E069	31590
chr1	93438108	93438623	E069	40808
chr1	93400049	93400806	E070	2749
chr1	93401684	93401829	E070	4384
chr1	93407249	93407329	E070	9949
chr1	93407540	93408010	E070	10240
chr1	93408809	93409073	E070	11509
chr1	93421704	93421823	E070	24404
chr1	93421849	93421959	E070	24549
chr1	93348501	93348646	E071	-48654
chr1	93348862	93349389	E071	-47911
chr1	93374886	93375287	E071	-22013
chr1	93375470	93375946	E071	-21354
chr1	93388368	93388425	E071	-8875
chr1	93395074	93395126	E071	-2174
chr1	93395262	93395469	E071	-1831
chr1	93395476	93395638	E071	-1662
chr1	93399119	93399316	E071	1819
chr1	93399397	93399563	E071	2097
chr1	93399901	93399999	E071	2601
chr1	93400049	93400806	E071	2749
chr1	93401684	93401829	E071	4384
chr1	93402249	93402344	E071	4949
chr1	93406253	93406443	E071	8953
chr1	93408695	93408757	E071	11395
chr1	93409807	93409924	E071	12507
chr1	93410075	93410197	E071	12775
chr1	93410636	93410715	E071	13336
chr1	93410897	93411007	E071	13597
chr1	93411087	93411201	E071	13787
chr1	93411573	93411731	E071	14273
chr1	93413201	93413363	E071	15901
chr1	93413747	93413884	E071	16447
chr1	93415652	93415926	E071	18352
chr1	93416028	93416280	E071	18728
chr1	93416304	93416406	E071	19004
chr1	93416622	93417201	E071	19322
chr1	93417658	93417790	E071	20358
chr1	93417911	93417961	E071	20611
chr1	93421704	93421823	E071	24404
chr1	93421849	93421959	E071	24549
chr1	93422195	93422584	E071	24895
chr1	93422586	93422693	E071	25286
chr1	93422753	93422818	E071	25453
chr1	93422865	93423244	E071	25565
chr1	93423690	93423788	E071	26390
chr1	93423872	93424033	E071	26572
chr1	93424075	93424184	E071	26775
chr1	93424219	93424301	E071	26919
chr1	93424333	93424410	E071	27033
chr1	93433605	93433702	E071	36305
chr1	93433803	93434038	E071	36503
chr1	93434090	93434266	E071	36790
chr1	93438108	93438623	E071	40808
chr1	93438671	93439486	E071	41371
chr1	93367434	93367557	E072	-29743
chr1	93374886	93375287	E072	-22013
chr1	93375470	93375946	E072	-21354
chr1	93387980	93388181	E072	-9119
chr1	93388368	93388425	E072	-8875
chr1	93395074	93395126	E072	-2174
chr1	93395262	93395469	E072	-1831
chr1	93395476	93395638	E072	-1662
chr1	93399397	93399563	E072	2097
chr1	93399901	93399999	E072	2601
chr1	93400049	93400806	E072	2749
chr1	93407249	93407329	E072	9949
chr1	93407540	93408010	E072	10240
chr1	93408695	93408757	E072	11395
chr1	93408809	93409073	E072	11509
chr1	93409807	93409924	E072	12507
chr1	93410075	93410197	E072	12775
chr1	93410636	93410715	E072	13336
chr1	93410897	93411007	E072	13597
chr1	93411087	93411201	E072	13787
chr1	93411573	93411731	E072	14273
chr1	93415652	93415926	E072	18352
chr1	93416028	93416280	E072	18728
chr1	93416304	93416406	E072	19004
chr1	93416622	93417201	E072	19322
chr1	93417658	93417790	E072	20358
chr1	93421704	93421823	E072	24404
chr1	93421849	93421959	E072	24549
chr1	93422195	93422584	E072	24895
chr1	93422586	93422693	E072	25286
chr1	93422753	93422818	E072	25453
chr1	93422865	93423244	E072	25565
chr1	93423690	93423788	E072	26390
chr1	93423872	93424033	E072	26572
chr1	93424075	93424184	E072	26775
chr1	93424219	93424301	E072	26919
chr1	93424333	93424410	E072	27033
chr1	93438108	93438623	E072	40808
chr1	93348501	93348646	E073	-48654
chr1	93348862	93349389	E073	-47911
chr1	93374886	93375287	E073	-22013
chr1	93395074	93395126	E073	-2174
chr1	93395262	93395469	E073	-1831
chr1	93395476	93395638	E073	-1662
chr1	93399119	93399316	E073	1819
chr1	93399397	93399563	E073	2097
chr1	93400049	93400806	E073	2749
chr1	93407249	93407329	E073	9949
chr1	93408695	93408757	E073	11395
chr1	93409807	93409924	E073	12507
chr1	93410075	93410197	E073	12775
chr1	93410897	93411007	E073	13597
chr1	93411087	93411201	E073	13787
chr1	93411573	93411731	E073	14273
chr1	93415652	93415926	E073	18352
chr1	93416028	93416280	E073	18728
chr1	93416304	93416406	E073	19004
chr1	93416622	93417201	E073	19322
chr1	93417658	93417790	E073	20358
chr1	93417911	93417961	E073	20611
chr1	93421704	93421823	E073	24404
chr1	93421849	93421959	E073	24549
chr1	93422195	93422584	E073	24895
chr1	93422586	93422693	E073	25286
chr1	93422753	93422818	E073	25453
chr1	93422865	93423244	E073	25565
chr1	93423690	93423788	E073	26390
chr1	93423872	93424033	E073	26572
chr1	93424075	93424184	E073	26775
chr1	93424219	93424301	E073	26919
chr1	93424333	93424410	E073	27033
chr1	93438108	93438623	E073	40808
chr1	93348315	93348424	E074	-48876
chr1	93348501	93348646	E074	-48654
chr1	93348862	93349389	E074	-47911
chr1	93374886	93375287	E074	-22013
chr1	93375470	93375946	E074	-21354
chr1	93388368	93388425	E074	-8875
chr1	93392406	93392469	E074	-4831
chr1	93392525	93392598	E074	-4702
chr1	93395074	93395126	E074	-2174
chr1	93395262	93395469	E074	-1831
chr1	93395476	93395638	E074	-1662
chr1	93399119	93399316	E074	1819
chr1	93399397	93399563	E074	2097
chr1	93399901	93399999	E074	2601
chr1	93400049	93400806	E074	2749
chr1	93406253	93406443	E074	8953
chr1	93407249	93407329	E074	9949
chr1	93408695	93408757	E074	11395
chr1	93408809	93409073	E074	11509
chr1	93409807	93409924	E074	12507
chr1	93410075	93410197	E074	12775
chr1	93410897	93411007	E074	13597
chr1	93411087	93411201	E074	13787
chr1	93411573	93411731	E074	14273
chr1	93413201	93413363	E074	15901
chr1	93413747	93413884	E074	16447
chr1	93415652	93415926	E074	18352
chr1	93416028	93416280	E074	18728
chr1	93416304	93416406	E074	19004
chr1	93416622	93417201	E074	19322
chr1	93417658	93417790	E074	20358
chr1	93417911	93417961	E074	20611
chr1	93418425	93418544	E074	21125
chr1	93419026	93419150	E074	21726
chr1	93419168	93419344	E074	21868
chr1	93421704	93421823	E074	24404
chr1	93421849	93421959	E074	24549
chr1	93422195	93422584	E074	24895
chr1	93422586	93422693	E074	25286
chr1	93422753	93422818	E074	25453
chr1	93422865	93423244	E074	25565
chr1	93423690	93423788	E074	26390
chr1	93423872	93424033	E074	26572
chr1	93424075	93424184	E074	26775
chr1	93424219	93424301	E074	26919
chr1	93424333	93424410	E074	27033
chr1	93433605	93433702	E074	36305
chr1	93433803	93434038	E074	36503
chr1	93438108	93438623	E074	40808
chr1	93399119	93399316	E081	1819
chr1	93399397	93399563	E081	2097
chr1	93399901	93399999	E081	2601
chr1	93400049	93400806	E081	2749
chr1	93401684	93401829	E081	4384
chr1	93402249	93402344	E081	4949
chr1	93408695	93408757	E081	11395
chr1	93408809	93409073	E081	11509
chr1	93400049	93400806	E082	2749
chr1	93407540	93408010	E082	10240
chr1	93408695	93408757	E082	11395
chr1	93408809	93409073	E082	11509

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93425530	93428497	E067	28230
chr1	93425530	93428497	E068	28230
chr1	93425530	93428497	E069	28230
chr1	93425530	93428497	E070	28230
chr1	93425530	93428497	E071	28230
chr1	93425530	93428497	E072	28230
chr1	93425530	93428497	E073	28230
chr1	93425530	93428497	E074	28230
chr1	93425530	93428497	E082	28230