rs7542608

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0345 (10332/29868,GnomAD)
G=0366 (10661/29118,TOPMED)
G=0261 (1305/5008,1000G)
G=0368 (1419/3854,ALSPAC)
G=0377 (1397/3708,TWINSUK)

Position: chr1:92935637 (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.92935637A>G
GRCh37.p13 chr 1	NC_000001.10:g.93401194A>G
FAM69A RefSeqGene	NG_033051.1:g.30886T>C

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	A=0.618	G=0.382
1000Genomes	American	Sub	694	A=0.710	G=0.290
1000Genomes	East Asian	Sub	1008	A=0.960	G=0.040
1000Genomes	Europe	Sub	1006	A=0.632	G=0.368
1000Genomes	Global	Study-wide	5008	A=0.739	G=0.261
1000Genomes	South Asian	Sub	978	A=0.810	G=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.632	G=0.368
The Genome Aggregation Database	African	Sub	8678	A=0.612	G=0.388
The Genome Aggregation Database	American	Sub	834	A=0.760	G=0.240
The Genome Aggregation Database	East Asian	Sub	1622	A=0.947	G=0.053
The Genome Aggregation Database	Europe	Sub	18432	A=0.641	G=0.358
The Genome Aggregation Database	Global	Study-wide	29868	A=0.654	G=0.345
The Genome Aggregation Database	Other	Sub	302	A=0.760	G=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.633	G=0.366
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.623	G=0.377

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
rs7542608	7.18E-05	alcohol consumption	23953852

eQTL of rs7542608 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93401194	FAM69A	ENSG00000154511.7	A>G	2.3665e-3	-25863	Cortex
Chr1:93401194	EVI5	ENSG00000067208.10	A>G	1.7380e-4	143233	Caudate_basal_ganglia

meQTL of rs7542608 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	-25907
chr1	93375470	93375946	E067	-25248
chr1	93387980	93388181	E067	-13013
chr1	93388368	93388425	E067	-12769
chr1	93395074	93395126	E067	-6068
chr1	93395262	93395469	E067	-5725
chr1	93395476	93395638	E067	-5556
chr1	93399397	93399563	E067	-1631
chr1	93399901	93399999	E067	-1195
chr1	93400049	93400806	E067	-388
chr1	93408809	93409073	E067	7615
chr1	93409807	93409924	E067	8613
chr1	93410075	93410197	E067	8881
chr1	93410636	93410715	E067	9442
chr1	93410897	93411007	E067	9703
chr1	93411087	93411201	E067	9893
chr1	93411573	93411731	E067	10379
chr1	93413201	93413363	E067	12007
chr1	93415652	93415926	E067	14458
chr1	93416028	93416280	E067	14834
chr1	93416304	93416406	E067	15110
chr1	93416622	93417201	E067	15428
chr1	93417658	93417790	E067	16464
chr1	93421704	93421823	E067	20510
chr1	93421849	93421959	E067	20655
chr1	93422195	93422584	E067	21001
chr1	93422586	93422693	E067	21392
chr1	93422753	93422818	E067	21559
chr1	93422865	93423244	E067	21671
chr1	93423872	93424033	E067	22678
chr1	93424075	93424184	E067	22881
chr1	93424219	93424301	E067	23025
chr1	93424333	93424410	E067	23139
chr1	93425050	93425102	E067	23856
chr1	93438108	93438623	E067	36914
chr1	93375470	93375946	E068	-25248
chr1	93387980	93388181	E068	-13013
chr1	93388368	93388425	E068	-12769
chr1	93393378	93393664	E068	-7530
chr1	93395074	93395126	E068	-6068
chr1	93395262	93395469	E068	-5725
chr1	93395476	93395638	E068	-5556
chr1	93397024	93397554	E068	-3640
chr1	93399119	93399316	E068	-1878
chr1	93399397	93399563	E068	-1631
chr1	93399901	93399999	E068	-1195
chr1	93406253	93406443	E068	5059
chr1	93407249	93407329	E068	6055
chr1	93407540	93408010	E068	6346
chr1	93408695	93408757	E068	7501
chr1	93408809	93409073	E068	7615
chr1	93409807	93409924	E068	8613
chr1	93410075	93410197	E068	8881
chr1	93410636	93410715	E068	9442
chr1	93410897	93411007	E068	9703
chr1	93411087	93411201	E068	9893
chr1	93411573	93411731	E068	10379
chr1	93413201	93413363	E068	12007
chr1	93413747	93413884	E068	12553
chr1	93415652	93415926	E068	14458
chr1	93416304	93416406	E068	15110
chr1	93416622	93417201	E068	15428
chr1	93417658	93417790	E068	16464
chr1	93421704	93421823	E068	20510
chr1	93421849	93421959	E068	20655
chr1	93422195	93422584	E068	21001
chr1	93422586	93422693	E068	21392
chr1	93422753	93422818	E068	21559
chr1	93422865	93423244	E068	21671
chr1	93423690	93423788	E068	22496
chr1	93423872	93424033	E068	22678
chr1	93424075	93424184	E068	22881
chr1	93424219	93424301	E068	23025
chr1	93424333	93424410	E068	23139
chr1	93433605	93433702	E068	32411
chr1	93433803	93434038	E068	32609
chr1	93434090	93434266	E068	32896
chr1	93367434	93367557	E069	-33637
chr1	93374886	93375287	E069	-25907
chr1	93375470	93375946	E069	-25248
chr1	93387980	93388181	E069	-13013
chr1	93388368	93388425	E069	-12769
chr1	93395074	93395126	E069	-6068
chr1	93395262	93395469	E069	-5725
chr1	93395476	93395638	E069	-5556
chr1	93399119	93399316	E069	-1878
chr1	93399397	93399563	E069	-1631
chr1	93399901	93399999	E069	-1195
chr1	93400049	93400806	E069	-388
chr1	93402249	93402344	E069	1055
chr1	93406253	93406443	E069	5059
chr1	93407540	93408010	E069	6346
chr1	93408695	93408757	E069	7501
chr1	93408809	93409073	E069	7615
chr1	93409807	93409924	E069	8613
chr1	93410075	93410197	E069	8881
chr1	93410636	93410715	E069	9442
chr1	93410897	93411007	E069	9703
chr1	93411087	93411201	E069	9893
chr1	93411573	93411731	E069	10379
chr1	93415652	93415926	E069	14458
chr1	93416028	93416280	E069	14834
chr1	93416304	93416406	E069	15110
chr1	93416622	93417201	E069	15428
chr1	93421704	93421823	E069	20510
chr1	93421849	93421959	E069	20655
chr1	93422195	93422584	E069	21001
chr1	93422586	93422693	E069	21392
chr1	93422753	93422818	E069	21559
chr1	93422865	93423244	E069	21671
chr1	93423690	93423788	E069	22496
chr1	93423872	93424033	E069	22678
chr1	93424075	93424184	E069	22881
chr1	93428506	93428818	E069	27312
chr1	93428890	93428938	E069	27696
chr1	93438108	93438623	E069	36914
chr1	93400049	93400806	E070	-388
chr1	93401684	93401829	E070	490
chr1	93407249	93407329	E070	6055
chr1	93407540	93408010	E070	6346
chr1	93408809	93409073	E070	7615
chr1	93421704	93421823	E070	20510
chr1	93421849	93421959	E070	20655
chr1	93374886	93375287	E071	-25907
chr1	93375470	93375946	E071	-25248
chr1	93388368	93388425	E071	-12769
chr1	93395074	93395126	E071	-6068
chr1	93395262	93395469	E071	-5725
chr1	93395476	93395638	E071	-5556
chr1	93399119	93399316	E071	-1878
chr1	93399397	93399563	E071	-1631
chr1	93399901	93399999	E071	-1195
chr1	93400049	93400806	E071	-388
chr1	93401684	93401829	E071	490
chr1	93402249	93402344	E071	1055
chr1	93406253	93406443	E071	5059
chr1	93408695	93408757	E071	7501
chr1	93409807	93409924	E071	8613
chr1	93410075	93410197	E071	8881
chr1	93410636	93410715	E071	9442
chr1	93410897	93411007	E071	9703
chr1	93411087	93411201	E071	9893
chr1	93411573	93411731	E071	10379
chr1	93413201	93413363	E071	12007
chr1	93413747	93413884	E071	12553
chr1	93415652	93415926	E071	14458
chr1	93416028	93416280	E071	14834
chr1	93416304	93416406	E071	15110
chr1	93416622	93417201	E071	15428
chr1	93417658	93417790	E071	16464
chr1	93417911	93417961	E071	16717
chr1	93421704	93421823	E071	20510
chr1	93421849	93421959	E071	20655
chr1	93422195	93422584	E071	21001
chr1	93422586	93422693	E071	21392
chr1	93422753	93422818	E071	21559
chr1	93422865	93423244	E071	21671
chr1	93423690	93423788	E071	22496
chr1	93423872	93424033	E071	22678
chr1	93424075	93424184	E071	22881
chr1	93424219	93424301	E071	23025
chr1	93424333	93424410	E071	23139
chr1	93433605	93433702	E071	32411
chr1	93433803	93434038	E071	32609
chr1	93434090	93434266	E071	32896
chr1	93438108	93438623	E071	36914
chr1	93438671	93439486	E071	37477
chr1	93367434	93367557	E072	-33637
chr1	93374886	93375287	E072	-25907
chr1	93375470	93375946	E072	-25248
chr1	93387980	93388181	E072	-13013
chr1	93388368	93388425	E072	-12769
chr1	93395074	93395126	E072	-6068
chr1	93395262	93395469	E072	-5725
chr1	93395476	93395638	E072	-5556
chr1	93399397	93399563	E072	-1631
chr1	93399901	93399999	E072	-1195
chr1	93400049	93400806	E072	-388
chr1	93407249	93407329	E072	6055
chr1	93407540	93408010	E072	6346
chr1	93408695	93408757	E072	7501
chr1	93408809	93409073	E072	7615
chr1	93409807	93409924	E072	8613
chr1	93410075	93410197	E072	8881
chr1	93410636	93410715	E072	9442
chr1	93410897	93411007	E072	9703
chr1	93411087	93411201	E072	9893
chr1	93411573	93411731	E072	10379
chr1	93415652	93415926	E072	14458
chr1	93416028	93416280	E072	14834
chr1	93416304	93416406	E072	15110
chr1	93416622	93417201	E072	15428
chr1	93417658	93417790	E072	16464
chr1	93421704	93421823	E072	20510
chr1	93421849	93421959	E072	20655
chr1	93422195	93422584	E072	21001
chr1	93422586	93422693	E072	21392
chr1	93422753	93422818	E072	21559
chr1	93422865	93423244	E072	21671
chr1	93423690	93423788	E072	22496
chr1	93423872	93424033	E072	22678
chr1	93424075	93424184	E072	22881
chr1	93424219	93424301	E072	23025
chr1	93424333	93424410	E072	23139
chr1	93438108	93438623	E072	36914
chr1	93374886	93375287	E073	-25907
chr1	93395074	93395126	E073	-6068
chr1	93395262	93395469	E073	-5725
chr1	93395476	93395638	E073	-5556
chr1	93399119	93399316	E073	-1878
chr1	93399397	93399563	E073	-1631
chr1	93400049	93400806	E073	-388
chr1	93407249	93407329	E073	6055
chr1	93408695	93408757	E073	7501
chr1	93409807	93409924	E073	8613
chr1	93410075	93410197	E073	8881
chr1	93410897	93411007	E073	9703
chr1	93411087	93411201	E073	9893
chr1	93411573	93411731	E073	10379
chr1	93415652	93415926	E073	14458
chr1	93416028	93416280	E073	14834
chr1	93416304	93416406	E073	15110
chr1	93416622	93417201	E073	15428
chr1	93417658	93417790	E073	16464
chr1	93417911	93417961	E073	16717
chr1	93421704	93421823	E073	20510
chr1	93421849	93421959	E073	20655
chr1	93422195	93422584	E073	21001
chr1	93422586	93422693	E073	21392
chr1	93422753	93422818	E073	21559
chr1	93422865	93423244	E073	21671
chr1	93423690	93423788	E073	22496
chr1	93423872	93424033	E073	22678
chr1	93424075	93424184	E073	22881
chr1	93424219	93424301	E073	23025
chr1	93424333	93424410	E073	23139
chr1	93438108	93438623	E073	36914
chr1	93374886	93375287	E074	-25907
chr1	93375470	93375946	E074	-25248
chr1	93388368	93388425	E074	-12769
chr1	93392406	93392469	E074	-8725
chr1	93392525	93392598	E074	-8596
chr1	93395074	93395126	E074	-6068
chr1	93395262	93395469	E074	-5725
chr1	93395476	93395638	E074	-5556
chr1	93399119	93399316	E074	-1878
chr1	93399397	93399563	E074	-1631
chr1	93399901	93399999	E074	-1195
chr1	93400049	93400806	E074	-388
chr1	93406253	93406443	E074	5059
chr1	93407249	93407329	E074	6055
chr1	93408695	93408757	E074	7501
chr1	93408809	93409073	E074	7615
chr1	93409807	93409924	E074	8613
chr1	93410075	93410197	E074	8881
chr1	93410897	93411007	E074	9703
chr1	93411087	93411201	E074	9893
chr1	93411573	93411731	E074	10379
chr1	93413201	93413363	E074	12007
chr1	93413747	93413884	E074	12553
chr1	93415652	93415926	E074	14458
chr1	93416028	93416280	E074	14834
chr1	93416304	93416406	E074	15110
chr1	93416622	93417201	E074	15428
chr1	93417658	93417790	E074	16464
chr1	93417911	93417961	E074	16717
chr1	93418425	93418544	E074	17231
chr1	93419026	93419150	E074	17832
chr1	93419168	93419344	E074	17974
chr1	93421704	93421823	E074	20510
chr1	93421849	93421959	E074	20655
chr1	93422195	93422584	E074	21001
chr1	93422586	93422693	E074	21392
chr1	93422753	93422818	E074	21559
chr1	93422865	93423244	E074	21671
chr1	93423690	93423788	E074	22496
chr1	93423872	93424033	E074	22678
chr1	93424075	93424184	E074	22881
chr1	93424219	93424301	E074	23025
chr1	93424333	93424410	E074	23139
chr1	93433605	93433702	E074	32411
chr1	93433803	93434038	E074	32609
chr1	93438108	93438623	E074	36914
chr1	93399119	93399316	E081	-1878
chr1	93399397	93399563	E081	-1631
chr1	93399901	93399999	E081	-1195
chr1	93400049	93400806	E081	-388
chr1	93401684	93401829	E081	490
chr1	93402249	93402344	E081	1055
chr1	93408695	93408757	E081	7501
chr1	93408809	93409073	E081	7615
chr1	93400049	93400806	E082	-388
chr1	93407540	93408010	E082	6346
chr1	93408695	93408757	E082	7501
chr1	93408809	93409073	E082	7615

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93425530	93428497	E067	24336
chr1	93425530	93428497	E068	24336
chr1	93425530	93428497	E069	24336
chr1	93425530	93428497	E070	24336
chr1	93425530	93428497	E071	24336
chr1	93425530	93428497	E072	24336
chr1	93425530	93428497	E073	24336
chr1	93425530	93428497	E074	24336
chr1	93425530	93428497	E082	24336