rs2263247

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

FAM69A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0280 (8392/29890,GnomAD)
T==0267 (7778/29118,TOPMED)
T==0193 (966/5008,1000G)
T==0366 (1412/3854,ALSPAC)
T==0377 (1398/3708,TWINSUK)

Position: chr1:92898510 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 237 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.92898510T>C
GRCh37.p13 chr 1	NC_000001.10:g.93364067T>C
FAM69A RefSeqGene	NG_033051.1:g.68013A>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=0.157	C=0.843
1000Genomes	American	Sub	694	T=0.270	C=0.730
1000Genomes	East Asian	Sub	1008	T=0.034	C=0.966
1000Genomes	Europe	Sub	1006	T=0.366	C=0.634
1000Genomes	Global	Study-wide	5008	T=0.193	C=0.807
1000Genomes	South Asian	Sub	978	T=0.180	C=0.820
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.366	C=0.634
The Genome Aggregation Database	African	Sub	8688	T=0.169	C=0.831
The Genome Aggregation Database	American	Sub	836	T=0.230	C=0.770
The Genome Aggregation Database	East Asian	Sub	1620	T=0.041	C=0.959
The Genome Aggregation Database	Europe	Sub	18444	T=0.357	C=0.642
The Genome Aggregation Database	Global	Study-wide	29890	T=0.280	C=0.719
The Genome Aggregation Database	Other	Sub	302	T=0.240	C=0.760
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.267	C=0.732
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.377	C=0.623

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
rs2263247	7.68E-05	alcohol consumption	23953852

eQTL of rs2263247 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93364067	FAM69A	ENSG00000154511.7	T>C	2.3665e-3	-62990	Cortex
Chr1:93364067	EVI5	ENSG00000067208.10	T>C	1.7380e-4	106106	Caudate_basal_ganglia

meQTL of rs2263247 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.0669262119126827	6.2034e-35

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	93317337	93317402	E067	-46665
chr1	93317473	93317740	E067	-46327
chr1	93324170	93325314	E067	-38753
chr1	93325436	93325502	E067	-38565
chr1	93325557	93325675	E067	-38392
chr1	93343820	93343872	E067	-20195
chr1	93345115	93345155	E067	-18912
chr1	93345345	93345583	E067	-18484
chr1	93374886	93375287	E067	10819
chr1	93375470	93375946	E067	11403
chr1	93387980	93388181	E067	23913
chr1	93388368	93388425	E067	24301
chr1	93395074	93395126	E067	31007
chr1	93395262	93395469	E067	31195
chr1	93395476	93395638	E067	31409
chr1	93399397	93399563	E067	35330
chr1	93399901	93399999	E067	35834
chr1	93400049	93400806	E067	35982
chr1	93408809	93409073	E067	44742
chr1	93409807	93409924	E067	45740
chr1	93410075	93410197	E067	46008
chr1	93410636	93410715	E067	46569
chr1	93410897	93411007	E067	46830
chr1	93411087	93411201	E067	47020
chr1	93411573	93411731	E067	47506
chr1	93413201	93413363	E067	49134
chr1	93317337	93317402	E068	-46665
chr1	93317473	93317740	E068	-46327
chr1	93325436	93325502	E068	-38565
chr1	93325557	93325675	E068	-38392
chr1	93341920	93342406	E068	-21661
chr1	93345115	93345155	E068	-18912
chr1	93345345	93345583	E068	-18484
chr1	93348315	93348424	E068	-15643
chr1	93348501	93348646	E068	-15421
chr1	93348862	93349389	E068	-14678
chr1	93375470	93375946	E068	11403
chr1	93387980	93388181	E068	23913
chr1	93388368	93388425	E068	24301
chr1	93393378	93393664	E068	29311
chr1	93395074	93395126	E068	31007
chr1	93395262	93395469	E068	31195
chr1	93395476	93395638	E068	31409
chr1	93397024	93397554	E068	32957
chr1	93399119	93399316	E068	35052
chr1	93399397	93399563	E068	35330
chr1	93399901	93399999	E068	35834
chr1	93406253	93406443	E068	42186
chr1	93407249	93407329	E068	43182
chr1	93407540	93408010	E068	43473
chr1	93408695	93408757	E068	44628
chr1	93408809	93409073	E068	44742
chr1	93409807	93409924	E068	45740
chr1	93410075	93410197	E068	46008
chr1	93410636	93410715	E068	46569
chr1	93410897	93411007	E068	46830
chr1	93411087	93411201	E068	47020
chr1	93411573	93411731	E068	47506
chr1	93413201	93413363	E068	49134
chr1	93413747	93413884	E068	49680
chr1	93325436	93325502	E069	-38565
chr1	93325557	93325675	E069	-38392
chr1	93343820	93343872	E069	-20195
chr1	93345115	93345155	E069	-18912
chr1	93345345	93345583	E069	-18484
chr1	93348315	93348424	E069	-15643
chr1	93348501	93348646	E069	-15421
chr1	93367434	93367557	E069	3367
chr1	93374886	93375287	E069	10819
chr1	93375470	93375946	E069	11403
chr1	93387980	93388181	E069	23913
chr1	93388368	93388425	E069	24301
chr1	93395074	93395126	E069	31007
chr1	93395262	93395469	E069	31195
chr1	93395476	93395638	E069	31409
chr1	93399119	93399316	E069	35052
chr1	93399397	93399563	E069	35330
chr1	93399901	93399999	E069	35834
chr1	93400049	93400806	E069	35982
chr1	93402249	93402344	E069	38182
chr1	93406253	93406443	E069	42186
chr1	93407540	93408010	E069	43473
chr1	93408695	93408757	E069	44628
chr1	93408809	93409073	E069	44742
chr1	93409807	93409924	E069	45740
chr1	93410075	93410197	E069	46008
chr1	93410636	93410715	E069	46569
chr1	93410897	93411007	E069	46830
chr1	93411087	93411201	E069	47020
chr1	93411573	93411731	E069	47506
chr1	93342489	93342613	E070	-21454
chr1	93342703	93342819	E070	-21248
chr1	93342952	93343219	E070	-20848
chr1	93343266	93343741	E070	-20326
chr1	93343820	93343872	E070	-20195
chr1	93345115	93345155	E070	-18912
chr1	93345345	93345583	E070	-18484
chr1	93400049	93400806	E070	35982
chr1	93401684	93401829	E070	37617
chr1	93407249	93407329	E070	43182
chr1	93407540	93408010	E070	43473
chr1	93408809	93409073	E070	44742
chr1	93317337	93317402	E071	-46665
chr1	93317473	93317740	E071	-46327
chr1	93319620	93320383	E071	-43684
chr1	93325436	93325502	E071	-38565
chr1	93325557	93325675	E071	-38392
chr1	93338384	93338515	E071	-25552
chr1	93343820	93343872	E071	-20195
chr1	93345115	93345155	E071	-18912
chr1	93345345	93345583	E071	-18484
chr1	93346729	93347461	E071	-16606
chr1	93348501	93348646	E071	-15421
chr1	93348862	93349389	E071	-14678
chr1	93374886	93375287	E071	10819
chr1	93375470	93375946	E071	11403
chr1	93388368	93388425	E071	24301
chr1	93395074	93395126	E071	31007
chr1	93395262	93395469	E071	31195
chr1	93395476	93395638	E071	31409
chr1	93399119	93399316	E071	35052
chr1	93399397	93399563	E071	35330
chr1	93399901	93399999	E071	35834
chr1	93400049	93400806	E071	35982
chr1	93401684	93401829	E071	37617
chr1	93402249	93402344	E071	38182
chr1	93406253	93406443	E071	42186
chr1	93408695	93408757	E071	44628
chr1	93409807	93409924	E071	45740
chr1	93410075	93410197	E071	46008
chr1	93410636	93410715	E071	46569
chr1	93410897	93411007	E071	46830
chr1	93411087	93411201	E071	47020
chr1	93411573	93411731	E071	47506
chr1	93413201	93413363	E071	49134
chr1	93413747	93413884	E071	49680
chr1	93317337	93317402	E072	-46665
chr1	93317473	93317740	E072	-46327
chr1	93318075	93318232	E072	-45835
chr1	93318311	93318384	E072	-45683
chr1	93318988	93319144	E072	-44923
chr1	93324170	93325314	E072	-38753
chr1	93338384	93338515	E072	-25552
chr1	93343820	93343872	E072	-20195
chr1	93345115	93345155	E072	-18912
chr1	93345345	93345583	E072	-18484
chr1	93346729	93347461	E072	-16606
chr1	93367434	93367557	E072	3367
chr1	93374886	93375287	E072	10819
chr1	93375470	93375946	E072	11403
chr1	93387980	93388181	E072	23913
chr1	93388368	93388425	E072	24301
chr1	93395074	93395126	E072	31007
chr1	93395262	93395469	E072	31195
chr1	93395476	93395638	E072	31409
chr1	93399397	93399563	E072	35330
chr1	93399901	93399999	E072	35834
chr1	93400049	93400806	E072	35982
chr1	93407249	93407329	E072	43182
chr1	93407540	93408010	E072	43473
chr1	93408695	93408757	E072	44628
chr1	93408809	93409073	E072	44742
chr1	93409807	93409924	E072	45740
chr1	93410075	93410197	E072	46008
chr1	93410636	93410715	E072	46569
chr1	93410897	93411007	E072	46830
chr1	93411087	93411201	E072	47020
chr1	93411573	93411731	E072	47506
chr1	93345115	93345155	E073	-18912
chr1	93345345	93345583	E073	-18484
chr1	93348501	93348646	E073	-15421
chr1	93348862	93349389	E073	-14678
chr1	93374886	93375287	E073	10819
chr1	93395074	93395126	E073	31007
chr1	93395262	93395469	E073	31195
chr1	93395476	93395638	E073	31409
chr1	93399119	93399316	E073	35052
chr1	93399397	93399563	E073	35330
chr1	93400049	93400806	E073	35982
chr1	93407249	93407329	E073	43182
chr1	93408695	93408757	E073	44628
chr1	93409807	93409924	E073	45740
chr1	93410075	93410197	E073	46008
chr1	93410897	93411007	E073	46830
chr1	93411087	93411201	E073	47020
chr1	93411573	93411731	E073	47506
chr1	93324170	93325314	E074	-38753
chr1	93325436	93325502	E074	-38565
chr1	93325557	93325675	E074	-38392
chr1	93336380	93336485	E074	-27582
chr1	93338384	93338515	E074	-25552
chr1	93345115	93345155	E074	-18912
chr1	93345345	93345583	E074	-18484
chr1	93348315	93348424	E074	-15643
chr1	93348501	93348646	E074	-15421
chr1	93348862	93349389	E074	-14678
chr1	93374886	93375287	E074	10819
chr1	93375470	93375946	E074	11403
chr1	93388368	93388425	E074	24301
chr1	93392406	93392469	E074	28339
chr1	93392525	93392598	E074	28458
chr1	93395074	93395126	E074	31007
chr1	93395262	93395469	E074	31195
chr1	93395476	93395638	E074	31409
chr1	93399119	93399316	E074	35052
chr1	93399397	93399563	E074	35330
chr1	93399901	93399999	E074	35834
chr1	93400049	93400806	E074	35982
chr1	93406253	93406443	E074	42186
chr1	93407249	93407329	E074	43182
chr1	93408695	93408757	E074	44628
chr1	93408809	93409073	E074	44742
chr1	93409807	93409924	E074	45740
chr1	93410075	93410197	E074	46008
chr1	93410897	93411007	E074	46830
chr1	93411087	93411201	E074	47020
chr1	93411573	93411731	E074	47506
chr1	93413201	93413363	E074	49134
chr1	93413747	93413884	E074	49680
chr1	93318311	93318384	E081	-45683
chr1	93342952	93343219	E081	-20848
chr1	93343266	93343741	E081	-20326
chr1	93399119	93399316	E081	35052
chr1	93399397	93399563	E081	35330
chr1	93399901	93399999	E081	35834
chr1	93400049	93400806	E081	35982
chr1	93401684	93401829	E081	37617
chr1	93402249	93402344	E081	38182
chr1	93408695	93408757	E081	44628
chr1	93408809	93409073	E081	44742
chr1	93342952	93343219	E082	-20848
chr1	93343266	93343741	E082	-20326
chr1	93343820	93343872	E082	-20195
chr1	93400049	93400806	E082	35982
chr1	93407540	93408010	E082	43473
chr1	93408695	93408757	E082	44628
chr1	93408809	93409073	E082	44742