rs10874744

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SNORA66 : Non Coding Transcript Variant
FAM69A : Intron Variant
RPL5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0323 (36985/114506,ExAC)
G==0393 (11769/29904,GnomAD)
G==0436 (12719/29118,TOPMED)
A=0431 (2471/5734,GO-ESP)
G==0308 (1543/5008,1000G)
G==0378 (1456/3854,ALSPAC)
G==0383 (1419/3708,TWINSUK)

Position: chr1:92840760 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 173 Enhancers around

Promoter: 28 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.92840760G>A
GRCh37.p13 chr 1	NC_000001.10:g.93306317G>A
FAM69A RefSeqGene	NG_033051.1:g.125763C>T
RPL5 RefSeqGene	NG_011779.1:g.13724G>A

Gene: RPL5, ribosomal protein L5(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RPL5 transcript	NM_000969.3:c.	N/A	Intron Variant

Gene: FAM69A, family with sequence similarity 69 member A(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM69A transcript variant 5	NM_001252273.1:c.	N/A	Intron Variant
FAM69A transcript variant 1	NM_001006605.4:c.	N/A	Genic Downstream Transcript Variant
FAM69A transcript variant 2	NM_001252269.1:c.	N/A	Genic Downstream Transcript Variant
FAM69A transcript variant 3	NM_001252270.1:c.	N/A	Genic Downstream Transcript Variant
FAM69A transcript variant 4	NM_001252271.1:c.	N/A	Genic Downstream Transcript Variant

Gene: SNORA66, small nucleolar RNA, H/ACA box 66(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SNORA66 transcript	NR_002444.2:n.42G>A	G>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.545	A=0.455
1000Genomes	American	Sub	694	G=0.310	A=0.690
1000Genomes	East Asian	Sub	1008	G=0.040	A=0.960
1000Genomes	Europe	Sub	1006	G=0.378	A=0.622
1000Genomes	Global	Study-wide	5008	G=0.308	A=0.692
1000Genomes	South Asian	Sub	978	G=0.190	A=0.810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.378	A=0.622
The Exome Aggregation Consortium	American	Sub	19956	G=0.362	A=0.637
The Exome Aggregation Consortium	Asian	Sub	24768	G=0.144	A=0.855
The Exome Aggregation Consortium	Europe	Sub	68922	G=0.375	A=0.624
The Exome Aggregation Consortium	Global	Study-wide	114506	G=0.323	A=0.677
The Exome Aggregation Consortium	Other	Sub	860	G=0.310	A=0.690
The Genome Aggregation Database	African	Sub	8696	G=0.542	A=0.458
The Genome Aggregation Database	American	Sub	836	G=0.250	A=0.750
The Genome Aggregation Database	East Asian	Sub	1614	G=0.053	A=0.947
The Genome Aggregation Database	Europe	Sub	18456	G=0.362	A=0.637
The Genome Aggregation Database	Global	Study-wide	29904	G=0.393	A=0.606
The Genome Aggregation Database	Other	Sub	302	G=0.260	A=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.436	A=0.563
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.383	A=0.617

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
rs10874744	7.39E-05	alcohol consumption	23953852

eQTL of rs10874744 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:93306317	FAM69A	ENSG00000154511.7	G>A	2.3665e-3	-120740	Cortex

meQTL of rs10874744 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05036103	chr1:93415910	FAM69A	-0.0608350145982972	1.1570e-32

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	93296963	93297042	E067	-9275
chr1	93299552	93299655	E067	-6662
chr1	93299831	93300066	E067	-6251
chr1	93304201	93304337	E067	-1980
chr1	93317337	93317402	E067	11020
chr1	93317473	93317740	E067	11156
chr1	93324170	93325314	E067	17853
chr1	93325436	93325502	E067	19119
chr1	93325557	93325675	E067	19240
chr1	93343820	93343872	E067	37503
chr1	93345115	93345155	E067	38798
chr1	93345345	93345583	E067	39028
chr1	93296963	93297042	E068	-9275
chr1	93299552	93299655	E068	-6662
chr1	93299831	93300066	E068	-6251
chr1	93300279	93300406	E068	-5911
chr1	93300475	93300532	E068	-5785
chr1	93300650	93300747	E068	-5570
chr1	93300762	93300802	E068	-5515
chr1	93301623	93301733	E068	-4584
chr1	93305014	93305105	E068	-1212
chr1	93305123	93305252	E068	-1065
chr1	93305604	93305649	E068	-668
chr1	93305765	93305832	E068	-485
chr1	93306031	93306085	E068	-232
chr1	93308618	93308852	E068	2301
chr1	93309181	93309247	E068	2864
chr1	93309346	93309396	E068	3029
chr1	93309449	93309521	E068	3132
chr1	93309558	93309608	E068	3241
chr1	93317337	93317402	E068	11020
chr1	93317473	93317740	E068	11156
chr1	93325436	93325502	E068	19119
chr1	93325557	93325675	E068	19240
chr1	93341920	93342406	E068	35603
chr1	93345115	93345155	E068	38798
chr1	93345345	93345583	E068	39028
chr1	93348315	93348424	E068	41998
chr1	93348501	93348646	E068	42184
chr1	93348862	93349389	E068	42545
chr1	93269866	93270085	E069	-36232
chr1	93299552	93299655	E069	-6662
chr1	93299831	93300066	E069	-6251
chr1	93300279	93300406	E069	-5911
chr1	93302005	93302055	E069	-4262
chr1	93303481	93303616	E069	-2701
chr1	93304201	93304337	E069	-1980
chr1	93305014	93305105	E069	-1212
chr1	93305123	93305252	E069	-1065
chr1	93305604	93305649	E069	-668
chr1	93305765	93305832	E069	-485
chr1	93306031	93306085	E069	-232
chr1	93306247	93306444	E069	0
chr1	93308498	93308578	E069	2181
chr1	93325436	93325502	E069	19119
chr1	93325557	93325675	E069	19240
chr1	93343820	93343872	E069	37503
chr1	93345115	93345155	E069	38798
chr1	93345345	93345583	E069	39028
chr1	93348315	93348424	E069	41998
chr1	93348501	93348646	E069	42184
chr1	93299552	93299655	E070	-6662
chr1	93299831	93300066	E070	-6251
chr1	93300279	93300406	E070	-5911
chr1	93300475	93300532	E070	-5785
chr1	93300650	93300747	E070	-5570
chr1	93300762	93300802	E070	-5515
chr1	93300870	93300942	E070	-5375
chr1	93342489	93342613	E070	36172
chr1	93342703	93342819	E070	36386
chr1	93342952	93343219	E070	36635
chr1	93343266	93343741	E070	36949
chr1	93343820	93343872	E070	37503
chr1	93345115	93345155	E070	38798
chr1	93345345	93345583	E070	39028
chr1	93270165	93271138	E071	-35179
chr1	93299831	93300066	E071	-6251
chr1	93300279	93300406	E071	-5911
chr1	93300475	93300532	E071	-5785
chr1	93300650	93300747	E071	-5570
chr1	93300762	93300802	E071	-5515
chr1	93300870	93300942	E071	-5375
chr1	93304201	93304337	E071	-1980
chr1	93305014	93305105	E071	-1212
chr1	93305123	93305252	E071	-1065
chr1	93317337	93317402	E071	11020
chr1	93317473	93317740	E071	11156
chr1	93319620	93320383	E071	13303
chr1	93325436	93325502	E071	19119
chr1	93325557	93325675	E071	19240
chr1	93338384	93338515	E071	32067
chr1	93343820	93343872	E071	37503
chr1	93345115	93345155	E071	38798
chr1	93345345	93345583	E071	39028
chr1	93346729	93347461	E071	40412
chr1	93348501	93348646	E071	42184
chr1	93348862	93349389	E071	42545
chr1	93296963	93297042	E072	-9275
chr1	93299831	93300066	E072	-6251
chr1	93300279	93300406	E072	-5911
chr1	93300475	93300532	E072	-5785
chr1	93305123	93305252	E072	-1065
chr1	93305604	93305649	E072	-668
chr1	93305765	93305832	E072	-485
chr1	93306031	93306085	E072	-232
chr1	93306247	93306444	E072	0
chr1	93317337	93317402	E072	11020
chr1	93317473	93317740	E072	11156
chr1	93318075	93318232	E072	11758
chr1	93318311	93318384	E072	11994
chr1	93318988	93319144	E072	12671
chr1	93324170	93325314	E072	17853
chr1	93338384	93338515	E072	32067
chr1	93343820	93343872	E072	37503
chr1	93345115	93345155	E072	38798
chr1	93345345	93345583	E072	39028
chr1	93346729	93347461	E072	40412
chr1	93299831	93300066	E073	-6251
chr1	93300279	93300406	E073	-5911
chr1	93300475	93300532	E073	-5785
chr1	93300650	93300747	E073	-5570
chr1	93300762	93300802	E073	-5515
chr1	93300870	93300942	E073	-5375
chr1	93303481	93303616	E073	-2701
chr1	93304201	93304337	E073	-1980
chr1	93305014	93305105	E073	-1212
chr1	93305123	93305252	E073	-1065
chr1	93305604	93305649	E073	-668
chr1	93305765	93305832	E073	-485
chr1	93306031	93306085	E073	-232
chr1	93306247	93306444	E073	0
chr1	93345115	93345155	E073	38798
chr1	93345345	93345583	E073	39028
chr1	93348501	93348646	E073	42184
chr1	93348862	93349389	E073	42545
chr1	93299552	93299655	E074	-6662
chr1	93299831	93300066	E074	-6251
chr1	93300279	93300406	E074	-5911
chr1	93300475	93300532	E074	-5785
chr1	93300650	93300747	E074	-5570
chr1	93300762	93300802	E074	-5515
chr1	93300870	93300942	E074	-5375
chr1	93303481	93303616	E074	-2701
chr1	93324170	93325314	E074	17853
chr1	93325436	93325502	E074	19119
chr1	93325557	93325675	E074	19240
chr1	93336380	93336485	E074	30063
chr1	93338384	93338515	E074	32067
chr1	93345115	93345155	E074	38798
chr1	93345345	93345583	E074	39028
chr1	93348315	93348424	E074	41998
chr1	93348501	93348646	E074	42184
chr1	93348862	93349389	E074	42545
chr1	93299552	93299655	E081	-6662
chr1	93299831	93300066	E081	-6251
chr1	93300279	93300406	E081	-5911
chr1	93300475	93300532	E081	-5785
chr1	93300650	93300747	E081	-5570
chr1	93300762	93300802	E081	-5515
chr1	93318311	93318384	E081	11994
chr1	93342952	93343219	E081	36635
chr1	93343266	93343741	E081	36949
chr1	93296963	93297042	E082	-9275
chr1	93300279	93300406	E082	-5911
chr1	93300475	93300532	E082	-5785
chr1	93300650	93300747	E082	-5570
chr1	93300762	93300802	E082	-5515
chr1	93302005	93302055	E082	-4262
chr1	93302690	93302834	E082	-3483
chr1	93303481	93303616	E082	-2701
chr1	93342952	93343219	E082	36635
chr1	93343266	93343741	E082	36949
chr1	93343820	93343872	E082	37503

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	93297077	93298603	E067	-7714
chr1	93298756	93298859	E067	-7458
chr1	93299016	93299089	E067	-7228
chr1	93297077	93298603	E068	-7714
chr1	93298756	93298859	E068	-7458
chr1	93299016	93299089	E068	-7228
chr1	93297077	93298603	E069	-7714
chr1	93298756	93298859	E069	-7458
chr1	93297077	93298603	E070	-7714
chr1	93298756	93298859	E070	-7458
chr1	93297077	93298603	E071	-7714
chr1	93298756	93298859	E071	-7458
chr1	93299016	93299089	E071	-7228
chr1	93297077	93298603	E072	-7714
chr1	93298756	93298859	E072	-7458
chr1	93299016	93299089	E072	-7228
chr1	93297077	93298603	E073	-7714
chr1	93298756	93298859	E073	-7458
chr1	93299016	93299089	E073	-7228
chr1	93297077	93298603	E074	-7714
chr1	93298756	93298859	E074	-7458
chr1	93299016	93299089	E074	-7228
chr1	93297077	93298603	E081	-7714
chr1	93298756	93298859	E081	-7458
chr1	93299016	93299089	E081	-7228
chr1	93297077	93298603	E082	-7714
chr1	93298756	93298859	E082	-7458
chr1	93299016	93299089	E082	-7228