rs1557997

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

RPA3 : Intron Variant
UMAD1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0356 (10640/29844,GnomAD)
G==0394 (11477/29118,TOPMED)
G==0338 (1694/5008,1000G)
G==0339 (1308/3854,ALSPAC)
G==0328 (1215/3708,TWINSUK)

Position: chr7:7664329 (GRCh38.p7) (7p21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 104 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.7664329G>A
GRCh37.p13 chr 7	NC_000007.13:g.7703960G>A

Gene: UMAD1, UBAP1-MVB12-associated (UMA) domain containing 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UMAD1 transcript variant 1	NM_001302348.1:c.	N/A	Intron Variant
UMAD1 transcript variant 2	NM_001302349.1:c.	N/A	Intron Variant
UMAD1 transcript variant 3	NM_001302350.1:c.	N/A	Intron Variant

Gene: RPA3, replication protein A3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RPA3 transcript	NM_002947.4:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.477	A=0.523
1000Genomes	American	Sub	694	G=0.310	A=0.690
1000Genomes	East Asian	Sub	1008	G=0.165	A=0.835
1000Genomes	Europe	Sub	1006	G=0.314	A=0.686
1000Genomes	Global	Study-wide	5008	G=0.338	A=0.662
1000Genomes	South Asian	Sub	978	G=0.380	A=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.339	A=0.661
The Genome Aggregation Database	African	Sub	8658	G=0.450	A=0.550
The Genome Aggregation Database	American	Sub	836	G=0.290	A=0.710
The Genome Aggregation Database	East Asian	Sub	1606	G=0.130	A=0.870
The Genome Aggregation Database	Europe	Sub	18442	G=0.336	A=0.663
The Genome Aggregation Database	Global	Study-wide	29844	G=0.356	A=0.643
The Genome Aggregation Database	Other	Sub	302	G=0.270	A=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.394	A=0.605
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.328	A=0.672

PMID	Title	Author	Journal
22102698	Genetic variation in nucleotide excision repair pathway genes, pesticide exposure and prostate cancer risk.	Barry KH	Carcinogenesis
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

SNP ID	p-value	Traits	Study
rs1557997	4.6E-05	alcohol consumption (maxi-drinks)	24277619

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

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 )
chr7	7713692	7713746	E067	9732
chr7	7720727	7721611	E067	16767
chr7	7721637	7721766	E067	17677
chr7	7721816	7721891	E067	17856
chr7	7722126	7722186	E067	18166
chr7	7722189	7722286	E067	18229
chr7	7722315	7722511	E067	18355
chr7	7722547	7722822	E067	18587
chr7	7722941	7723021	E067	18981
chr7	7734643	7734777	E067	30683
chr7	7734839	7735552	E067	30879
chr7	7720727	7721611	E068	16767
chr7	7721637	7721766	E068	17677
chr7	7721816	7721891	E068	17856
chr7	7722126	7722186	E068	18166
chr7	7722189	7722286	E068	18229
chr7	7722315	7722511	E068	18355
chr7	7722547	7722822	E068	18587
chr7	7722941	7723021	E068	18981
chr7	7726212	7727299	E068	22252
chr7	7734489	7734539	E068	30529
chr7	7734643	7734777	E068	30683
chr7	7734839	7735552	E068	30879
chr7	7735630	7735680	E068	31670
chr7	7735826	7735897	E068	31866
chr7	7735954	7736736	E068	31994
chr7	7736774	7736834	E068	32814
chr7	7713862	7713922	E069	9902
chr7	7720727	7721611	E069	16767
chr7	7721637	7721766	E069	17677
chr7	7734489	7734539	E069	30529
chr7	7734643	7734777	E069	30683
chr7	7734839	7735552	E069	30879
chr7	7702293	7702438	E070	-1522
chr7	7727501	7727699	E070	23541
chr7	7741063	7741133	E070	37103
chr7	7741199	7741305	E070	37239
chr7	7741362	7741477	E070	37402
chr7	7743505	7743575	E070	39545
chr7	7744527	7744716	E070	40567
chr7	7744876	7745169	E070	40916
chr7	7745961	7746052	E070	42001
chr7	7746306	7746425	E070	42346
chr7	7746533	7746623	E070	42573
chr7	7746652	7746848	E070	42692
chr7	7746898	7747220	E070	42938
chr7	7748037	7748104	E070	44077
chr7	7748140	7748271	E070	44180
chr7	7748505	7748555	E070	44545
chr7	7748581	7748631	E070	44621
chr7	7748700	7748784	E070	44740
chr7	7748835	7749367	E070	44875
chr7	7749419	7749523	E070	45459
chr7	7720727	7721611	E071	16767
chr7	7721637	7721766	E071	17677
chr7	7721816	7721891	E071	17856
chr7	7722547	7722822	E071	18587
chr7	7722941	7723021	E071	18981
chr7	7734643	7734777	E071	30683
chr7	7734839	7735552	E071	30879
chr7	7744527	7744716	E071	40567
chr7	7744876	7745169	E071	40916
chr7	7745751	7745834	E071	41791
chr7	7745961	7746052	E071	42001
chr7	7748700	7748784	E071	44740
chr7	7722315	7722511	E072	18355
chr7	7722547	7722822	E072	18587
chr7	7726212	7727299	E072	22252
chr7	7746652	7746848	E072	42692
chr7	7746898	7747220	E072	42938
chr7	7720727	7721611	E073	16767
chr7	7721637	7721766	E073	17677
chr7	7726212	7727299	E073	22252
chr7	7727501	7727699	E073	23541
chr7	7727723	7727992	E073	23763
chr7	7734839	7735552	E073	30879
chr7	7682142	7682192	E074	-21768
chr7	7682470	7682561	E074	-21399
chr7	7719366	7719679	E074	15406
chr7	7720521	7720654	E074	16561
chr7	7720727	7721611	E074	16767
chr7	7721637	7721766	E074	17677
chr7	7721816	7721891	E074	17856
chr7	7722547	7722822	E074	18587
chr7	7734839	7735552	E074	30879
chr7	7744527	7744716	E074	40567
chr7	7746306	7746425	E074	42346
chr7	7746533	7746623	E074	42573
chr7	7746652	7746848	E074	42692
chr7	7746898	7747220	E074	42938
chr7	7722547	7722822	E081	18587
chr7	7722941	7723021	E081	18981
chr7	7746306	7746425	E081	42346
chr7	7746533	7746623	E081	42573
chr7	7746652	7746848	E081	42692
chr7	7746898	7747220	E081	42938
chr7	7722315	7722511	E082	18355
chr7	7722547	7722822	E082	18587
chr7	7746306	7746425	E082	42346
chr7	7746533	7746623	E082	42573
chr7	7746652	7746848	E082	42692
chr7	7746898	7747220	E082	42938
chr7	7747419	7747876	E082	43459
chr7	7747880	7747985	E082	43920

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	7678930	7681522	E067	-22438
chr7	7678930	7681522	E068	-22438
chr7	7678930	7681522	E069	-22438
chr7	7678930	7681522	E070	-22438
chr7	7678930	7681522	E071	-22438
chr7	7678930	7681522	E072	-22438
chr7	7678930	7681522	E073	-22438
chr7	7678930	7681522	E074	-22438
chr7	7678930	7681522	E081	-22438
chr7	7678930	7681522	E082	-22438

rs1557997

Genomic Coordinates

Gene: UMAD1, UBAP1-MVB12-associated (UMA) domain containing 1(plus strand)

Gene: RPA3, replication protein A3(minus strand)

Population Frequency

P-Value

eQTL of rs1557997 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1557997 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)