rs10779795

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PHF13 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0328 (9828/29938,GnomAD)
G=0307 (8960/29118,TOPMED)
G=0366 (1832/5008,1000G)
G=0331 (1274/3854,ALSPAC)
G=0344 (1277/3708,TWINSUK)

Position: chr1:6617004 (GRCh38.p7) (1p36.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 209 Enhancers around

Promoter: 53 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.6617004A>G
GRCh37.p13 chr 1	NC_000001.10:g.6677064A>G

Gene: PHF13, PHD finger protein 13(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHF13 transcript	NM_153812.2:c.	N/A	Intron Variant
PHF13 transcript variant X1	XM_011540762.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.694	G=0.306
1000Genomes	American	Sub	694	A=0.670	G=0.330
1000Genomes	East Asian	Sub	1008	A=0.613	G=0.387
1000Genomes	Europe	Sub	1006	A=0.673	G=0.327
1000Genomes	Global	Study-wide	5008	A=0.634	G=0.366
1000Genomes	South Asian	Sub	978	A=0.510	G=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.669	G=0.331
The Genome Aggregation Database	African	Sub	8718	A=0.692	G=0.308
The Genome Aggregation Database	American	Sub	836	A=0.720	G=0.280
The Genome Aggregation Database	East Asian	Sub	1616	A=0.574	G=0.426
The Genome Aggregation Database	Europe	Sub	18468	A=0.669	G=0.330
The Genome Aggregation Database	Global	Study-wide	29938	A=0.671	G=0.328
The Genome Aggregation Database	Other	Sub	300	A=0.630	G=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.692	G=0.307
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.656	G=0.344

PMID	Title	Author	Journal
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

P-Value

SNP ID	p-value	Traits	Study
rs10779795	0.000853	alcohol dependence	24277619

eQTL of rs10779795 in Brain tissues (GTEx Analysis Release V7)

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

meQTL of rs10779795 in Fetal Brain

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 )
chr1	6638260	6638597	E067	-38467
chr1	6638687	6638847	E067	-38217
chr1	6638887	6639107	E067	-37957
chr1	6641511	6641555	E067	-35509
chr1	6641788	6642808	E067	-34256
chr1	6646736	6646919	E067	-30145
chr1	6647085	6648478	E067	-28586
chr1	6651994	6652253	E067	-24811
chr1	6652302	6652381	E067	-24683
chr1	6652594	6652734	E067	-24330
chr1	6652847	6652897	E067	-24167
chr1	6656573	6656638	E067	-20426
chr1	6656764	6656871	E067	-20193
chr1	6657001	6657085	E067	-19979
chr1	6657134	6657643	E067	-19421
chr1	6657753	6657901	E067	-19163
chr1	6657957	6658162	E067	-18902
chr1	6658603	6658686	E067	-18378
chr1	6686857	6686906	E067	9793
chr1	6687111	6687194	E067	10047
chr1	6713236	6713355	E067	36172
chr1	6713546	6713594	E067	36482
chr1	6638260	6638597	E068	-38467
chr1	6638687	6638847	E068	-38217
chr1	6638887	6639107	E068	-37957
chr1	6641511	6641555	E068	-35509
chr1	6641788	6642808	E068	-34256
chr1	6646736	6646919	E068	-30145
chr1	6647085	6648478	E068	-28586
chr1	6650915	6651002	E068	-26062
chr1	6651268	6651386	E068	-25678
chr1	6651392	6651549	E068	-25515
chr1	6651994	6652253	E068	-24811
chr1	6652302	6652381	E068	-24683
chr1	6652594	6652734	E068	-24330
chr1	6652847	6652897	E068	-24167
chr1	6653171	6653241	E068	-23823
chr1	6656573	6656638	E068	-20426
chr1	6656764	6656871	E068	-20193
chr1	6657001	6657085	E068	-19979
chr1	6657134	6657643	E068	-19421
chr1	6657753	6657901	E068	-19163
chr1	6657957	6658162	E068	-18902
chr1	6658603	6658686	E068	-18378
chr1	6659017	6659208	E068	-17856
chr1	6664916	6665010	E068	-12054
chr1	6665114	6665226	E068	-11838
chr1	6669409	6669721	E068	-7343
chr1	6638260	6638597	E069	-38467
chr1	6638687	6638847	E069	-38217
chr1	6638887	6639107	E069	-37957
chr1	6641511	6641555	E069	-35509
chr1	6641788	6642808	E069	-34256
chr1	6646736	6646919	E069	-30145
chr1	6647085	6648478	E069	-28586
chr1	6651268	6651386	E069	-25678
chr1	6651392	6651549	E069	-25515
chr1	6651994	6652253	E069	-24811
chr1	6652302	6652381	E069	-24683
chr1	6652594	6652734	E069	-24330
chr1	6652847	6652897	E069	-24167
chr1	6656573	6656638	E069	-20426
chr1	6656764	6656871	E069	-20193
chr1	6657001	6657085	E069	-19979
chr1	6657134	6657643	E069	-19421
chr1	6657753	6657901	E069	-19163
chr1	6657957	6658162	E069	-18902
chr1	6658603	6658686	E069	-18378
chr1	6659017	6659208	E069	-17856
chr1	6664916	6665010	E069	-12054
chr1	6665114	6665226	E069	-11838
chr1	6669409	6669721	E069	-7343
chr1	6669759	6670017	E069	-7047
chr1	6686857	6686906	E069	9793
chr1	6687111	6687194	E069	10047
chr1	6713546	6713594	E069	36482
chr1	6713713	6713960	E069	36649
chr1	6641511	6641555	E070	-35509
chr1	6641788	6642808	E070	-34256
chr1	6647085	6648478	E070	-28586
chr1	6656573	6656638	E070	-20426
chr1	6656764	6656871	E070	-20193
chr1	6657001	6657085	E070	-19979
chr1	6671846	6671981	E070	-5083
chr1	6686857	6686906	E070	9793
chr1	6687111	6687194	E070	10047
chr1	6687284	6687370	E070	10220
chr1	6711439	6711492	E070	34375
chr1	6713236	6713355	E070	36172
chr1	6638260	6638597	E071	-38467
chr1	6638687	6638847	E071	-38217
chr1	6638887	6639107	E071	-37957
chr1	6641511	6641555	E071	-35509
chr1	6647085	6648478	E071	-28586
chr1	6648579	6648711	E071	-28353
chr1	6648755	6648858	E071	-28206
chr1	6648898	6649021	E071	-28043
chr1	6649073	6649127	E071	-27937
chr1	6649206	6649566	E071	-27498
chr1	6649661	6649755	E071	-27309
chr1	6649765	6649926	E071	-27138
chr1	6651268	6651386	E071	-25678
chr1	6651392	6651549	E071	-25515
chr1	6651994	6652253	E071	-24811
chr1	6652302	6652381	E071	-24683
chr1	6652594	6652734	E071	-24330
chr1	6652847	6652897	E071	-24167
chr1	6656573	6656638	E071	-20426
chr1	6656764	6656871	E071	-20193
chr1	6657001	6657085	E071	-19979
chr1	6657134	6657643	E071	-19421
chr1	6657753	6657901	E071	-19163
chr1	6657957	6658162	E071	-18902
chr1	6658603	6658686	E071	-18378
chr1	6664916	6665010	E071	-12054
chr1	6665114	6665226	E071	-11838
chr1	6671846	6671981	E071	-5083
chr1	6686857	6686906	E071	9793
chr1	6638260	6638597	E072	-38467
chr1	6638687	6638847	E072	-38217
chr1	6638887	6639107	E072	-37957
chr1	6644308	6644482	E072	-32582
chr1	6646157	6646208	E072	-30856
chr1	6646736	6646919	E072	-30145
chr1	6647085	6648478	E072	-28586
chr1	6649206	6649566	E072	-27498
chr1	6649661	6649755	E072	-27309
chr1	6649765	6649926	E072	-27138
chr1	6650915	6651002	E072	-26062
chr1	6651268	6651386	E072	-25678
chr1	6651392	6651549	E072	-25515
chr1	6651994	6652253	E072	-24811
chr1	6656573	6656638	E072	-20426
chr1	6656764	6656871	E072	-20193
chr1	6657001	6657085	E072	-19979
chr1	6657134	6657643	E072	-19421
chr1	6657753	6657901	E072	-19163
chr1	6657957	6658162	E072	-18902
chr1	6659017	6659208	E072	-17856
chr1	6669409	6669721	E072	-7343
chr1	6669759	6670017	E072	-7047
chr1	6686857	6686906	E072	9793
chr1	6638260	6638597	E073	-38467
chr1	6638687	6638847	E073	-38217
chr1	6641511	6641555	E073	-35509
chr1	6641788	6642808	E073	-34256
chr1	6644308	6644482	E073	-32582
chr1	6644635	6644756	E073	-32308
chr1	6644818	6645072	E073	-31992
chr1	6645238	6645777	E073	-31287
chr1	6645934	6646021	E073	-31043
chr1	6646157	6646208	E073	-30856
chr1	6646736	6646919	E073	-30145
chr1	6647085	6648478	E073	-28586
chr1	6651268	6651386	E073	-25678
chr1	6651392	6651549	E073	-25515
chr1	6651994	6652253	E073	-24811
chr1	6652302	6652381	E073	-24683
chr1	6652594	6652734	E073	-24330
chr1	6652847	6652897	E073	-24167
chr1	6653171	6653241	E073	-23823
chr1	6656573	6656638	E073	-20426
chr1	6656764	6656871	E073	-20193
chr1	6657001	6657085	E073	-19979
chr1	6657134	6657643	E073	-19421
chr1	6657753	6657901	E073	-19163
chr1	6657957	6658162	E073	-18902
chr1	6658603	6658686	E073	-18378
chr1	6664916	6665010	E073	-12054
chr1	6665114	6665226	E073	-11838
chr1	6671846	6671981	E073	-5083
chr1	6672072	6672154	E073	-4910
chr1	6686857	6686906	E073	9793
chr1	6687111	6687194	E073	10047
chr1	6687284	6687370	E073	10220
chr1	6638260	6638597	E074	-38467
chr1	6638687	6638847	E074	-38217
chr1	6638887	6639107	E074	-37957
chr1	6646736	6646919	E074	-30145
chr1	6647085	6648478	E074	-28586
chr1	6648579	6648711	E074	-28353
chr1	6648755	6648858	E074	-28206
chr1	6656573	6656638	E074	-20426
chr1	6656764	6656871	E074	-20193
chr1	6657001	6657085	E074	-19979
chr1	6657134	6657643	E074	-19421
chr1	6657753	6657901	E074	-19163
chr1	6657957	6658162	E074	-18902
chr1	6658603	6658686	E074	-18378
chr1	6671846	6671981	E074	-5083
chr1	6672072	6672154	E074	-4910
chr1	6641511	6641555	E081	-35509
chr1	6641788	6642808	E081	-34256
chr1	6671846	6671981	E081	-5083
chr1	6672072	6672154	E081	-4910
chr1	6676123	6676183	E081	-881
chr1	6676370	6676578	E081	-486
chr1	6686857	6686906	E081	9793
chr1	6697930	6698042	E081	20866
chr1	6698319	6698611	E081	21255
chr1	6713236	6713355	E081	36172
chr1	6713546	6713594	E081	36482
chr1	6713713	6713960	E081	36649
chr1	6641511	6641555	E082	-35509
chr1	6641788	6642808	E082	-34256
chr1	6672072	6672154	E082	-4910
chr1	6697930	6698042	E082	20866
chr1	6698319	6698611	E082	21255
chr1	6713236	6713355	E082	36172

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	6660603	6664818	E067	-12246
chr1	6672478	6675107	E067	-1957
chr1	6675119	6675282	E067	-1782
chr1	6675302	6675535	E067	-1529
chr1	6675620	6675880	E067	-1184
chr1	6684611	6686176	E067	7547
chr1	6660603	6664818	E068	-12246
chr1	6672478	6675107	E068	-1957
chr1	6675119	6675282	E068	-1782
chr1	6675302	6675535	E068	-1529
chr1	6675620	6675880	E068	-1184
chr1	6684611	6686176	E068	7547
chr1	6660603	6664818	E069	-12246
chr1	6672478	6675107	E069	-1957
chr1	6675119	6675282	E069	-1782
chr1	6675302	6675535	E069	-1529
chr1	6675620	6675880	E069	-1184
chr1	6684611	6686176	E069	7547
chr1	6672478	6675107	E070	-1957
chr1	6675119	6675282	E070	-1782
chr1	6675302	6675535	E070	-1529
chr1	6675620	6675880	E070	-1184
chr1	6684611	6686176	E070	7547
chr1	6660603	6664818	E071	-12246
chr1	6672478	6675107	E071	-1957
chr1	6675119	6675282	E071	-1782
chr1	6675302	6675535	E071	-1529
chr1	6675620	6675880	E071	-1184
chr1	6684611	6686176	E071	7547
chr1	6660603	6664818	E072	-12246
chr1	6672478	6675107	E072	-1957
chr1	6675119	6675282	E072	-1782
chr1	6675302	6675535	E072	-1529
chr1	6675620	6675880	E072	-1184
chr1	6684611	6686176	E072	7547
chr1	6660603	6664818	E073	-12246
chr1	6672478	6675107	E073	-1957
chr1	6675119	6675282	E073	-1782
chr1	6675302	6675535	E073	-1529
chr1	6675620	6675880	E073	-1184
chr1	6684611	6686176	E073	7547
chr1	6630982	6631068	E074	-45996
chr1	6660603	6664818	E074	-12246
chr1	6672478	6675107	E074	-1957
chr1	6675302	6675535	E074	-1529
chr1	6675620	6675880	E074	-1184
chr1	6684611	6686176	E074	7547
chr1	6660603	6664818	E082	-12246
chr1	6672478	6675107	E082	-1957
chr1	6675119	6675282	E082	-1782
chr1	6675302	6675535	E082	-1529
chr1	6675620	6675880	E082	-1184
chr1	6684611	6686176	E082	7547