rs6027132

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PHACTR3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0478 (14318/29904,GnomAD)
T=0470 (13688/29118,TOPMED)
T=0500 (2502/5008,1000G)
C==0373 (1438/3854,ALSPAC)
C==0373 (1383/3708,TWINSUK)

Position: chr20:59809396 (GRCh38.p7) (20q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 421 Enhancers around

Promoter: 14 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.59809396C>T
GRCh37.p13 chr 20	NC_000020.10:g.58384451C>T
PHACTR3 RefSeqGene	NG_029537.1:g.236888C>T

Gene: PHACTR3, phosphatase and actin regulator 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHACTR3 transcript variant 4	NM_001199505.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 5	NM_001199506.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 6	NM_001281507.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 1	NM_080672.4:c.	N/A	Intron Variant
PHACTR3 transcript variant 2	NM_183244.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 3	NM_183246.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X2	XM_011528525.2:c.	N/A	Intron Variant
PHACTR3 transcript variant X4	XM_011528526.2:c.	N/A	Intron Variant
PHACTR3 transcript variant X1	XM_017027626.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X3	XM_017027627.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X5	XM_017027628.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X6	XM_017027629.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X7	XM_017027630.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X8	XM_017027631.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.744	T=0.256
1000Genomes	American	Sub	694	C=0.330	T=0.670
1000Genomes	East Asian	Sub	1008	C=0.442	T=0.558
1000Genomes	Europe	Sub	1006	C=0.410	T=0.590
1000Genomes	Global	Study-wide	5008	C=0.500	T=0.500
1000Genomes	South Asian	Sub	978	C=0.440	T=0.560
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.373	T=0.627
The Genome Aggregation Database	African	Sub	8680	C=0.708	T=0.292
The Genome Aggregation Database	American	Sub	838	C=0.340	T=0.660
The Genome Aggregation Database	East Asian	Sub	1612	C=0.462	T=0.538
The Genome Aggregation Database	Europe	Sub	18472	C=0.378	T=0.621
The Genome Aggregation Database	Global	Study-wide	29904	C=0.478	T=0.521
The Genome Aggregation Database	Other	Sub	302	C=0.540	T=0.460
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.529	T=0.470
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.373	T=0.627

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs6027132	1.74E-05	alcohol consumption	23743675

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 )
chr20	58346072	58346273	E067	-38178
chr20	58346362	58346412	E067	-38039
chr20	58346447	58346527	E067	-37924
chr20	58346541	58346645	E067	-37806
chr20	58346706	58346862	E067	-37589
chr20	58349847	58349938	E067	-34513
chr20	58350082	58350132	E067	-34319
chr20	58350226	58350311	E067	-34140
chr20	58350607	58350695	E067	-33756
chr20	58351599	58351639	E067	-32812
chr20	58358628	58358678	E067	-25773
chr20	58358702	58358783	E067	-25668
chr20	58359058	58359181	E067	-25270
chr20	58361672	58361902	E067	-22549
chr20	58362138	58362178	E067	-22273
chr20	58362249	58362324	E067	-22127
chr20	58362392	58362446	E067	-22005
chr20	58377612	58378256	E067	-6195
chr20	58378979	58379078	E067	-5373
chr20	58379528	58379939	E067	-4512
chr20	58380117	58380366	E067	-4085
chr20	58385358	58385418	E067	907
chr20	58385439	58385701	E067	988
chr20	58385741	58385952	E067	1290
chr20	58386348	58386432	E067	1897
chr20	58386929	58387022	E067	2478
chr20	58387078	58387119	E067	2627
chr20	58387127	58387245	E067	2676
chr20	58387489	58387652	E067	3038
chr20	58387720	58387774	E067	3269
chr20	58387910	58387975	E067	3459
chr20	58388324	58388374	E067	3873
chr20	58389173	58389250	E067	4722
chr20	58389255	58389321	E067	4804
chr20	58389571	58389685	E067	5120
chr20	58389722	58389836	E067	5271
chr20	58392595	58392664	E067	8144
chr20	58394875	58395205	E067	10424
chr20	58395340	58396182	E067	10889
chr20	58396568	58396632	E067	12117
chr20	58397874	58397924	E067	13423
chr20	58399133	58399214	E067	14682
chr20	58399322	58399377	E067	14871
chr20	58399473	58399731	E067	15022
chr20	58399737	58399939	E067	15286
chr20	58400145	58400195	E067	15694
chr20	58400250	58400340	E067	15799
chr20	58404054	58405274	E067	19603
chr20	58405716	58405934	E067	21265
chr20	58405994	58406552	E067	21543
chr20	58406558	58407506	E067	22107
chr20	58407952	58408048	E067	23501
chr20	58410059	58410534	E067	25608
chr20	58410558	58411316	E067	26107
chr20	58346706	58346862	E068	-37589
chr20	58347007	58347192	E068	-37259
chr20	58352456	58352680	E068	-31771
chr20	58358628	58358678	E068	-25773
chr20	58358702	58358783	E068	-25668
chr20	58377612	58378256	E068	-6195
chr20	58378979	58379078	E068	-5373
chr20	58379528	58379939	E068	-4512
chr20	58385358	58385418	E068	907
chr20	58385439	58385701	E068	988
chr20	58385741	58385952	E068	1290
chr20	58386348	58386432	E068	1897
chr20	58387078	58387119	E068	2627
chr20	58389173	58389250	E068	4722
chr20	58389255	58389321	E068	4804
chr20	58389571	58389685	E068	5120
chr20	58389722	58389836	E068	5271
chr20	58394875	58395205	E068	10424
chr20	58395340	58396182	E068	10889
chr20	58396568	58396632	E068	12117
chr20	58398460	58399074	E068	14009
chr20	58399133	58399214	E068	14682
chr20	58399322	58399377	E068	14871
chr20	58399473	58399731	E068	15022
chr20	58399737	58399939	E068	15286
chr20	58400145	58400195	E068	15694
chr20	58400250	58400340	E068	15799
chr20	58400393	58400523	E068	15942
chr20	58404054	58405274	E068	19603
chr20	58405716	58405934	E068	21265
chr20	58405994	58406552	E068	21543
chr20	58406558	58407506	E068	22107
chr20	58410059	58410534	E068	25608
chr20	58336410	58336455	E069	-47996
chr20	58336496	58336546	E069	-47905
chr20	58336580	58336648	E069	-47803
chr20	58346072	58346273	E069	-38178
chr20	58346362	58346412	E069	-38039
chr20	58346447	58346527	E069	-37924
chr20	58346541	58346645	E069	-37806
chr20	58346706	58346862	E069	-37589
chr20	58351599	58351639	E069	-32812
chr20	58352456	58352680	E069	-31771
chr20	58352846	58352955	E069	-31496
chr20	58357965	58358428	E069	-26023
chr20	58358628	58358678	E069	-25773
chr20	58358702	58358783	E069	-25668
chr20	58359058	58359181	E069	-25270
chr20	58359500	58359567	E069	-24884
chr20	58359581	58359635	E069	-24816
chr20	58360158	58360291	E069	-24160
chr20	58360539	58360708	E069	-23743
chr20	58360714	58360858	E069	-23593
chr20	58361672	58361902	E069	-22549
chr20	58362138	58362178	E069	-22273
chr20	58362249	58362324	E069	-22127
chr20	58377612	58378256	E069	-6195
chr20	58378979	58379078	E069	-5373
chr20	58379528	58379939	E069	-4512
chr20	58380117	58380366	E069	-4085
chr20	58380380	58380458	E069	-3993
chr20	58385358	58385418	E069	907
chr20	58385439	58385701	E069	988
chr20	58385741	58385952	E069	1290
chr20	58386348	58386432	E069	1897
chr20	58386929	58387022	E069	2478
chr20	58387078	58387119	E069	2627
chr20	58387127	58387245	E069	2676
chr20	58388324	58388374	E069	3873
chr20	58389173	58389250	E069	4722
chr20	58389255	58389321	E069	4804
chr20	58389571	58389685	E069	5120
chr20	58389722	58389836	E069	5271
chr20	58394875	58395205	E069	10424
chr20	58395340	58396182	E069	10889
chr20	58396568	58396632	E069	12117
chr20	58397874	58397924	E069	13423
chr20	58398460	58399074	E069	14009
chr20	58399133	58399214	E069	14682
chr20	58399322	58399377	E069	14871
chr20	58399473	58399731	E069	15022
chr20	58399737	58399939	E069	15286
chr20	58400145	58400195	E069	15694
chr20	58400250	58400340	E069	15799
chr20	58400393	58400523	E069	15942
chr20	58405716	58405934	E069	21265
chr20	58405994	58406552	E069	21543
chr20	58406558	58407506	E069	22107
chr20	58407952	58408048	E069	23501
chr20	58410059	58410534	E069	25608
chr20	58410558	58411316	E069	26107
chr20	58346362	58346412	E070	-38039
chr20	58346447	58346527	E070	-37924
chr20	58346541	58346645	E070	-37806
chr20	58346706	58346862	E070	-37589
chr20	58385358	58385418	E070	907
chr20	58385439	58385701	E070	988
chr20	58385741	58385952	E070	1290
chr20	58386348	58386432	E070	1897
chr20	58394875	58395205	E070	10424
chr20	58395340	58396182	E070	10889
chr20	58410059	58410534	E070	25608
chr20	58336410	58336455	E071	-47996
chr20	58336496	58336546	E071	-47905
chr20	58336580	58336648	E071	-47803
chr20	58340995	58341045	E071	-43406
chr20	58346072	58346273	E071	-38178
chr20	58346362	58346412	E071	-38039
chr20	58346447	58346527	E071	-37924
chr20	58346541	58346645	E071	-37806
chr20	58346706	58346862	E071	-37589
chr20	58350607	58350695	E071	-33756
chr20	58351599	58351639	E071	-32812
chr20	58352456	58352680	E071	-31771
chr20	58358628	58358678	E071	-25773
chr20	58358702	58358783	E071	-25668
chr20	58361672	58361902	E071	-22549
chr20	58362138	58362178	E071	-22273
chr20	58377612	58378256	E071	-6195
chr20	58378979	58379078	E071	-5373
chr20	58379528	58379939	E071	-4512
chr20	58385358	58385418	E071	907
chr20	58385439	58385701	E071	988
chr20	58385741	58385952	E071	1290
chr20	58387489	58387652	E071	3038
chr20	58387720	58387774	E071	3269
chr20	58387910	58387975	E071	3459
chr20	58388324	58388374	E071	3873
chr20	58389173	58389250	E071	4722
chr20	58389255	58389321	E071	4804
chr20	58389571	58389685	E071	5120
chr20	58389722	58389836	E071	5271
chr20	58394875	58395205	E071	10424
chr20	58395340	58396182	E071	10889
chr20	58396568	58396632	E071	12117
chr20	58397874	58397924	E071	13423
chr20	58399473	58399731	E071	15022
chr20	58399737	58399939	E071	15286
chr20	58400145	58400195	E071	15694
chr20	58405716	58405934	E071	21265
chr20	58405994	58406552	E071	21543
chr20	58406558	58407506	E071	22107
chr20	58407952	58408048	E071	23501
chr20	58408307	58408361	E071	23856
chr20	58408456	58408539	E071	24005
chr20	58410059	58410534	E071	25608
chr20	58346072	58346273	E072	-38178
chr20	58346362	58346412	E072	-38039
chr20	58346447	58346527	E072	-37924
chr20	58346541	58346645	E072	-37806
chr20	58346706	58346862	E072	-37589
chr20	58347007	58347192	E072	-37259
chr20	58350082	58350132	E072	-34319
chr20	58350226	58350311	E072	-34140
chr20	58350607	58350695	E072	-33756
chr20	58358628	58358678	E072	-25773
chr20	58358702	58358783	E072	-25668
chr20	58359058	58359181	E072	-25270
chr20	58359500	58359567	E072	-24884
chr20	58359581	58359635	E072	-24816
chr20	58360158	58360291	E072	-24160
chr20	58360539	58360708	E072	-23743
chr20	58360714	58360858	E072	-23593
chr20	58362138	58362178	E072	-22273
chr20	58362249	58362324	E072	-22127
chr20	58377612	58378256	E072	-6195
chr20	58378979	58379078	E072	-5373
chr20	58379528	58379939	E072	-4512
chr20	58380117	58380366	E072	-4085
chr20	58380380	58380458	E072	-3993
chr20	58385358	58385418	E072	907
chr20	58385439	58385701	E072	988
chr20	58385741	58385952	E072	1290
chr20	58386348	58386432	E072	1897
chr20	58386929	58387022	E072	2478
chr20	58387078	58387119	E072	2627
chr20	58387127	58387245	E072	2676
chr20	58387489	58387652	E072	3038
chr20	58387720	58387774	E072	3269
chr20	58387910	58387975	E072	3459
chr20	58388324	58388374	E072	3873
chr20	58389173	58389250	E072	4722
chr20	58389255	58389321	E072	4804
chr20	58389571	58389685	E072	5120
chr20	58389722	58389836	E072	5271
chr20	58394875	58395205	E072	10424
chr20	58395340	58396182	E072	10889
chr20	58396568	58396632	E072	12117
chr20	58397874	58397924	E072	13423
chr20	58399133	58399214	E072	14682
chr20	58399322	58399377	E072	14871
chr20	58399473	58399731	E072	15022
chr20	58399737	58399939	E072	15286
chr20	58400145	58400195	E072	15694
chr20	58400250	58400340	E072	15799
chr20	58400393	58400523	E072	15942
chr20	58400770	58400846	E072	16319
chr20	58400951	58401110	E072	16500
chr20	58401192	58402169	E072	16741
chr20	58402221	58402514	E072	17770
chr20	58402552	58402602	E072	18101
chr20	58402667	58402825	E072	18216
chr20	58402917	58403028	E072	18466
chr20	58403122	58403162	E072	18671
chr20	58404054	58405274	E072	19603
chr20	58405716	58405934	E072	21265
chr20	58405994	58406552	E072	21543
chr20	58406558	58407506	E072	22107
chr20	58409732	58409782	E072	25281
chr20	58410059	58410534	E072	25608
chr20	58410558	58411316	E072	26107
chr20	58346072	58346273	E073	-38178
chr20	58346362	58346412	E073	-38039
chr20	58346447	58346527	E073	-37924
chr20	58346541	58346645	E073	-37806
chr20	58377612	58378256	E073	-6195
chr20	58378979	58379078	E073	-5373
chr20	58379528	58379939	E073	-4512
chr20	58380117	58380366	E073	-4085
chr20	58380380	58380458	E073	-3993
chr20	58385358	58385418	E073	907
chr20	58385439	58385701	E073	988
chr20	58385741	58385952	E073	1290
chr20	58386348	58386432	E073	1897
chr20	58386929	58387022	E073	2478
chr20	58387078	58387119	E073	2627
chr20	58387127	58387245	E073	2676
chr20	58387489	58387652	E073	3038
chr20	58387720	58387774	E073	3269
chr20	58387910	58387975	E073	3459
chr20	58388324	58388374	E073	3873
chr20	58389173	58389250	E073	4722
chr20	58389255	58389321	E073	4804
chr20	58389571	58389685	E073	5120
chr20	58389722	58389836	E073	5271
chr20	58394875	58395205	E073	10424
chr20	58395340	58396182	E073	10889
chr20	58396568	58396632	E073	12117
chr20	58397874	58397924	E073	13423
chr20	58399133	58399214	E073	14682
chr20	58399322	58399377	E073	14871
chr20	58399473	58399731	E073	15022
chr20	58399737	58399939	E073	15286
chr20	58400145	58400195	E073	15694
chr20	58400250	58400340	E073	15799
chr20	58402221	58402514	E073	17770
chr20	58402552	58402602	E073	18101
chr20	58402667	58402825	E073	18216
chr20	58402917	58403028	E073	18466
chr20	58403122	58403162	E073	18671
chr20	58404054	58405274	E073	19603
chr20	58405716	58405934	E073	21265
chr20	58405994	58406552	E073	21543
chr20	58406558	58407506	E073	22107
chr20	58410059	58410534	E073	25608
chr20	58410558	58411316	E073	26107
chr20	58413041	58414073	E073	28590
chr20	58340727	58340903	E074	-43548
chr20	58340945	58340989	E074	-43462
chr20	58340995	58341045	E074	-43406
chr20	58346072	58346273	E074	-38178
chr20	58346362	58346412	E074	-38039
chr20	58346447	58346527	E074	-37924
chr20	58346541	58346645	E074	-37806
chr20	58346706	58346862	E074	-37589
chr20	58347007	58347192	E074	-37259
chr20	58350607	58350695	E074	-33756
chr20	58351599	58351639	E074	-32812
chr20	58352456	58352680	E074	-31771
chr20	58352846	58352955	E074	-31496
chr20	58358628	58358678	E074	-25773
chr20	58358702	58358783	E074	-25668
chr20	58359058	58359181	E074	-25270
chr20	58360539	58360708	E074	-23743
chr20	58360714	58360858	E074	-23593
chr20	58377612	58378256	E074	-6195
chr20	58378979	58379078	E074	-5373
chr20	58379528	58379939	E074	-4512
chr20	58380117	58380366	E074	-4085
chr20	58380380	58380458	E074	-3993
chr20	58389173	58389250	E074	4722
chr20	58389255	58389321	E074	4804
chr20	58389571	58389685	E074	5120
chr20	58389722	58389836	E074	5271
chr20	58392279	58392351	E074	7828
chr20	58392520	58392578	E074	8069
chr20	58392595	58392664	E074	8144
chr20	58394276	58394357	E074	9825
chr20	58394875	58395205	E074	10424
chr20	58395340	58396182	E074	10889
chr20	58396568	58396632	E074	12117
chr20	58399133	58399214	E074	14682
chr20	58399322	58399377	E074	14871
chr20	58399473	58399731	E074	15022
chr20	58399737	58399939	E074	15286
chr20	58400145	58400195	E074	15694
chr20	58400250	58400340	E074	15799
chr20	58400393	58400523	E074	15942
chr20	58401192	58402169	E074	16741
chr20	58402221	58402514	E074	17770
chr20	58405716	58405934	E074	21265
chr20	58405994	58406552	E074	21543
chr20	58406558	58407506	E074	22107
chr20	58407952	58408048	E074	23501
chr20	58410059	58410534	E074	25608
chr20	58414839	58416074	E074	30388
chr20	58359058	58359181	E081	-25270
chr20	58359500	58359567	E081	-24884
chr20	58359581	58359635	E081	-24816
chr20	58385358	58385418	E081	907
chr20	58385439	58385701	E081	988
chr20	58385741	58385952	E081	1290
chr20	58386348	58386432	E081	1897
chr20	58386929	58387022	E081	2478
chr20	58387078	58387119	E081	2627
chr20	58387127	58387245	E081	2676
chr20	58387489	58387652	E081	3038
chr20	58387720	58387774	E081	3269
chr20	58387910	58387975	E081	3459
chr20	58388324	58388374	E081	3873
chr20	58389255	58389321	E081	4804
chr20	58392279	58392351	E081	7828
chr20	58392520	58392578	E081	8069
chr20	58392595	58392664	E081	8144
chr20	58394276	58394357	E081	9825
chr20	58394875	58395205	E081	10424
chr20	58395340	58396182	E081	10889
chr20	58396568	58396632	E081	12117
chr20	58397874	58397924	E081	13423
chr20	58398460	58399074	E081	14009
chr20	58399133	58399214	E081	14682
chr20	58399322	58399377	E081	14871
chr20	58399473	58399731	E081	15022
chr20	58399737	58399939	E081	15286
chr20	58400145	58400195	E081	15694
chr20	58400250	58400340	E081	15799
chr20	58400393	58400523	E081	15942
chr20	58400770	58400846	E081	16319
chr20	58400951	58401110	E081	16500
chr20	58404054	58405274	E081	19603
chr20	58410059	58410534	E081	25608
chr20	58410558	58411316	E081	26107
chr20	58385358	58385418	E082	907
chr20	58385439	58385701	E082	988
chr20	58385741	58385952	E082	1290
chr20	58386348	58386432	E082	1897
chr20	58387078	58387119	E082	2627
chr20	58387127	58387245	E082	2676
chr20	58387489	58387652	E082	3038
chr20	58387720	58387774	E082	3269
chr20	58387910	58387975	E082	3459
chr20	58392279	58392351	E082	7828
chr20	58392520	58392578	E082	8069
chr20	58392595	58392664	E082	8144
chr20	58395340	58396182	E082	10889
chr20	58396568	58396632	E082	12117
chr20	58397874	58397924	E082	13423
chr20	58398460	58399074	E082	14009
chr20	58399133	58399214	E082	14682
chr20	58399322	58399377	E082	14871
chr20	58399473	58399731	E082	15022
chr20	58399737	58399939	E082	15286
chr20	58400145	58400195	E082	15694
chr20	58400250	58400340	E082	15799
chr20	58400393	58400523	E082	15942
chr20	58404054	58405274	E082	19603
chr20	58405716	58405934	E082	21265

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	58411536	58412586	E067	27085
chr20	58412797	58412991	E067	28346
chr20	58411536	58412586	E068	27085
chr20	58412797	58412991	E068	28346
chr20	58411536	58412586	E069	27085
chr20	58412797	58412991	E069	28346
chr20	58411536	58412586	E070	27085
chr20	58411536	58412586	E072	27085
chr20	58412797	58412991	E072	28346
chr20	58411536	58412586	E073	27085
chr20	58412797	58412991	E073	28346
chr20	58411536	58412586	E074	27085
chr20	58412797	58412991	E074	28346
chr20	58411536	58412586	E082	27085

rs6027132

Genomic Coordinates

Gene: PHACTR3, phosphatase and actin regulator 3(plus strand)

Population Frequency

P-Value

eQTL of rs6027132 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6027132 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)