rs6688203

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

PPT1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0106 (3175/29892,GnomAD)
A=0110 (3210/29118,TOPMED)
A=0137 (687/5008,1000G)
A=0101 (388/3854,ALSPAC)
A=0092 (340/3708,TWINSUK)

Position: chr1:40084258 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 186 Enhancers around

Promoter: 37 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.40084258C>A
GRCh37.p13 chr 1	NC_000001.10:g.40549930C>A
PPT1 RefSeqGene	LRG_690

Gene: PPT1, palmitoyl-protein thioesterase 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PPT1 transcript variant 1	NM_000310.3:c.	N/A	Intron Variant
PPT1 transcript variant 2	NM_001142604.1:c.	N/A	Intron Variant
PPT1 transcript variant X1	XM_005271008.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.836	A=0.164
1000Genomes	American	Sub	694	C=0.880	A=0.120
1000Genomes	East Asian	Sub	1008	C=0.826	A=0.174
1000Genomes	Europe	Sub	1006	C=0.921	A=0.079
1000Genomes	Global	Study-wide	5008	C=0.863	A=0.137
1000Genomes	South Asian	Sub	978	C=0.860	A=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.899	A=0.101
The Genome Aggregation Database	African	Sub	8692	C=0.850	A=0.150
The Genome Aggregation Database	American	Sub	836	C=0.860	A=0.140
The Genome Aggregation Database	East Asian	Sub	1616	C=0.858	A=0.142
The Genome Aggregation Database	Europe	Sub	18446	C=0.917	A=0.082
The Genome Aggregation Database	Global	Study-wide	29892	C=0.893	A=0.106
The Genome Aggregation Database	Other	Sub	302	C=0.990	A=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.889	A=0.110
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.908	A=0.092

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs6688203	0.00066	alcohol dependence	21314694

eQTL of rs6688203 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 rs6688203 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	40512987	40513213	E067	-36717
chr1	40513387	40513455	E067	-36475
chr1	40513520	40513659	E067	-36271
chr1	40514011	40514096	E067	-35834
chr1	40514667	40514768	E067	-35162
chr1	40515068	40515248	E067	-34682
chr1	40515263	40515696	E067	-34234
chr1	40515738	40515876	E067	-34054
chr1	40516476	40516848	E067	-33082
chr1	40521869	40521909	E067	-28021
chr1	40522173	40522247	E067	-27683
chr1	40522252	40522292	E067	-27638
chr1	40522847	40523094	E067	-26836
chr1	40523180	40523428	E067	-26502
chr1	40526167	40526264	E067	-23666
chr1	40526289	40526366	E067	-23564
chr1	40549927	40549969	E067	0
chr1	40550097	40550222	E067	167
chr1	40510906	40511170	E068	-38760
chr1	40511556	40511724	E068	-38206
chr1	40512987	40513213	E068	-36717
chr1	40513387	40513455	E068	-36475
chr1	40513520	40513659	E068	-36271
chr1	40514011	40514096	E068	-35834
chr1	40514667	40514768	E068	-35162
chr1	40515068	40515248	E068	-34682
chr1	40515263	40515696	E068	-34234
chr1	40515738	40515876	E068	-34054
chr1	40521869	40521909	E068	-28021
chr1	40522173	40522247	E068	-27683
chr1	40522252	40522292	E068	-27638
chr1	40523958	40524004	E068	-25926
chr1	40524076	40524146	E068	-25784
chr1	40524300	40524769	E068	-25161
chr1	40524776	40526066	E068	-23864
chr1	40527414	40527477	E068	-22453
chr1	40549422	40549502	E068	-428
chr1	40549927	40549969	E068	0
chr1	40550097	40550222	E068	167
chr1	40550337	40550393	E068	407
chr1	40550466	40550809	E068	536
chr1	40502110	40502218	E069	-47712
chr1	40502299	40502647	E069	-47283
chr1	40502768	40502853	E069	-47077
chr1	40512987	40513213	E069	-36717
chr1	40513387	40513455	E069	-36475
chr1	40514667	40514768	E069	-35162
chr1	40515068	40515248	E069	-34682
chr1	40515263	40515696	E069	-34234
chr1	40515738	40515876	E069	-34054
chr1	40516476	40516848	E069	-33082
chr1	40521869	40521909	E069	-28021
chr1	40522173	40522247	E069	-27683
chr1	40522252	40522292	E069	-27638
chr1	40522847	40523094	E069	-26836
chr1	40523180	40523428	E069	-26502
chr1	40523958	40524004	E069	-25926
chr1	40524076	40524146	E069	-25784
chr1	40532784	40532931	E069	-16999
chr1	40532933	40533086	E069	-16844
chr1	40549927	40549969	E069	0
chr1	40550097	40550222	E069	167
chr1	40561540	40561802	E069	11610
chr1	40502110	40502218	E070	-47712
chr1	40502299	40502647	E070	-47283
chr1	40502768	40502853	E070	-47077
chr1	40502929	40502985	E070	-46945
chr1	40503665	40503705	E070	-46225
chr1	40503760	40503895	E070	-46035
chr1	40503926	40503976	E070	-45954
chr1	40504421	40504735	E070	-45195
chr1	40522847	40523094	E070	-26836
chr1	40523180	40523428	E070	-26502
chr1	40561540	40561802	E070	11610
chr1	40598082	40598136	E070	48152
chr1	40501889	40502042	E071	-47888
chr1	40502110	40502218	E071	-47712
chr1	40502299	40502647	E071	-47283
chr1	40509211	40509329	E071	-40601
chr1	40511556	40511724	E071	-38206
chr1	40512212	40512434	E071	-37496
chr1	40512987	40513213	E071	-36717
chr1	40513387	40513455	E071	-36475
chr1	40513520	40513659	E071	-36271
chr1	40514667	40514768	E071	-35162
chr1	40515068	40515248	E071	-34682
chr1	40515263	40515696	E071	-34234
chr1	40515738	40515876	E071	-34054
chr1	40522173	40522247	E071	-27683
chr1	40522252	40522292	E071	-27638
chr1	40522847	40523094	E071	-26836
chr1	40523180	40523428	E071	-26502
chr1	40523958	40524004	E071	-25926
chr1	40524076	40524146	E071	-25784
chr1	40524300	40524769	E071	-25161
chr1	40524776	40526066	E071	-23864
chr1	40526167	40526264	E071	-23666
chr1	40526289	40526366	E071	-23564
chr1	40531508	40531585	E071	-18345
chr1	40532784	40532931	E071	-16999
chr1	40549927	40549969	E071	0
chr1	40550097	40550222	E071	167
chr1	40550337	40550393	E071	407
chr1	40550466	40550809	E071	536
chr1	40550959	40551053	E071	1029
chr1	40561540	40561802	E071	11610
chr1	40502110	40502218	E072	-47712
chr1	40502299	40502647	E072	-47283
chr1	40502768	40502853	E072	-47077
chr1	40502929	40502985	E072	-46945
chr1	40510906	40511170	E072	-38760
chr1	40514667	40514768	E072	-35162
chr1	40515068	40515248	E072	-34682
chr1	40515263	40515696	E072	-34234
chr1	40515738	40515876	E072	-34054
chr1	40521869	40521909	E072	-28021
chr1	40522173	40522247	E072	-27683
chr1	40522252	40522292	E072	-27638
chr1	40522847	40523094	E072	-26836
chr1	40523180	40523428	E072	-26502
chr1	40523958	40524004	E072	-25926
chr1	40526167	40526264	E072	-23666
chr1	40549927	40549969	E072	0
chr1	40550097	40550222	E072	167
chr1	40561540	40561802	E072	11610
chr1	40502110	40502218	E073	-47712
chr1	40502299	40502647	E073	-47283
chr1	40502768	40502853	E073	-47077
chr1	40514667	40514768	E073	-35162
chr1	40515068	40515248	E073	-34682
chr1	40515263	40515696	E073	-34234
chr1	40515738	40515876	E073	-34054
chr1	40522173	40522247	E073	-27683
chr1	40522252	40522292	E073	-27638
chr1	40522847	40523094	E073	-26836
chr1	40523180	40523428	E073	-26502
chr1	40549422	40549502	E073	-428
chr1	40549927	40549969	E073	0
chr1	40510906	40511170	E074	-38760
chr1	40511556	40511724	E074	-38206
chr1	40512987	40513213	E074	-36717
chr1	40513387	40513455	E074	-36475
chr1	40514667	40514768	E074	-35162
chr1	40515068	40515248	E074	-34682
chr1	40515263	40515696	E074	-34234
chr1	40515738	40515876	E074	-34054
chr1	40521869	40521909	E074	-28021
chr1	40522173	40522247	E074	-27683
chr1	40522252	40522292	E074	-27638
chr1	40522847	40523094	E074	-26836
chr1	40523180	40523428	E074	-26502
chr1	40523958	40524004	E074	-25926
chr1	40524076	40524146	E074	-25784
chr1	40524300	40524769	E074	-25161
chr1	40549927	40549969	E074	0
chr1	40550097	40550222	E074	167
chr1	40550337	40550393	E074	407
chr1	40550466	40550809	E074	536
chr1	40550959	40551053	E074	1029
chr1	40501209	40501277	E081	-48653
chr1	40501351	40501448	E081	-48482
chr1	40501889	40502042	E081	-47888
chr1	40502110	40502218	E081	-47712
chr1	40502299	40502647	E081	-47283
chr1	40502768	40502853	E081	-47077
chr1	40502929	40502985	E081	-46945
chr1	40503665	40503705	E081	-46225
chr1	40503760	40503895	E081	-46035
chr1	40503926	40503976	E081	-45954
chr1	40504421	40504735	E081	-45195
chr1	40509211	40509329	E081	-40601
chr1	40510906	40511170	E081	-38760
chr1	40561540	40561802	E081	11610
chr1	40500306	40500410	E082	-49520
chr1	40500510	40501034	E082	-48896
chr1	40501209	40501277	E082	-48653
chr1	40501889	40502042	E082	-47888
chr1	40502110	40502218	E082	-47712
chr1	40502299	40502647	E082	-47283
chr1	40502768	40502853	E082	-47077
chr1	40502929	40502985	E082	-46945
chr1	40503665	40503705	E082	-46225
chr1	40503760	40503895	E082	-46035
chr1	40503926	40503976	E082	-45954
chr1	40504421	40504735	E082	-45195
chr1	40561540	40561802	E082	11610

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	40504789	40507357	E067	-42573
chr1	40507396	40507500	E067	-42430
chr1	40562445	40563750	E067	12515
chr1	40598450	40598990	E067	48520
chr1	40504789	40507357	E068	-42573
chr1	40507396	40507500	E068	-42430
chr1	40562445	40563750	E068	12515
chr1	40598450	40598990	E068	48520
chr1	40504789	40507357	E069	-42573
chr1	40507396	40507500	E069	-42430
chr1	40562445	40563750	E069	12515
chr1	40598450	40598990	E069	48520
chr1	40504789	40507357	E070	-42573
chr1	40507396	40507500	E070	-42430
chr1	40562445	40563750	E070	12515
chr1	40598450	40598990	E070	48520
chr1	40504789	40507357	E071	-42573
chr1	40507396	40507500	E071	-42430
chr1	40562445	40563750	E071	12515
chr1	40598450	40598990	E071	48520
chr1	40504789	40507357	E072	-42573
chr1	40507396	40507500	E072	-42430
chr1	40562445	40563750	E072	12515
chr1	40504789	40507357	E073	-42573
chr1	40507396	40507500	E073	-42430
chr1	40562445	40563750	E073	12515
chr1	40598450	40598990	E073	48520
chr1	40504789	40507357	E074	-42573
chr1	40507396	40507500	E074	-42430
chr1	40562445	40563750	E074	12515
chr1	40598450	40598990	E074	48520
chr1	40504789	40507357	E081	-42573
chr1	40507396	40507500	E081	-42430
chr1	40562445	40563750	E081	12515
chr1	40504789	40507357	E082	-42573
chr1	40507396	40507500	E082	-42430
chr1	40562445	40563750	E082	12515