rs12402428

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC105378669 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0135 (4050/29994,GnomAD)
C=0151 (4421/29118,TOPMED)
C=0186 (931/5008,1000G)
C=0104 (401/3854,ALSPAC)
C=0097 (358/3708,TWINSUK)

Position: chr1:40038053 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 194 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.40038053T>C
GRCh37.p13 chr 1	NC_000001.10:g.40503725T>C

Gene: LOC105378669, uncharacterized LOC105378669(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378669 transcript variant X1	XR_001738012.1:n.	N/A	Intron Variant
LOC105378669 transcript variant X2	XR_001738013.1:n.	N/A	Intron Variant
LOC105378669 transcript variant X3	XR_001738014.1:n.	N/A	Intron Variant
LOC105378669 transcript variant X4	XR_001738015.1:n.	N/A	Intron Variant
LOC105378669 transcript variant X5	XR_001738016.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.744	C=0.256
1000Genomes	American	Sub	694	T=0.910	C=0.090
1000Genomes	East Asian	Sub	1008	T=0.747	C=0.253
1000Genomes	Europe	Sub	1006	T=0.917	C=0.083
1000Genomes	Global	Study-wide	5008	T=0.814	C=0.186
1000Genomes	South Asian	Sub	978	T=0.800	C=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.896	C=0.104
The Genome Aggregation Database	African	Sub	8724	T=0.780	C=0.220
The Genome Aggregation Database	American	Sub	838	T=0.900	C=0.100
The Genome Aggregation Database	East Asian	Sub	1622	T=0.784	C=0.216
The Genome Aggregation Database	Europe	Sub	18508	T=0.908	C=0.091
The Genome Aggregation Database	Global	Study-wide	29994	T=0.865	C=0.135
The Genome Aggregation Database	Other	Sub	302	T=0.960	C=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.848	C=0.151
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.903	C=0.097

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
rs12402428	0.000652	alcohol dependence	21314694

eQTL of rs12402428 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 rs12402428 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	9262
chr1	40513387	40513455	E067	9662
chr1	40513520	40513659	E067	9795
chr1	40514011	40514096	E067	10286
chr1	40514667	40514768	E067	10942
chr1	40515068	40515248	E067	11343
chr1	40515263	40515696	E067	11538
chr1	40515738	40515876	E067	12013
chr1	40516476	40516848	E067	12751
chr1	40521869	40521909	E067	18144
chr1	40522173	40522247	E067	18448
chr1	40522252	40522292	E067	18527
chr1	40522847	40523094	E067	19122
chr1	40523180	40523428	E067	19455
chr1	40526167	40526264	E067	22442
chr1	40526289	40526366	E067	22564
chr1	40549927	40549969	E067	46202
chr1	40550097	40550222	E067	46372
chr1	40461559	40462039	E068	-41686
chr1	40510906	40511170	E068	7181
chr1	40511556	40511724	E068	7831
chr1	40512987	40513213	E068	9262
chr1	40513387	40513455	E068	9662
chr1	40513520	40513659	E068	9795
chr1	40514011	40514096	E068	10286
chr1	40514667	40514768	E068	10942
chr1	40515068	40515248	E068	11343
chr1	40515263	40515696	E068	11538
chr1	40515738	40515876	E068	12013
chr1	40521869	40521909	E068	18144
chr1	40522173	40522247	E068	18448
chr1	40522252	40522292	E068	18527
chr1	40523958	40524004	E068	20233
chr1	40524076	40524146	E068	20351
chr1	40524300	40524769	E068	20575
chr1	40524776	40526066	E068	21051
chr1	40527414	40527477	E068	23689
chr1	40549422	40549502	E068	45697
chr1	40549927	40549969	E068	46202
chr1	40550097	40550222	E068	46372
chr1	40550337	40550393	E068	46612
chr1	40550466	40550809	E068	46741
chr1	40497884	40498378	E069	-5347
chr1	40502110	40502218	E069	-1507
chr1	40502299	40502647	E069	-1078
chr1	40502768	40502853	E069	-872
chr1	40512987	40513213	E069	9262
chr1	40513387	40513455	E069	9662
chr1	40514667	40514768	E069	10942
chr1	40515068	40515248	E069	11343
chr1	40515263	40515696	E069	11538
chr1	40515738	40515876	E069	12013
chr1	40516476	40516848	E069	12751
chr1	40521869	40521909	E069	18144
chr1	40522173	40522247	E069	18448
chr1	40522252	40522292	E069	18527
chr1	40522847	40523094	E069	19122
chr1	40523180	40523428	E069	19455
chr1	40523958	40524004	E069	20233
chr1	40524076	40524146	E069	20351
chr1	40532784	40532931	E069	29059
chr1	40532933	40533086	E069	29208
chr1	40549927	40549969	E069	46202
chr1	40550097	40550222	E069	46372
chr1	40502110	40502218	E070	-1507
chr1	40502299	40502647	E070	-1078
chr1	40502768	40502853	E070	-872
chr1	40502929	40502985	E070	-740
chr1	40503665	40503705	E070	-20
chr1	40503760	40503895	E070	35
chr1	40503926	40503976	E070	201
chr1	40504421	40504735	E070	696
chr1	40522847	40523094	E070	19122
chr1	40523180	40523428	E070	19455
chr1	40497884	40498378	E071	-5347
chr1	40501889	40502042	E071	-1683
chr1	40502110	40502218	E071	-1507
chr1	40502299	40502647	E071	-1078
chr1	40509211	40509329	E071	5486
chr1	40511556	40511724	E071	7831
chr1	40512212	40512434	E071	8487
chr1	40512987	40513213	E071	9262
chr1	40513387	40513455	E071	9662
chr1	40513520	40513659	E071	9795
chr1	40514667	40514768	E071	10942
chr1	40515068	40515248	E071	11343
chr1	40515263	40515696	E071	11538
chr1	40515738	40515876	E071	12013
chr1	40522173	40522247	E071	18448
chr1	40522252	40522292	E071	18527
chr1	40522847	40523094	E071	19122
chr1	40523180	40523428	E071	19455
chr1	40523958	40524004	E071	20233
chr1	40524076	40524146	E071	20351
chr1	40524300	40524769	E071	20575
chr1	40524776	40526066	E071	21051
chr1	40526167	40526264	E071	22442
chr1	40526289	40526366	E071	22564
chr1	40531508	40531585	E071	27783
chr1	40532784	40532931	E071	29059
chr1	40549927	40549969	E071	46202
chr1	40550097	40550222	E071	46372
chr1	40550337	40550393	E071	46612
chr1	40550466	40550809	E071	46741
chr1	40550959	40551053	E071	47234
chr1	40497884	40498378	E072	-5347
chr1	40502110	40502218	E072	-1507
chr1	40502299	40502647	E072	-1078
chr1	40502768	40502853	E072	-872
chr1	40502929	40502985	E072	-740
chr1	40510906	40511170	E072	7181
chr1	40514667	40514768	E072	10942
chr1	40515068	40515248	E072	11343
chr1	40515263	40515696	E072	11538
chr1	40515738	40515876	E072	12013
chr1	40521869	40521909	E072	18144
chr1	40522173	40522247	E072	18448
chr1	40522252	40522292	E072	18527
chr1	40522847	40523094	E072	19122
chr1	40523180	40523428	E072	19455
chr1	40523958	40524004	E072	20233
chr1	40526167	40526264	E072	22442
chr1	40549927	40549969	E072	46202
chr1	40550097	40550222	E072	46372
chr1	40502110	40502218	E073	-1507
chr1	40502299	40502647	E073	-1078
chr1	40502768	40502853	E073	-872
chr1	40514667	40514768	E073	10942
chr1	40515068	40515248	E073	11343
chr1	40515263	40515696	E073	11538
chr1	40515738	40515876	E073	12013
chr1	40522173	40522247	E073	18448
chr1	40522252	40522292	E073	18527
chr1	40522847	40523094	E073	19122
chr1	40523180	40523428	E073	19455
chr1	40549422	40549502	E073	45697
chr1	40549927	40549969	E073	46202
chr1	40461404	40461500	E074	-42225
chr1	40461559	40462039	E074	-41686
chr1	40510906	40511170	E074	7181
chr1	40511556	40511724	E074	7831
chr1	40512987	40513213	E074	9262
chr1	40513387	40513455	E074	9662
chr1	40514667	40514768	E074	10942
chr1	40515068	40515248	E074	11343
chr1	40515263	40515696	E074	11538
chr1	40515738	40515876	E074	12013
chr1	40521869	40521909	E074	18144
chr1	40522173	40522247	E074	18448
chr1	40522252	40522292	E074	18527
chr1	40522847	40523094	E074	19122
chr1	40523180	40523428	E074	19455
chr1	40523958	40524004	E074	20233
chr1	40524076	40524146	E074	20351
chr1	40524300	40524769	E074	20575
chr1	40549927	40549969	E074	46202
chr1	40550097	40550222	E074	46372
chr1	40550337	40550393	E074	46612
chr1	40550466	40550809	E074	46741
chr1	40550959	40551053	E074	47234
chr1	40470041	40470207	E081	-33518
chr1	40470528	40471364	E081	-32361
chr1	40471379	40471429	E081	-32296
chr1	40471493	40471573	E081	-32152
chr1	40486300	40486350	E081	-17375
chr1	40486379	40486711	E081	-17014
chr1	40501209	40501277	E081	-2448
chr1	40501351	40501448	E081	-2277
chr1	40501889	40502042	E081	-1683
chr1	40502110	40502218	E081	-1507
chr1	40502299	40502647	E081	-1078
chr1	40502768	40502853	E081	-872
chr1	40502929	40502985	E081	-740
chr1	40503665	40503705	E081	-20
chr1	40503760	40503895	E081	35
chr1	40503926	40503976	E081	201
chr1	40504421	40504735	E081	696
chr1	40509211	40509329	E081	5486
chr1	40510906	40511170	E081	7181
chr1	40467675	40467740	E082	-35985
chr1	40470528	40471364	E082	-32361
chr1	40471379	40471429	E082	-32296
chr1	40500306	40500410	E082	-3315
chr1	40500510	40501034	E082	-2691
chr1	40501209	40501277	E082	-2448
chr1	40501889	40502042	E082	-1683
chr1	40502110	40502218	E082	-1507
chr1	40502299	40502647	E082	-1078
chr1	40502768	40502853	E082	-872
chr1	40502929	40502985	E082	-740
chr1	40503665	40503705	E082	-20
chr1	40503760	40503895	E082	35
chr1	40503926	40503976	E082	201
chr1	40504421	40504735	E082	696

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	40504789	40507357	E067	1064
chr1	40507396	40507500	E067	3671
chr1	40504789	40507357	E068	1064
chr1	40507396	40507500	E068	3671
chr1	40504789	40507357	E069	1064
chr1	40507396	40507500	E069	3671
chr1	40504789	40507357	E070	1064
chr1	40507396	40507500	E070	3671
chr1	40504789	40507357	E071	1064
chr1	40507396	40507500	E071	3671
chr1	40504789	40507357	E072	1064
chr1	40507396	40507500	E072	3671
chr1	40504789	40507357	E073	1064
chr1	40507396	40507500	E073	3671
chr1	40504789	40507357	E074	1064
chr1	40507396	40507500	E074	3671
chr1	40504789	40507357	E081	1064
chr1	40507396	40507500	E081	3671
chr1	40504789	40507357	E082	1064
chr1	40507396	40507500	E082	3671