rs10201643

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

LYPD6B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0493 (14755/29906,GnomAD)
G=0436 (12701/29118,TOPMED)
G=0428 (2141/5008,1000G)
T==0400 (1543/3854,ALSPAC)
T==0390 (1446/3708,TWINSUK)

Position: chr2:149049127 (GRCh38.p7) (2q23.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 64 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.149049127T>G
GRCh37.p13 chr 2	NC_000002.11:g.149905641T>G

Gene: LYPD6B, LY6/PLAUR domain containing 6B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LYPD6B transcript variant 3	NM_001317003.1:c.	N/A	Intron Variant
LYPD6B transcript variant 5	NM_001317005.1:c.	N/A	Intron Variant
LYPD6B transcript variant 6	NM_001317006.1:c.	N/A	Intron Variant
LYPD6B transcript variant 1	NM_177964.4:c.	N/A	Intron Variant
LYPD6B transcript variant 2	NM_001317002.1:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant 4	NM_001317004.1:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X7	XM_011510623.2:c.	N/A	Intron Variant
LYPD6B transcript variant X2	XM_017003364.1:c.	N/A	Intron Variant
LYPD6B transcript variant X8	XM_017003365.1:c.	N/A	Intron Variant
LYPD6B transcript variant X9	XM_017003366.1:c.	N/A	Intron Variant
LYPD6B transcript variant X3	XM_005246306.4:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X4	XM_006712279.2:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X5	XM_006712280.3:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X6	XM_006712281.3:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X1	XM_011510620.2:c.	N/A	Genic Upstream Transcript Variant
LYPD6B transcript variant X10	XM_011510625.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.821	G=0.179
1000Genomes	American	Sub	694	T=0.430	G=0.570
1000Genomes	East Asian	Sub	1008	T=0.704	G=0.296
1000Genomes	Europe	Sub	1006	T=0.386	G=0.614
1000Genomes	Global	Study-wide	5008	T=0.572	G=0.428
1000Genomes	South Asian	Sub	978	T=0.390	G=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.400	G=0.600
The Genome Aggregation Database	African	Sub	8704	T=0.763	G=0.237
The Genome Aggregation Database	American	Sub	836	T=0.440	G=0.560
The Genome Aggregation Database	East Asian	Sub	1616	T=0.752	G=0.248
The Genome Aggregation Database	Europe	Sub	18448	T=0.369	G=0.630
The Genome Aggregation Database	Global	Study-wide	29906	T=0.506	G=0.493
The Genome Aggregation Database	Other	Sub	302	T=0.410	G=0.590
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.563	G=0.436
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.390	G=0.610

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs10201643	0.0000196	alcoholism	pha002893
rs10201643	0.00002	alcohol dependence	20201924

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 )
chr2	149855746	149855800	E067	-49841
chr2	149855877	149856491	E067	-49150
chr2	149856612	149856662	E067	-48979
chr2	149856819	149856947	E067	-48694
chr2	149873784	149874238	E067	-31403
chr2	149855746	149855800	E068	-49841
chr2	149855877	149856491	E068	-49150
chr2	149856612	149856662	E068	-48979
chr2	149856819	149856947	E068	-48694
chr2	149857160	149857268	E068	-48373
chr2	149873784	149874238	E068	-31403
chr2	149855877	149856491	E069	-49150
chr2	149856612	149856662	E069	-48979
chr2	149856819	149856947	E069	-48694
chr2	149857160	149857268	E069	-48373
chr2	149858124	149858274	E069	-47367
chr2	149859275	149859325	E069	-46316
chr2	149873784	149874238	E069	-31403
chr2	149874326	149874761	E069	-30880
chr2	149855746	149855800	E070	-49841
chr2	149855877	149856491	E070	-49150
chr2	149884133	149884705	E070	-20936
chr2	149884750	149884924	E070	-20717
chr2	149855746	149855800	E071	-49841
chr2	149855877	149856491	E071	-49150
chr2	149856612	149856662	E071	-48979
chr2	149856819	149856947	E071	-48694
chr2	149857160	149857268	E071	-48373
chr2	149858124	149858274	E071	-47367
chr2	149873784	149874238	E071	-31403
chr2	149878345	149878523	E071	-27118
chr2	149855746	149855800	E072	-49841
chr2	149855877	149856491	E072	-49150
chr2	149856612	149856662	E072	-48979
chr2	149856819	149856947	E072	-48694
chr2	149857160	149857268	E072	-48373
chr2	149858124	149858274	E072	-47367
chr2	149859275	149859325	E072	-46316
chr2	149873784	149874238	E072	-31403
chr2	149855746	149855800	E073	-49841
chr2	149855877	149856491	E073	-49150
chr2	149856612	149856662	E073	-48979
chr2	149856819	149856947	E073	-48694
chr2	149858124	149858274	E073	-47367
chr2	149859275	149859325	E073	-46316
chr2	149862077	149862614	E073	-43027
chr2	149873784	149874238	E073	-31403
chr2	149855746	149855800	E074	-49841
chr2	149855877	149856491	E074	-49150
chr2	149856612	149856662	E074	-48979
chr2	149856819	149856947	E074	-48694
chr2	149857160	149857268	E074	-48373
chr2	149858124	149858274	E074	-47367
chr2	149878345	149878523	E074	-27118
chr2	149855746	149855800	E081	-49841
chr2	149855877	149856491	E081	-49150
chr2	149856612	149856662	E081	-48979
chr2	149856819	149856947	E081	-48694
chr2	149858124	149858274	E081	-47367
chr2	149859275	149859325	E081	-46316
chr2	149855746	149855800	E082	-49841
chr2	149855877	149856491	E082	-49150
chr2	149856612	149856662	E082	-48979
chr2	149856819	149856947	E082	-48694

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	149895682	149895807	E067	-9834
chr2	149894497	149895676	E069	-9965
chr2	149895682	149895807	E069	-9834
chr2	149894497	149895676	E070	-9965
chr2	149895682	149895807	E070	-9834
chr2	149894497	149895676	E071	-9965
chr2	149894497	149895676	E072	-9965
chr2	149894497	149895676	E073	-9965
chr2	149894497	149895676	E082	-9965
chr2	149895682	149895807	E082	-9834

rs10201643

Genomic Coordinates

Gene: LYPD6B, LY6/PLAUR domain containing 6B(plus strand)

Population Frequency

P-Value

eQTL of rs10201643 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs10201643 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)