rs1148556

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

MBD6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0066 (1990/29964,GnomAD)
T=0087 (2538/29118,TOPMED)
T=0072 (361/5008,1000G)
T=0028 (109/3854,ALSPAC)
T=0029 (107/3708,TWINSUK)

Position: chr12:57523742 (GRCh38.p7) (12q13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 122 Enhancers around

Promoter: 104 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.57523742C>T
GRCh37.p13 chr 12	NC_000012.11:g.57917525C>T
DDIT3 RefSeqGene	NG_027674.1:g.1776G>A

Gene: MBD6, methyl-CpG binding domain protein 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MBD6 transcript	NM_052897.3:c.	N/A	Intron Variant
MBD6 transcript variant X1	XM_005268617.1:c.	N/A	Intron Variant
MBD6 transcript variant X3	XM_005268618.1:c.	N/A	Intron Variant
MBD6 transcript variant X12	XM_005268620.2:c.	N/A	Intron Variant
MBD6 transcript variant X2	XM_006719217.1:c.	N/A	Intron Variant
MBD6 transcript variant X4	XM_006719218.1:c.	N/A	Intron Variant
MBD6 transcript variant X5	XM_011537851.2:c.	N/A	Intron Variant
MBD6 transcript variant X11	XR_001748569.1:n.	N/A	Intron Variant
MBD6 transcript variant X6	XR_429073.1:n.	N/A	Intron Variant
MBD6 transcript variant X7	XR_429075.1:n.	N/A	Intron Variant
MBD6 transcript variant X8	XR_429076.1:n.	N/A	Intron Variant
MBD6 transcript variant X9	XR_429078.1:n.	N/A	Intron Variant
MBD6 transcript variant X10	XR_429079.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.820	T=0.180
1000Genomes	American	Sub	694	C=0.980	T=0.020
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=0.951	T=0.049
1000Genomes	Global	Study-wide	5008	C=0.928	T=0.072
1000Genomes	South Asian	Sub	978	C=0.940	T=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.972	T=0.028
The Genome Aggregation Database	African	Sub	8716	C=0.864	T=0.136
The Genome Aggregation Database	American	Sub	838	C=0.970	T=0.030
The Genome Aggregation Database	East Asian	Sub	1622	C=0.999	T=0.001
The Genome Aggregation Database	Europe	Sub	18486	C=0.958	T=0.041
The Genome Aggregation Database	Global	Study-wide	29964	C=0.933	T=0.066
The Genome Aggregation Database	Other	Sub	302	C=0.950	T=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.912	T=0.087
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.971	T=0.029

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

P-Value

SNP ID	p-value	Traits	Study
rs1148556	0.00028	alcohol dependence	20201924

eQTL of rs1148556 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 rs1148556 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 )
chr12	57883035	57883177	E067	-34348
chr12	57883183	57883359	E067	-34166
chr12	57910447	57911081	E067	-6444
chr12	57911093	57911330	E067	-6195
chr12	57911348	57911490	E067	-6035
chr12	57911504	57911591	E067	-5934
chr12	57918415	57919003	E067	890
chr12	57941538	57941615	E067	24013
chr12	57942846	57943177	E067	25321
chr12	57911093	57911330	E068	-6195
chr12	57911348	57911490	E068	-6035
chr12	57911504	57911591	E068	-5934
chr12	57919004	57919195	E068	1479
chr12	57919198	57919312	E068	1673
chr12	57919329	57919413	E068	1804
chr12	57929056	57929165	E068	11531
chr12	57929382	57929462	E068	11857
chr12	57929508	57929639	E068	11983
chr12	57937337	57937458	E068	19812
chr12	57937463	57937751	E068	19938
chr12	57937883	57937951	E068	20358
chr12	57938775	57938892	E068	21250
chr12	57946085	57946151	E068	28560
chr12	57946312	57946362	E068	28787
chr12	57883035	57883177	E069	-34348
chr12	57883183	57883359	E069	-34166
chr12	57883714	57883783	E069	-33742
chr12	57884001	57884051	E069	-33474
chr12	57911093	57911330	E069	-6195
chr12	57911348	57911490	E069	-6035
chr12	57918415	57919003	E069	890
chr12	57919004	57919195	E069	1479
chr12	57919198	57919312	E069	1673
chr12	57937337	57937458	E069	19812
chr12	57937463	57937751	E069	19938
chr12	57937883	57937951	E069	20358
chr12	57938775	57938892	E069	21250
chr12	57918415	57919003	E070	890
chr12	57919004	57919195	E070	1479
chr12	57919198	57919312	E070	1673
chr12	57919329	57919413	E070	1804
chr12	57919497	57919547	E070	1972
chr12	57919596	57919669	E070	2071
chr12	57919727	57920070	E070	2202
chr12	57920074	57920277	E070	2549
chr12	57920377	57920427	E070	2852
chr12	57920470	57920903	E070	2945
chr12	57937337	57937458	E070	19812
chr12	57937463	57937751	E070	19938
chr12	57938775	57938892	E070	21250
chr12	57948692	57948811	E070	31167
chr12	57948820	57948870	E070	31295
chr12	57950684	57950748	E070	33159
chr12	57911348	57911490	E071	-6035
chr12	57911504	57911591	E071	-5934
chr12	57937337	57937458	E071	19812
chr12	57937463	57937751	E071	19938
chr12	57937883	57937951	E071	20358
chr12	57938775	57938892	E071	21250
chr12	57941538	57941615	E071	24013
chr12	57942846	57943177	E071	25321
chr12	57947093	57947283	E071	29568
chr12	57910447	57911081	E072	-6444
chr12	57911093	57911330	E072	-6195
chr12	57911348	57911490	E072	-6035
chr12	57911504	57911591	E072	-5934
chr12	57911874	57912541	E072	-4984
chr12	57937337	57937458	E072	19812
chr12	57937463	57937751	E072	19938
chr12	57937883	57937951	E072	20358
chr12	57938775	57938892	E072	21250
chr12	57910447	57911081	E073	-6444
chr12	57911093	57911330	E073	-6195
chr12	57911348	57911490	E073	-6035
chr12	57911504	57911591	E073	-5934
chr12	57918415	57919003	E073	890
chr12	57919004	57919195	E073	1479
chr12	57919198	57919312	E073	1673
chr12	57919329	57919413	E073	1804
chr12	57919497	57919547	E073	1972
chr12	57919596	57919669	E073	2071
chr12	57919727	57920070	E073	2202
chr12	57920074	57920277	E073	2549
chr12	57937337	57937458	E073	19812
chr12	57937463	57937751	E073	19938
chr12	57937883	57937951	E073	20358
chr12	57883035	57883177	E074	-34348
chr12	57883183	57883359	E074	-34166
chr12	57918415	57919003	E074	890
chr12	57883035	57883177	E081	-34348
chr12	57883183	57883359	E081	-34166
chr12	57918415	57919003	E081	890
chr12	57919004	57919195	E081	1479
chr12	57919198	57919312	E081	1673
chr12	57919329	57919413	E081	1804
chr12	57919497	57919547	E081	1972
chr12	57919596	57919669	E081	2071
chr12	57919727	57920070	E081	2202
chr12	57920074	57920277	E081	2549
chr12	57938775	57938892	E081	21250
chr12	57942846	57943177	E081	25321
chr12	57946312	57946362	E081	28787
chr12	57946408	57946458	E081	28883
chr12	57946495	57946547	E081	28970
chr12	57948692	57948811	E081	31167
chr12	57948820	57948870	E081	31295
chr12	57950250	57950469	E081	32725
chr12	57883183	57883359	E082	-34166
chr12	57883714	57883783	E082	-33742
chr12	57918415	57919003	E082	890
chr12	57919004	57919195	E082	1479
chr12	57919198	57919312	E082	1673
chr12	57919329	57919413	E082	1804
chr12	57919497	57919547	E082	1972
chr12	57919596	57919669	E082	2071
chr12	57919727	57920070	E082	2202
chr12	57937337	57937458	E082	19812
chr12	57937463	57937751	E082	19938
chr12	57937883	57937951	E082	20358
chr12	57938775	57938892	E082	21250
chr12	57948692	57948811	E082	31167
chr12	57948820	57948870	E082	31295

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	57881085	57882695	E067	-34830
chr12	57912852	57915051	E067	-2474
chr12	57939511	57941533	E067	21986
chr12	57943248	57944621	E067	25723
chr12	57944681	57944857	E067	27156
chr12	57944886	57945001	E067	27361
chr12	57945065	57945105	E067	27540
chr12	57945115	57945274	E067	27590
chr12	57945433	57945560	E067	27908
chr12	57945589	57945751	E067	28064
chr12	57945845	57945940	E067	28320
chr12	57947293	57947404	E067	29768
chr12	57881085	57882695	E068	-34830
chr12	57912852	57915051	E068	-2474
chr12	57939511	57941533	E068	21986
chr12	57943248	57944621	E068	25723
chr12	57944681	57944857	E068	27156
chr12	57944886	57945001	E068	27361
chr12	57945065	57945105	E068	27540
chr12	57945115	57945274	E068	27590
chr12	57945433	57945560	E068	27908
chr12	57945589	57945751	E068	28064
chr12	57947293	57947404	E068	29768
chr12	57881085	57882695	E069	-34830
chr12	57912852	57915051	E069	-2474
chr12	57939511	57941533	E069	21986
chr12	57943248	57944621	E069	25723
chr12	57944681	57944857	E069	27156
chr12	57944886	57945001	E069	27361
chr12	57945065	57945105	E069	27540
chr12	57945115	57945274	E069	27590
chr12	57945433	57945560	E069	27908
chr12	57945589	57945751	E069	28064
chr12	57945845	57945940	E069	28320
chr12	57947293	57947404	E069	29768
chr12	57881085	57882695	E070	-34830
chr12	57912852	57915051	E070	-2474
chr12	57939511	57941533	E070	21986
chr12	57943248	57944621	E070	25723
chr12	57944681	57944857	E070	27156
chr12	57944886	57945001	E070	27361
chr12	57945065	57945105	E070	27540
chr12	57945115	57945274	E070	27590
chr12	57945433	57945560	E070	27908
chr12	57945589	57945751	E070	28064
chr12	57945845	57945940	E070	28320
chr12	57947293	57947404	E070	29768
chr12	57881085	57882695	E071	-34830
chr12	57912852	57915051	E071	-2474
chr12	57939511	57941533	E071	21986
chr12	57943248	57944621	E071	25723
chr12	57944681	57944857	E071	27156
chr12	57881085	57882695	E072	-34830
chr12	57912852	57915051	E072	-2474
chr12	57939511	57941533	E072	21986
chr12	57943248	57944621	E072	25723
chr12	57944681	57944857	E072	27156
chr12	57944886	57945001	E072	27361
chr12	57945065	57945105	E072	27540
chr12	57945115	57945274	E072	27590
chr12	57945433	57945560	E072	27908
chr12	57945589	57945751	E072	28064
chr12	57945845	57945940	E072	28320
chr12	57947293	57947404	E072	29768
chr12	57881085	57882695	E073	-34830
chr12	57912852	57915051	E073	-2474
chr12	57939511	57941533	E073	21986
chr12	57943248	57944621	E073	25723
chr12	57944681	57944857	E073	27156
chr12	57944886	57945001	E073	27361
chr12	57945065	57945105	E073	27540
chr12	57945115	57945274	E073	27590
chr12	57945433	57945560	E073	27908
chr12	57945589	57945751	E073	28064
chr12	57945845	57945940	E073	28320
chr12	57947293	57947404	E073	29768
chr12	57881085	57882695	E074	-34830
chr12	57912852	57915051	E074	-2474
chr12	57939511	57941533	E074	21986
chr12	57943248	57944621	E074	25723
chr12	57944681	57944857	E074	27156
chr12	57881085	57882695	E081	-34830
chr12	57912852	57915051	E081	-2474
chr12	57943248	57944621	E081	25723
chr12	57944681	57944857	E081	27156
chr12	57944886	57945001	E081	27361
chr12	57945065	57945105	E081	27540
chr12	57945115	57945274	E081	27590
chr12	57945433	57945560	E081	27908
chr12	57945589	57945751	E081	28064
chr12	57945845	57945940	E081	28320
chr12	57947293	57947404	E081	29768
chr12	57881085	57882695	E082	-34830
chr12	57912852	57915051	E082	-2474
chr12	57939511	57941533	E082	21986
chr12	57943248	57944621	E082	25723
chr12	57944681	57944857	E082	27156
chr12	57944886	57945001	E082	27361
chr12	57945065	57945105	E082	27540
chr12	57945115	57945274	E082	27590
chr12	57945433	57945560	E082	27908
chr12	57945589	57945751	E082	28064
chr12	57945845	57945940	E082	28320
chr12	57947293	57947404	E082	29768