rs11578798

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

OBSCN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0157 (4698/29886,GnomAD)
A=0159 (4645/29116,TOPMED)
A=0140 (699/5008,1000G)
A=0168 (649/3854,ALSPAC)
A=0168 (622/3708,TWINSUK)

Position: chr1:228355602 (GRCh38.p7) (1q42.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 64 Enhancers around

Promoter: 15 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.228355602T>A
GRCh37.p13 chr 1	NC_000001.10:g.228543303T>A
OBSCN RefSeqGene	NG_032122.1:g.152443T>A

Gene: OBSCN, obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OBSCN transcript variant 2	NM_001098623.2:c.	N/A	Intron Variant
OBSCN transcript variant IC	NM_001271223.2:c.	N/A	Intron Variant
OBSCN transcript variant 1	NM_052843.3:c.	N/A	Intron Variant
OBSCN transcript variant X6	XM_005273287.4:c.	N/A	Intron Variant
OBSCN transcript variant X7	XM_005273291.4:c.	N/A	Intron Variant
OBSCN transcript variant X18	XM_005273298.4:c.	N/A	Intron Variant
OBSCN transcript variant X32	XM_005273307.4:c.	N/A	Intron Variant
OBSCN transcript variant X25	XM_006711822.3:c.	N/A	Intron Variant
OBSCN transcript variant X27	XM_006711823.3:c.	N/A	Intron Variant
OBSCN transcript variant X39	XM_006711827.3:c.	N/A	Intron Variant
OBSCN transcript variant X42	XM_006711829.3:c.	N/A	Intron Variant
OBSCN transcript variant X34	XM_011544297.2:c.	N/A	Intron Variant
OBSCN transcript variant X41	XM_011544299.2:c.	N/A	Intron Variant
OBSCN transcript variant X1	XM_017002443.1:c.	N/A	Intron Variant
OBSCN transcript variant X2	XM_017002444.1:c.	N/A	Intron Variant
OBSCN transcript variant X3	XM_017002445.1:c.	N/A	Intron Variant
OBSCN transcript variant X4	XM_017002446.1:c.	N/A	Intron Variant
OBSCN transcript variant X5	XM_017002447.1:c.	N/A	Intron Variant
OBSCN transcript variant X8	XM_017002448.1:c.	N/A	Intron Variant
OBSCN transcript variant X9	XM_017002449.1:c.	N/A	Intron Variant
OBSCN transcript variant X10	XM_017002450.1:c.	N/A	Intron Variant
OBSCN transcript variant X11	XM_017002451.1:c.	N/A	Intron Variant
OBSCN transcript variant X12	XM_017002452.1:c.	N/A	Intron Variant
OBSCN transcript variant X13	XM_017002453.1:c.	N/A	Intron Variant
OBSCN transcript variant X14	XM_017002454.1:c.	N/A	Intron Variant
OBSCN transcript variant X15	XM_017002455.1:c.	N/A	Intron Variant
OBSCN transcript variant X16	XM_017002456.1:c.	N/A	Intron Variant
OBSCN transcript variant X17	XM_017002457.1:c.	N/A	Intron Variant
OBSCN transcript variant X19	XM_017002458.1:c.	N/A	Intron Variant
OBSCN transcript variant X20	XM_017002459.1:c.	N/A	Intron Variant
OBSCN transcript variant X21	XM_017002460.1:c.	N/A	Intron Variant
OBSCN transcript variant X22	XM_017002461.1:c.	N/A	Intron Variant
OBSCN transcript variant X23	XM_017002462.1:c.	N/A	Intron Variant
OBSCN transcript variant X24	XM_017002463.1:c.	N/A	Intron Variant
OBSCN transcript variant X26	XM_017002464.1:c.	N/A	Intron Variant
OBSCN transcript variant X28	XM_017002465.1:c.	N/A	Intron Variant
OBSCN transcript variant X29	XM_017002466.1:c.	N/A	Intron Variant
OBSCN transcript variant X30	XM_017002467.1:c.	N/A	Intron Variant
OBSCN transcript variant X31	XM_017002468.1:c.	N/A	Intron Variant
OBSCN transcript variant X33	XM_017002469.1:c.	N/A	Intron Variant
OBSCN transcript variant X35	XM_017002470.1:c.	N/A	Intron Variant
OBSCN transcript variant X36	XM_017002471.1:c.	N/A	Intron Variant
OBSCN transcript variant X37	XM_017002472.1:c.	N/A	Intron Variant
OBSCN transcript variant X38	XM_017002473.1:c.	N/A	Intron Variant
OBSCN transcript variant X40	XR_001737476.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.899	A=0.101
1000Genomes	American	Sub	694	T=0.760	A=0.240
1000Genomes	East Asian	Sub	1008	T=0.848	A=0.152
1000Genomes	Europe	Sub	1006	T=0.849	A=0.151
1000Genomes	Global	Study-wide	5008	T=0.860	A=0.140
1000Genomes	South Asian	Sub	978	T=0.900	A=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.832	A=0.168
The Genome Aggregation Database	African	Sub	8708	T=0.859	A=0.141
The Genome Aggregation Database	American	Sub	836	T=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1612	T=0.867	A=0.133
The Genome Aggregation Database	Europe	Sub	18428	T=0.839	A=0.160
The Genome Aggregation Database	Global	Study-wide	29886	T=0.842	A=0.157
The Genome Aggregation Database	Other	Sub	302	T=0.810	A=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.840	A=0.159
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.832	A=0.168

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
rs11578798	0.000875	alcohol dependence	21314694

eQTL of rs11578798 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 rs11578798 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	228562480	228563070	E067	19177
chr1	228563142	228563204	E067	19839
chr1	228591901	228591963	E067	48598
chr1	228591981	228592069	E067	48678
chr1	228592198	228592266	E067	48895
chr1	228562480	228563070	E068	19177
chr1	228568128	228568204	E068	24825
chr1	228568507	228568602	E068	25204
chr1	228568722	228568795	E068	25419
chr1	228569039	228569093	E068	25736
chr1	228569169	228569356	E068	25866
chr1	228578720	228578878	E068	35417
chr1	228579620	228579674	E068	36317
chr1	228581001	228581423	E068	37698
chr1	228588423	228588478	E068	45120
chr1	228588585	228588668	E068	45282
chr1	228591981	228592069	E068	48678
chr1	228592198	228592266	E068	48895
chr1	228562480	228563070	E069	19177
chr1	228563142	228563204	E069	19839
chr1	228591981	228592069	E069	48678
chr1	228592198	228592266	E069	48895
chr1	228564929	228565007	E070	21626
chr1	228565258	228565356	E070	21955
chr1	228591901	228591963	E070	48598
chr1	228591981	228592069	E070	48678
chr1	228592198	228592266	E070	48895
chr1	228562016	228562228	E071	18713
chr1	228562271	228562373	E071	18968
chr1	228562480	228563070	E071	19177
chr1	228563142	228563204	E071	19839
chr1	228563250	228563520	E071	19947
chr1	228581503	228581564	E071	38200
chr1	228581640	228581746	E071	38337
chr1	228581879	228581970	E071	38576
chr1	228591901	228591963	E071	48598
chr1	228591981	228592069	E071	48678
chr1	228592198	228592266	E071	48895
chr1	228562016	228562228	E072	18713
chr1	228562271	228562373	E072	18968
chr1	228562480	228563070	E072	19177
chr1	228563142	228563204	E072	19839
chr1	228563250	228563520	E072	19947
chr1	228581001	228581423	E072	37698
chr1	228581503	228581564	E072	38200
chr1	228591981	228592069	E072	48678
chr1	228592198	228592266	E072	48895
chr1	228562480	228563070	E073	19177
chr1	228563142	228563204	E073	19839
chr1	228563250	228563520	E073	19947
chr1	228581640	228581746	E073	38337
chr1	228581879	228581970	E073	38576
chr1	228591901	228591963	E073	48598
chr1	228591981	228592069	E073	48678
chr1	228562016	228562228	E074	18713
chr1	228562271	228562373	E074	18968
chr1	228591901	228591963	E074	48598
chr1	228591981	228592069	E074	48678
chr1	228592198	228592266	E074	48895
chr1	228591901	228591963	E081	48598
chr1	228591981	228592069	E081	48678
chr1	228592198	228592266	E081	48895
chr1	228591901	228591963	E082	48598
chr1	228591981	228592069	E082	48678

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	228565771	228567126	E067	22468
chr1	228567151	228567225	E067	23848
chr1	228565771	228567126	E068	22468
chr1	228567151	228567225	E068	23848
chr1	228565771	228567126	E069	22468
chr1	228565771	228567126	E070	22468
chr1	228565771	228567126	E071	22468
chr1	228567151	228567225	E071	23848
chr1	228565771	228567126	E072	22468
chr1	228567151	228567225	E072	23848
chr1	228565771	228567126	E073	22468
chr1	228567151	228567225	E073	23848
chr1	228565771	228567126	E074	22468
chr1	228565771	228567126	E082	22468
chr1	228567151	228567225	E082	23848