rs911216

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0215 (6444/29886,GnomAD)
C=0224 (6539/29118,TOPMED)
C=0210 (1050/5008,1000G)
C=0223 (860/3854,ALSPAC)
C=0196 (728/3708,TWINSUK)

Position: chr1:33909598 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 157 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.33909598A>C
GRCh37.p13 chr 1	NC_000001.10:g.34375199A>C

Gene: CSMD2, CUB and Sushi multiple domains 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CSMD2 transcript variant 1	NM_001281956.1:c.	N/A	Intron Variant
CSMD2 transcript variant 2	NM_052896.4:c.	N/A	Intron Variant
CSMD2 transcript variant X1	XM_017000185.1:c.	N/A	Intron Variant
CSMD2 transcript variant X2	XM_017000186.1:c.	N/A	Intron Variant
CSMD2 transcript variant X3	XM_017000187.1:c.	N/A	Intron Variant
CSMD2 transcript variant X4	XM_017000188.1:c.	N/A	Intron Variant
CSMD2 transcript variant X5	XM_017000189.1:c.	N/A	Intron Variant
CSMD2 transcript variant X6	XM_017000190.1:c.	N/A	Intron Variant
CSMD2 transcript variant X7	XM_017000191.1:c.	N/A	Intron Variant
CSMD2 transcript variant X8	XM_017000192.1:c.	N/A	Intron Variant
CSMD2 transcript variant X9	XM_017000193.1:c.	N/A	Intron Variant
CSMD2 transcript variant X10	XM_017000194.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.730	C=0.270
1000Genomes	American	Sub	694	A=0.860	C=0.140
1000Genomes	East Asian	Sub	1008	A=0.906	C=0.094
1000Genomes	Europe	Sub	1006	A=0.769	C=0.231
1000Genomes	Global	Study-wide	5008	A=0.790	C=0.210
1000Genomes	South Asian	Sub	978	A=0.720	C=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.777	C=0.223
The Genome Aggregation Database	African	Sub	8692	A=0.760	C=0.240
The Genome Aggregation Database	American	Sub	836	A=0.870	C=0.130
The Genome Aggregation Database	East Asian	Sub	1618	A=0.896	C=0.104
The Genome Aggregation Database	Europe	Sub	18440	A=0.781	C=0.218
The Genome Aggregation Database	Global	Study-wide	29886	A=0.784	C=0.215
The Genome Aggregation Database	Other	Sub	300	A=0.810	C=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.775	C=0.224
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.804	C=0.196

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
rs911216	0.00073	alcohol dependence	20201924

eQTL of rs911216 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 rs911216 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	34342662	34342906	E067	-32293
chr1	34351996	34352471	E067	-22728
chr1	34358698	34358778	E067	-16421
chr1	34358817	34359067	E067	-16132
chr1	34359086	34359387	E067	-15812
chr1	34367893	34368489	E067	-6710
chr1	34368500	34368768	E067	-6431
chr1	34368890	34369110	E067	-6089
chr1	34373839	34373889	E067	-1310
chr1	34373974	34374177	E067	-1022
chr1	34374204	34374258	E067	-941
chr1	34374324	34374722	E067	-477
chr1	34374777	34374826	E067	-373
chr1	34391239	34391482	E067	16040
chr1	34396173	34396420	E067	20974
chr1	34407181	34407231	E067	31982
chr1	34340278	34340375	E068	-34824
chr1	34351996	34352471	E068	-22728
chr1	34358698	34358778	E068	-16421
chr1	34358817	34359067	E068	-16132
chr1	34359086	34359387	E068	-15812
chr1	34373839	34373889	E068	-1310
chr1	34373974	34374177	E068	-1022
chr1	34374204	34374258	E068	-941
chr1	34374324	34374722	E068	-477
chr1	34374777	34374826	E068	-373
chr1	34396173	34396420	E068	20974
chr1	34396494	34396632	E068	21295
chr1	34407181	34407231	E068	31982
chr1	34407800	34407895	E068	32601
chr1	34423496	34423768	E068	48297
chr1	34424620	34424715	E068	49421
chr1	34424776	34424903	E068	49577
chr1	34351996	34352471	E069	-22728
chr1	34358817	34359067	E069	-16132
chr1	34359086	34359387	E069	-15812
chr1	34362921	34363085	E069	-12114
chr1	34363137	34363241	E069	-11958
chr1	34363686	34363926	E069	-11273
chr1	34364119	34364376	E069	-10823
chr1	34364566	34364731	E069	-10468
chr1	34367893	34368489	E069	-6710
chr1	34368500	34368768	E069	-6431
chr1	34373974	34374177	E069	-1022
chr1	34374204	34374258	E069	-941
chr1	34374324	34374722	E069	-477
chr1	34374777	34374826	E069	-373
chr1	34391239	34391482	E069	16040
chr1	34396173	34396420	E069	20974
chr1	34396494	34396632	E069	21295
chr1	34415322	34415372	E069	40123
chr1	34424776	34424903	E069	49577
chr1	34332014	34332146	E070	-43053
chr1	34363686	34363926	E070	-11273
chr1	34364119	34364376	E070	-10823
chr1	34367893	34368489	E070	-6710
chr1	34368500	34368768	E070	-6431
chr1	34368890	34369110	E070	-6089
chr1	34338448	34338592	E071	-36607
chr1	34340278	34340375	E071	-34824
chr1	34340417	34340588	E071	-34611
chr1	34341617	34341696	E071	-33503
chr1	34351996	34352471	E071	-22728
chr1	34358817	34359067	E071	-16132
chr1	34359086	34359387	E071	-15812
chr1	34364119	34364376	E071	-10823
chr1	34364566	34364731	E071	-10468
chr1	34365008	34365124	E071	-10075
chr1	34365430	34365486	E071	-9713
chr1	34367893	34368489	E071	-6710
chr1	34368500	34368768	E071	-6431
chr1	34368890	34369110	E071	-6089
chr1	34373839	34373889	E071	-1310
chr1	34373974	34374177	E071	-1022
chr1	34374204	34374258	E071	-941
chr1	34374324	34374722	E071	-477
chr1	34374777	34374826	E071	-373
chr1	34396173	34396420	E071	20974
chr1	34396494	34396632	E071	21295
chr1	34406191	34406325	E071	30992
chr1	34406368	34406522	E071	31169
chr1	34407181	34407231	E071	31982
chr1	34415322	34415372	E071	40123
chr1	34340278	34340375	E072	-34824
chr1	34340417	34340588	E072	-34611
chr1	34341617	34341696	E072	-33503
chr1	34342662	34342906	E072	-32293
chr1	34358698	34358778	E072	-16421
chr1	34358817	34359067	E072	-16132
chr1	34359086	34359387	E072	-15812
chr1	34362921	34363085	E072	-12114
chr1	34363137	34363241	E072	-11958
chr1	34363686	34363926	E072	-11273
chr1	34364119	34364376	E072	-10823
chr1	34364566	34364731	E072	-10468
chr1	34365430	34365486	E072	-9713
chr1	34367893	34368489	E072	-6710
chr1	34368500	34368768	E072	-6431
chr1	34368890	34369110	E072	-6089
chr1	34373974	34374177	E072	-1022
chr1	34374204	34374258	E072	-941
chr1	34374324	34374722	E072	-477
chr1	34374777	34374826	E072	-373
chr1	34396173	34396420	E072	20974
chr1	34396494	34396632	E072	21295
chr1	34423496	34423768	E072	48297
chr1	34358698	34358778	E073	-16421
chr1	34358817	34359067	E073	-16132
chr1	34359086	34359387	E073	-15812
chr1	34373974	34374177	E073	-1022
chr1	34374204	34374258	E073	-941
chr1	34374324	34374722	E073	-477
chr1	34374777	34374826	E073	-373
chr1	34423496	34423768	E073	48297
chr1	34351996	34352471	E074	-22728
chr1	34363686	34363926	E074	-11273
chr1	34364119	34364376	E074	-10823
chr1	34364566	34364731	E074	-10468
chr1	34365008	34365124	E074	-10075
chr1	34368890	34369110	E074	-6089
chr1	34373974	34374177	E074	-1022
chr1	34374204	34374258	E074	-941
chr1	34374324	34374722	E074	-477
chr1	34374777	34374826	E074	-373
chr1	34396173	34396420	E074	20974
chr1	34396494	34396632	E074	21295
chr1	34406191	34406325	E074	30992
chr1	34406368	34406522	E074	31169
chr1	34332014	34332146	E081	-43053
chr1	34333602	34333728	E081	-41471
chr1	34351996	34352471	E081	-22728
chr1	34358698	34358778	E081	-16421
chr1	34358817	34359067	E081	-16132
chr1	34359086	34359387	E081	-15812
chr1	34367893	34368489	E081	-6710
chr1	34368500	34368768	E081	-6431
chr1	34368890	34369110	E081	-6089
chr1	34373974	34374177	E081	-1022
chr1	34374204	34374258	E081	-941
chr1	34374324	34374722	E081	-477
chr1	34420847	34420901	E081	45648
chr1	34422012	34422119	E081	46813
chr1	34423496	34423768	E081	48297
chr1	34332014	34332146	E082	-43053
chr1	34340417	34340588	E082	-34611
chr1	34351996	34352471	E082	-22728
chr1	34358817	34359067	E082	-16132
chr1	34359086	34359387	E082	-15812
chr1	34363686	34363926	E082	-11273
chr1	34364119	34364376	E082	-10823
chr1	34367893	34368489	E082	-6710
chr1	34368500	34368768	E082	-6431
chr1	34368890	34369110	E082	-6089
chr1	34371831	34372051	E082	-3148
chr1	34374204	34374258	E082	-941
chr1	34422012	34422119	E082	46813
chr1	34423496	34423768	E082	48297