rs11657899

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CDK12 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0365 (10936/29914,GnomAD)
G==0446 (12997/29118,TOPMED)
G==0360 (1801/5008,1000G)
G==0251 (969/3854,ALSPAC)
G==0258 (956/3708,TWINSUK)

Position: chr17:39470710 (GRCh38.p7) (17q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 20 Enhancers around

Promoter: 52 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 17	NC_000017.11:g.39470710G>A
GRCh37.p13 chr 17	NC_000017.10:g.37626963G>A

Gene: CDK12, cyclin-dependent kinase 12(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDK12 transcript variant 2	NM_015083.2:c.	N/A	Intron Variant
CDK12 transcript variant 1	NM_016507.3:c.	N/A	Intron Variant
CDK12 transcript variant X1	XM_005257456.3:c.	N/A	Intron Variant
CDK12 transcript variant X25	XM_005257458.4:c.	N/A	Intron Variant
CDK12 transcript variant X2	XM_011524892.2:c.	N/A	Intron Variant
CDK12 transcript variant X3	XM_011524893.2:c.	N/A	Intron Variant
CDK12 transcript variant X4	XM_011524894.2:c.	N/A	Intron Variant
CDK12 transcript variant X5	XM_011524895.2:c.	N/A	Intron Variant
CDK12 transcript variant X6	XM_011524896.2:c.	N/A	Intron Variant
CDK12 transcript variant X8	XM_011524897.2:c.	N/A	Intron Variant
CDK12 transcript variant X9	XM_011524898.2:c.	N/A	Intron Variant
CDK12 transcript variant X10	XM_011524899.2:c.	N/A	Intron Variant
CDK12 transcript variant X13	XM_011524900.2:c.	N/A	Intron Variant
CDK12 transcript variant X14	XM_011524901.2:c.	N/A	Intron Variant
CDK12 transcript variant X11	XM_011524902.2:c.	N/A	Intron Variant
CDK12 transcript variant X12	XM_011524903.2:c.	N/A	Intron Variant
CDK12 transcript variant X18	XM_011524905.2:c.	N/A	Intron Variant
CDK12 transcript variant X19	XM_011524906.2:c.	N/A	Intron Variant
CDK12 transcript variant X20	XM_011524907.2:c.	N/A	Intron Variant
CDK12 transcript variant X7	XM_017024744.1:c.	N/A	Intron Variant
CDK12 transcript variant X8	XM_017024745.1:c.	N/A	Intron Variant
CDK12 transcript variant X12	XM_017024746.1:c.	N/A	Intron Variant
CDK12 transcript variant X15	XM_017024747.1:c.	N/A	Intron Variant
CDK12 transcript variant X16	XM_017024748.1:c.	N/A	Intron Variant
CDK12 transcript variant X17	XM_017024749.1:c.	N/A	Intron Variant
CDK12 transcript variant X21	XM_017024750.1:c.	N/A	Intron Variant
CDK12 transcript variant X22	XM_017024751.1:c.	N/A	Intron Variant
CDK12 transcript variant X23	XM_017024752.1:c.	N/A	Intron Variant
CDK12 transcript variant X26	XM_017024753.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.717	A=0.283
1000Genomes	American	Sub	694	G=0.330	A=0.670
1000Genomes	East Asian	Sub	1008	G=0.262	A=0.738
1000Genomes	Europe	Sub	1006	G=0.250	A=0.750
1000Genomes	Global	Study-wide	5008	G=0.360	A=0.640
1000Genomes	South Asian	Sub	978	G=0.110	A=0.890
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.251	A=0.749
The Genome Aggregation Database	African	Sub	8684	G=0.663	A=0.337
The Genome Aggregation Database	American	Sub	838	G=0.310	A=0.690
The Genome Aggregation Database	East Asian	Sub	1616	G=0.304	A=0.696
The Genome Aggregation Database	Europe	Sub	18474	G=0.234	A=0.766
The Genome Aggregation Database	Global	Study-wide	29914	G=0.365	A=0.634
The Genome Aggregation Database	Other	Sub	302	G=0.350	A=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.446	A=0.553
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.258	A=0.742

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
rs11657899	0.000969	alcohol dependence	20201924

eQTL of rs11657899 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 rs11657899 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg07936489	chr17:37558343	FBXL20	0.0188505998011327	9.8035e-14
cg15445000	chr17:37608096	MED1	-0.0454517621155827	1.1448e-11
cg00129232	chr17:37814104	STARD3	0.00606136462437292	4.4652e-10
cg20243544	chr17:37824526	PNMT	-0.0145629994946833	6.8706e-10
cg07936489	chr17:37558343	FBXL20	0.0188506	9.8000e-14

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 )
chr17	37621883	37621933	E067	-5030
chr17	37622132	37622327	E067	-4636
chr17	37623934	37623984	E068	-2979
chr17	37621883	37621933	E069	-5030
chr17	37622132	37622327	E069	-4636
chr17	37605267	37605460	E070	-21503
chr17	37605507	37605677	E070	-21286
chr17	37606120	37606170	E070	-20793
chr17	37622132	37622327	E070	-4636
chr17	37622132	37622327	E071	-4636
chr17	37673549	37673764	E071	46586
chr17	37673849	37673895	E071	46886
chr17	37673549	37673764	E074	46586
chr17	37673849	37673895	E074	46886
chr17	37621883	37621933	E081	-5030
chr17	37622132	37622327	E081	-4636
chr17	37623934	37623984	E081	-2979
chr17	37605267	37605460	E082	-21503
chr17	37605507	37605677	E082	-21286
chr17	37622132	37622327	E082	-4636

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr17	37606792	37607810	E067	-19153
chr17	37608111	37608237	E067	-18726
chr17	37617313	37619882	E067	-7081
chr17	37619960	37620016	E067	-6947
chr17	37620123	37620173	E067	-6790
chr17	37606792	37607810	E068	-19153
chr17	37608111	37608237	E068	-18726
chr17	37617058	37617146	E068	-9817
chr17	37617313	37619882	E068	-7081
chr17	37619960	37620016	E068	-6947
chr17	37620123	37620173	E068	-6790
chr17	37606792	37607810	E069	-19153
chr17	37608111	37608237	E069	-18726
chr17	37617313	37619882	E069	-7081
chr17	37619960	37620016	E069	-6947
chr17	37620123	37620173	E069	-6790
chr17	37606792	37607810	E070	-19153
chr17	37608111	37608237	E070	-18726
chr17	37617313	37619882	E070	-7081
chr17	37619960	37620016	E070	-6947
chr17	37620123	37620173	E070	-6790
chr17	37606792	37607810	E071	-19153
chr17	37608111	37608237	E071	-18726
chr17	37617058	37617146	E071	-9817
chr17	37617313	37619882	E071	-7081
chr17	37619960	37620016	E071	-6947
chr17	37620123	37620173	E071	-6790
chr17	37606792	37607810	E072	-19153
chr17	37608111	37608237	E072	-18726
chr17	37617058	37617146	E072	-9817
chr17	37617313	37619882	E072	-7081
chr17	37619960	37620016	E072	-6947
chr17	37620123	37620173	E072	-6790
chr17	37606792	37607810	E073	-19153
chr17	37608111	37608237	E073	-18726
chr17	37617313	37619882	E073	-7081
chr17	37619960	37620016	E073	-6947
chr17	37620123	37620173	E073	-6790
chr17	37606792	37607810	E074	-19153
chr17	37617058	37617146	E074	-9817
chr17	37617313	37619882	E074	-7081
chr17	37619960	37620016	E074	-6947
chr17	37620123	37620173	E074	-6790
chr17	37606792	37607810	E081	-19153
chr17	37617313	37619882	E081	-7081
chr17	37619960	37620016	E081	-6947
chr17	37620123	37620173	E081	-6790
chr17	37606792	37607810	E082	-19153
chr17	37608111	37608237	E082	-18726
chr17	37617313	37619882	E082	-7081
chr17	37619960	37620016	E082	-6947
chr17	37620123	37620173	E082	-6790