rs7503705

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CDK12 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0367 (10997/29930,GnomAD)
A==0447 (13017/29118,TOPMED)
A==0360 (1801/5008,1000G)
A==0253 (975/3854,ALSPAC)
A==0261 (968/3708,TWINSUK)

Position: chr17:39513451 (GRCh38.p7) (17q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 85 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 17	NC_000017.11:g.39513451A>G
GRCh37.p13 chr 17	NC_000017.10:g.37669704A>G

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	A=0.716	G=0.284
1000Genomes	American	Sub	694	A=0.330	G=0.670
1000Genomes	East Asian	Sub	1008	A=0.262	G=0.738
1000Genomes	Europe	Sub	1006	A=0.251	G=0.749
1000Genomes	Global	Study-wide	5008	A=0.360	G=0.640
1000Genomes	South Asian	Sub	978	A=0.110	G=0.890
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.253	G=0.747
The Genome Aggregation Database	African	Sub	8714	A=0.665	G=0.335
The Genome Aggregation Database	American	Sub	838	A=0.300	G=0.700
The Genome Aggregation Database	East Asian	Sub	1606	A=0.305	G=0.695
The Genome Aggregation Database	Europe	Sub	18472	A=0.235	G=0.764
The Genome Aggregation Database	Global	Study-wide	29930	A=0.367	G=0.632
The Genome Aggregation Database	Other	Sub	300	A=0.340	G=0.660
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.447	G=0.553
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.261	G=0.739

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
rs7503705	0.000671	alcohol dependence	20201924

eQTL of rs7503705 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 rs7503705 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	-47771
chr17	37622132	37622327	E067	-47377
chr17	37682359	37682484	E067	12655
chr17	37623934	37623984	E068	-45720
chr17	37717356	37717425	E068	47652
chr17	37717464	37717514	E068	47760
chr17	37719197	37719618	E068	49493
chr17	37621883	37621933	E069	-47771
chr17	37622132	37622327	E069	-47377
chr17	37682359	37682484	E069	12655
chr17	37622132	37622327	E070	-47377
chr17	37704820	37705114	E070	35116
chr17	37705133	37705247	E070	35429
chr17	37705250	37705451	E070	35546
chr17	37711731	37711952	E070	42027
chr17	37712456	37712574	E070	42752
chr17	37712575	37712739	E070	42871
chr17	37712763	37712972	E070	43059
chr17	37713079	37713129	E070	43375
chr17	37713691	37713773	E070	43987
chr17	37713887	37713947	E070	44183
chr17	37713977	37714039	E070	44273
chr17	37714072	37714122	E070	44368
chr17	37717290	37717340	E070	47586
chr17	37717356	37717425	E070	47652
chr17	37717464	37717514	E070	47760
chr17	37717697	37718041	E070	47993
chr17	37718627	37719124	E070	48923
chr17	37622132	37622327	E071	-47377
chr17	37673549	37673764	E071	3845
chr17	37673849	37673895	E071	4145
chr17	37682109	37682171	E071	12405
chr17	37682359	37682484	E071	12655
chr17	37682109	37682171	E072	12405
chr17	37682359	37682484	E072	12655
chr17	37709454	37710157	E072	39750
chr17	37682359	37682484	E073	12655
chr17	37719197	37719618	E073	49493
chr17	37673549	37673764	E074	3845
chr17	37673849	37673895	E074	4145
chr17	37682109	37682171	E074	12405
chr17	37682359	37682484	E074	12655
chr17	37685414	37685471	E074	15710
chr17	37685845	37685981	E074	16141
chr17	37621883	37621933	E081	-47771
chr17	37622132	37622327	E081	-47377
chr17	37623934	37623984	E081	-45720
chr17	37703929	37704658	E081	34225
chr17	37704820	37705114	E081	35116
chr17	37705133	37705247	E081	35429
chr17	37705250	37705451	E081	35546
chr17	37708024	37708319	E081	38320
chr17	37708331	37708457	E081	38627
chr17	37708578	37708660	E081	38874
chr17	37711731	37711952	E081	42027
chr17	37712456	37712574	E081	42752
chr17	37712575	37712739	E081	42871
chr17	37712763	37712972	E081	43059
chr17	37713079	37713129	E081	43375
chr17	37713691	37713773	E081	43987
chr17	37717290	37717340	E081	47586
chr17	37717356	37717425	E081	47652
chr17	37717464	37717514	E081	47760
chr17	37717697	37718041	E081	47993
chr17	37718627	37719124	E081	48923
chr17	37719197	37719618	E081	49493
chr17	37622132	37622327	E082	-47377
chr17	37704820	37705114	E082	35116
chr17	37709038	37709111	E082	39334
chr17	37709454	37710157	E082	39750
chr17	37712456	37712574	E082	42752
chr17	37712575	37712739	E082	42871
chr17	37712763	37712972	E082	43059
chr17	37713079	37713129	E082	43375
chr17	37714412	37714462	E082	44708
chr17	37715983	37716059	E082	46279
chr17	37716459	37716503	E082	46755
chr17	37716899	37716949	E082	47195
chr17	37716974	37717024	E082	47270
chr17	37717290	37717340	E082	47586
chr17	37717356	37717425	E082	47652
chr17	37717464	37717514	E082	47760
chr17	37717697	37718041	E082	47993
chr17	37718627	37719124	E082	48923
chr17	37719197	37719618	E082	49493

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr17	37619960	37620016	E067	-49688
chr17	37620123	37620173	E067	-49531
chr17	37619960	37620016	E068	-49688
chr17	37620123	37620173	E068	-49531
chr17	37619960	37620016	E069	-49688
chr17	37620123	37620173	E069	-49531
chr17	37619960	37620016	E070	-49688
chr17	37620123	37620173	E070	-49531
chr17	37619960	37620016	E071	-49688
chr17	37620123	37620173	E071	-49531
chr17	37619960	37620016	E072	-49688
chr17	37620123	37620173	E072	-49531
chr17	37619960	37620016	E073	-49688
chr17	37620123	37620173	E073	-49531
chr17	37619960	37620016	E074	-49688
chr17	37620123	37620173	E074	-49531
chr17	37619960	37620016	E081	-49688
chr17	37620123	37620173	E081	-49531
chr17	37619960	37620016	E082	-49688
chr17	37620123	37620173	E082	-49531