rs11915803

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CCDC13 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0220 (6609/29950,GnomAD)
C=0169 (4920/29118,TOPMED)
C=0182 (912/5008,1000G)
C=0274 (1056/3854,ALSPAC)
C=0287 (1064/3708,TWINSUK)

Position: chr3:42758799 (GRCh38.p7) (3p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 379 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.42758799T>C
GRCh37.p13 chr 3	NC_000003.11:g.42800291T>C

Gene: CCDC13, coiled-coil domain containing 13(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCDC13 transcript	NM_144719.3:c.	N/A	Intron Variant
CCDC13 transcript variant X2	XM_005264898.3:c.	N/A	Intron Variant
CCDC13 transcript variant X8	XM_005264899.4:c.	N/A	Intron Variant
CCDC13 transcript variant X3	XM_011533418.2:c.	N/A	Intron Variant
CCDC13 transcript variant X6	XM_011533420.2:c.	N/A	Intron Variant
CCDC13 transcript variant X7	XM_011533421.2:c.	N/A	Intron Variant
CCDC13 transcript variant X4	XM_011533419.2:c.	N/A	Genic Upstream Transcript Variant
CCDC13 transcript variant X5	XM_017005781.1:c.	N/A	Genic Upstream Transcript Variant
CCDC13 transcript variant X1	XR_940385.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.936	C=0.064
1000Genomes	American	Sub	694	T=0.840	C=0.160
1000Genomes	East Asian	Sub	1008	T=0.831	C=0.169
1000Genomes	Europe	Sub	1006	T=0.730	C=0.270
1000Genomes	Global	Study-wide	5008	T=0.818	C=0.182
1000Genomes	South Asian	Sub	978	T=0.720	C=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.726	C=0.274
The Genome Aggregation Database	African	Sub	8714	T=0.908	C=0.092
The Genome Aggregation Database	American	Sub	836	T=0.860	C=0.140
The Genome Aggregation Database	East Asian	Sub	1618	T=0.860	C=0.140
The Genome Aggregation Database	Europe	Sub	18480	T=0.708	C=0.291
The Genome Aggregation Database	Global	Study-wide	29950	T=0.779	C=0.220
The Genome Aggregation Database	Other	Sub	302	T=0.750	C=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.831	C=0.169
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.713	C=0.287

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
rs11915803	0.000868	alcohol dependence	20201924

eQTL of rs11915803 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:42800291	HHATL	ENSG00000010282.10	T>C	4.9210e-8	55972	Cerebellum
Chr3:42800291	HHATL	ENSG00000010282.10	T>C	3.6591e-4	55972	Hypothalamus
Chr3:42800291	HHATL	ENSG00000010282.10	T>C	5.9614e-6	55972	Hippocampus
Chr3:42800291	HHATL	ENSG00000010282.10	T>C	2.2311e-5	55972	Substantia_nigra
Chr3:42800291	ACKR2	ENSG00000144648.10	T>C	1.4850e-2	-45953	Putamen_basal_ganglia

meQTL of rs11915803 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 )
chr3	42753058	42753252	E067	-47039
chr3	42753474	42753613	E067	-46678
chr3	42764594	42764644	E067	-35647
chr3	42764693	42764931	E067	-35360
chr3	42766734	42766849	E067	-33442
chr3	42767014	42767343	E067	-32948
chr3	42769682	42769826	E067	-30465
chr3	42770346	42770400	E067	-29891
chr3	42770515	42770617	E067	-29674
chr3	42770964	42771019	E067	-29272
chr3	42771339	42771539	E067	-28752
chr3	42771886	42772037	E067	-28254
chr3	42773656	42773953	E067	-26338
chr3	42774508	42774760	E067	-25531
chr3	42775003	42775478	E067	-24813
chr3	42775654	42775825	E067	-24466
chr3	42775976	42776036	E067	-24255
chr3	42776218	42776268	E067	-24023
chr3	42776721	42776845	E067	-23446
chr3	42777037	42777089	E067	-23202
chr3	42777418	42777524	E067	-22767
chr3	42777595	42777886	E067	-22405
chr3	42777972	42778037	E067	-22254
chr3	42780955	42781012	E067	-19279
chr3	42781287	42781702	E067	-18589
chr3	42781774	42781934	E067	-18357
chr3	42782136	42782306	E067	-17985
chr3	42785318	42785585	E067	-14706
chr3	42785598	42786099	E067	-14192
chr3	42786553	42786603	E067	-13688
chr3	42786895	42787106	E067	-13185
chr3	42787158	42787302	E067	-12989
chr3	42787336	42787449	E067	-12842
chr3	42787649	42787913	E067	-12378
chr3	42788030	42788394	E067	-11897
chr3	42788584	42788669	E067	-11622
chr3	42788837	42788877	E067	-11414
chr3	42789019	42789149	E067	-11142
chr3	42789153	42789270	E067	-11021
chr3	42789412	42789462	E067	-10829
chr3	42789955	42790015	E067	-10276
chr3	42790187	42790280	E067	-10011
chr3	42804579	42804793	E067	4288
chr3	42837112	42837614	E067	36821
chr3	42841135	42841185	E067	40844
chr3	42842694	42842794	E067	42403
chr3	42753058	42753252	E068	-47039
chr3	42753474	42753613	E068	-46678
chr3	42760526	42760794	E068	-39497
chr3	42761696	42761870	E068	-38421
chr3	42764594	42764644	E068	-35647
chr3	42764693	42764931	E068	-35360
chr3	42766734	42766849	E068	-33442
chr3	42767014	42767343	E068	-32948
chr3	42769682	42769826	E068	-30465
chr3	42770346	42770400	E068	-29891
chr3	42770515	42770617	E068	-29674
chr3	42770964	42771019	E068	-29272
chr3	42771339	42771539	E068	-28752
chr3	42771886	42772037	E068	-28254
chr3	42775654	42775825	E068	-24466
chr3	42775976	42776036	E068	-24255
chr3	42776218	42776268	E068	-24023
chr3	42776721	42776845	E068	-23446
chr3	42777037	42777089	E068	-23202
chr3	42777418	42777524	E068	-22767
chr3	42777595	42777886	E068	-22405
chr3	42777972	42778037	E068	-22254
chr3	42780955	42781012	E068	-19279
chr3	42781287	42781702	E068	-18589
chr3	42781774	42781934	E068	-18357
chr3	42782136	42782306	E068	-17985
chr3	42785318	42785585	E068	-14706
chr3	42785598	42786099	E068	-14192
chr3	42786553	42786603	E068	-13688
chr3	42786895	42787106	E068	-13185
chr3	42787158	42787302	E068	-12989
chr3	42787336	42787449	E068	-12842
chr3	42787649	42787913	E068	-12378
chr3	42788030	42788394	E068	-11897
chr3	42788584	42788669	E068	-11622
chr3	42788837	42788877	E068	-11414
chr3	42789019	42789149	E068	-11142
chr3	42789153	42789270	E068	-11021
chr3	42789412	42789462	E068	-10829
chr3	42789955	42790015	E068	-10276
chr3	42790187	42790280	E068	-10011
chr3	42791227	42791864	E068	-8427
chr3	42797220	42798074	E068	-2217
chr3	42798152	42798205	E068	-2086
chr3	42802890	42803277	E068	2599
chr3	42803621	42803752	E068	3330
chr3	42803782	42803898	E068	3491
chr3	42804579	42804793	E068	4288
chr3	42804902	42804958	E068	4611
chr3	42806057	42806145	E068	5766
chr3	42837112	42837614	E068	36821
chr3	42843603	42843653	E068	43312
chr3	42753058	42753252	E069	-47039
chr3	42753474	42753613	E069	-46678
chr3	42766734	42766849	E069	-33442
chr3	42769682	42769826	E069	-30465
chr3	42770346	42770400	E069	-29891
chr3	42770515	42770617	E069	-29674
chr3	42770964	42771019	E069	-29272
chr3	42771339	42771539	E069	-28752
chr3	42771886	42772037	E069	-28254
chr3	42773656	42773953	E069	-26338
chr3	42775654	42775825	E069	-24466
chr3	42775976	42776036	E069	-24255
chr3	42776218	42776268	E069	-24023
chr3	42776721	42776845	E069	-23446
chr3	42777037	42777089	E069	-23202
chr3	42777418	42777524	E069	-22767
chr3	42777595	42777886	E069	-22405
chr3	42777972	42778037	E069	-22254
chr3	42778078	42778128	E069	-22163
chr3	42780955	42781012	E069	-19279
chr3	42781287	42781702	E069	-18589
chr3	42781774	42781934	E069	-18357
chr3	42782136	42782306	E069	-17985
chr3	42785318	42785585	E069	-14706
chr3	42785598	42786099	E069	-14192
chr3	42786553	42786603	E069	-13688
chr3	42786895	42787106	E069	-13185
chr3	42787158	42787302	E069	-12989
chr3	42787336	42787449	E069	-12842
chr3	42787649	42787913	E069	-12378
chr3	42788030	42788394	E069	-11897
chr3	42788584	42788669	E069	-11622
chr3	42788837	42788877	E069	-11414
chr3	42789019	42789149	E069	-11142
chr3	42789153	42789270	E069	-11021
chr3	42789412	42789462	E069	-10829
chr3	42789955	42790015	E069	-10276
chr3	42790187	42790280	E069	-10011
chr3	42791227	42791864	E069	-8427
chr3	42793158	42793269	E069	-7022
chr3	42793369	42793495	E069	-6796
chr3	42802890	42803277	E069	2599
chr3	42803621	42803752	E069	3330
chr3	42803782	42803898	E069	3491
chr3	42804579	42804793	E069	4288
chr3	42804902	42804958	E069	4611
chr3	42805287	42805337	E069	4996
chr3	42837112	42837614	E069	36821
chr3	42843603	42843653	E069	43312
chr3	42773656	42773953	E070	-26338
chr3	42774508	42774760	E070	-25531
chr3	42775003	42775478	E070	-24813
chr3	42787158	42787302	E070	-12989
chr3	42787336	42787449	E070	-12842
chr3	42787649	42787913	E070	-12378
chr3	42788030	42788394	E070	-11897
chr3	42789019	42789149	E070	-11142
chr3	42789153	42789270	E070	-11021
chr3	42789412	42789462	E070	-10829
chr3	42813864	42813988	E070	13573
chr3	42841873	42841953	E070	41582
chr3	42753058	42753252	E071	-47039
chr3	42753474	42753613	E071	-46678
chr3	42763276	42763490	E071	-36801
chr3	42764594	42764644	E071	-35647
chr3	42764693	42764931	E071	-35360
chr3	42766734	42766849	E071	-33442
chr3	42767014	42767343	E071	-32948
chr3	42769682	42769826	E071	-30465
chr3	42770346	42770400	E071	-29891
chr3	42770515	42770617	E071	-29674
chr3	42770964	42771019	E071	-29272
chr3	42771339	42771539	E071	-28752
chr3	42771886	42772037	E071	-28254
chr3	42775654	42775825	E071	-24466
chr3	42775976	42776036	E071	-24255
chr3	42776218	42776268	E071	-24023
chr3	42776721	42776845	E071	-23446
chr3	42777037	42777089	E071	-23202
chr3	42777418	42777524	E071	-22767
chr3	42780955	42781012	E071	-19279
chr3	42781287	42781702	E071	-18589
chr3	42781774	42781934	E071	-18357
chr3	42782136	42782306	E071	-17985
chr3	42782725	42782857	E071	-17434
chr3	42782876	42782926	E071	-17365
chr3	42783347	42783453	E071	-16838
chr3	42785318	42785585	E071	-14706
chr3	42785598	42786099	E071	-14192
chr3	42786553	42786603	E071	-13688
chr3	42786895	42787106	E071	-13185
chr3	42787158	42787302	E071	-12989
chr3	42787336	42787449	E071	-12842
chr3	42787649	42787913	E071	-12378
chr3	42788030	42788394	E071	-11897
chr3	42788584	42788669	E071	-11622
chr3	42788837	42788877	E071	-11414
chr3	42789019	42789149	E071	-11142
chr3	42789153	42789270	E071	-11021
chr3	42789412	42789462	E071	-10829
chr3	42789955	42790015	E071	-10276
chr3	42790187	42790280	E071	-10011
chr3	42791227	42791864	E071	-8427
chr3	42793158	42793269	E071	-7022
chr3	42793369	42793495	E071	-6796
chr3	42802890	42803277	E071	2599
chr3	42803621	42803752	E071	3330
chr3	42803782	42803898	E071	3491
chr3	42804579	42804793	E071	4288
chr3	42837112	42837614	E071	36821
chr3	42841135	42841185	E071	40844
chr3	42841464	42841603	E071	41173
chr3	42753058	42753252	E072	-47039
chr3	42753474	42753613	E072	-46678
chr3	42760526	42760794	E072	-39497
chr3	42763276	42763490	E072	-36801
chr3	42766734	42766849	E072	-33442
chr3	42767014	42767343	E072	-32948
chr3	42769682	42769826	E072	-30465
chr3	42770346	42770400	E072	-29891
chr3	42770515	42770617	E072	-29674
chr3	42770964	42771019	E072	-29272
chr3	42771339	42771539	E072	-28752
chr3	42771886	42772037	E072	-28254
chr3	42773656	42773953	E072	-26338
chr3	42775003	42775478	E072	-24813
chr3	42775654	42775825	E072	-24466
chr3	42775976	42776036	E072	-24255
chr3	42776218	42776268	E072	-24023
chr3	42776721	42776845	E072	-23446
chr3	42777037	42777089	E072	-23202
chr3	42777418	42777524	E072	-22767
chr3	42777595	42777886	E072	-22405
chr3	42777972	42778037	E072	-22254
chr3	42778078	42778128	E072	-22163
chr3	42780955	42781012	E072	-19279
chr3	42781287	42781702	E072	-18589
chr3	42781774	42781934	E072	-18357
chr3	42782136	42782306	E072	-17985
chr3	42783347	42783453	E072	-16838
chr3	42785318	42785585	E072	-14706
chr3	42785598	42786099	E072	-14192
chr3	42786553	42786603	E072	-13688
chr3	42786895	42787106	E072	-13185
chr3	42787158	42787302	E072	-12989
chr3	42787336	42787449	E072	-12842
chr3	42787649	42787913	E072	-12378
chr3	42788030	42788394	E072	-11897
chr3	42788584	42788669	E072	-11622
chr3	42788837	42788877	E072	-11414
chr3	42789019	42789149	E072	-11142
chr3	42789153	42789270	E072	-11021
chr3	42789412	42789462	E072	-10829
chr3	42789955	42790015	E072	-10276
chr3	42790187	42790280	E072	-10011
chr3	42791227	42791864	E072	-8427
chr3	42793369	42793495	E072	-6796
chr3	42802890	42803277	E072	2599
chr3	42804579	42804793	E072	4288
chr3	42804902	42804958	E072	4611
chr3	42805287	42805337	E072	4996
chr3	42764693	42764931	E073	-35360
chr3	42766734	42766849	E073	-33442
chr3	42767014	42767343	E073	-32948
chr3	42769682	42769826	E073	-30465
chr3	42770346	42770400	E073	-29891
chr3	42770515	42770617	E073	-29674
chr3	42770964	42771019	E073	-29272
chr3	42771339	42771539	E073	-28752
chr3	42771886	42772037	E073	-28254
chr3	42773656	42773953	E073	-26338
chr3	42774508	42774760	E073	-25531
chr3	42775003	42775478	E073	-24813
chr3	42775654	42775825	E073	-24466
chr3	42775976	42776036	E073	-24255
chr3	42776218	42776268	E073	-24023
chr3	42776721	42776845	E073	-23446
chr3	42777037	42777089	E073	-23202
chr3	42780955	42781012	E073	-19279
chr3	42781287	42781702	E073	-18589
chr3	42781774	42781934	E073	-18357
chr3	42782136	42782306	E073	-17985
chr3	42782725	42782857	E073	-17434
chr3	42782876	42782926	E073	-17365
chr3	42783347	42783453	E073	-16838
chr3	42785318	42785585	E073	-14706
chr3	42785598	42786099	E073	-14192
chr3	42786553	42786603	E073	-13688
chr3	42786895	42787106	E073	-13185
chr3	42787158	42787302	E073	-12989
chr3	42787336	42787449	E073	-12842
chr3	42787649	42787913	E073	-12378
chr3	42788030	42788394	E073	-11897
chr3	42788584	42788669	E073	-11622
chr3	42790187	42790280	E073	-10011
chr3	42791227	42791864	E073	-8427
chr3	42793158	42793269	E073	-7022
chr3	42793369	42793495	E073	-6796
chr3	42813864	42813988	E073	13573
chr3	42832482	42832572	E073	32191
chr3	42842694	42842794	E073	42403
chr3	42843603	42843653	E073	43312
chr3	42753058	42753252	E074	-47039
chr3	42753474	42753613	E074	-46678
chr3	42760526	42760794	E074	-39497
chr3	42761696	42761870	E074	-38421
chr3	42763276	42763490	E074	-36801
chr3	42764594	42764644	E074	-35647
chr3	42764693	42764931	E074	-35360
chr3	42766734	42766849	E074	-33442
chr3	42767014	42767343	E074	-32948
chr3	42769682	42769826	E074	-30465
chr3	42770346	42770400	E074	-29891
chr3	42770515	42770617	E074	-29674
chr3	42770964	42771019	E074	-29272
chr3	42771339	42771539	E074	-28752
chr3	42771886	42772037	E074	-28254
chr3	42773656	42773953	E074	-26338
chr3	42775003	42775478	E074	-24813
chr3	42775654	42775825	E074	-24466
chr3	42775976	42776036	E074	-24255
chr3	42776218	42776268	E074	-24023
chr3	42776721	42776845	E074	-23446
chr3	42777037	42777089	E074	-23202
chr3	42777418	42777524	E074	-22767
chr3	42777595	42777886	E074	-22405
chr3	42777972	42778037	E074	-22254
chr3	42778078	42778128	E074	-22163
chr3	42780955	42781012	E074	-19279
chr3	42781287	42781702	E074	-18589
chr3	42781774	42781934	E074	-18357
chr3	42782136	42782306	E074	-17985
chr3	42782725	42782857	E074	-17434
chr3	42782876	42782926	E074	-17365
chr3	42783347	42783453	E074	-16838
chr3	42785318	42785585	E074	-14706
chr3	42785598	42786099	E074	-14192
chr3	42786553	42786603	E074	-13688
chr3	42786895	42787106	E074	-13185
chr3	42787158	42787302	E074	-12989
chr3	42787336	42787449	E074	-12842
chr3	42787649	42787913	E074	-12378
chr3	42788030	42788394	E074	-11897
chr3	42788584	42788669	E074	-11622
chr3	42788837	42788877	E074	-11414
chr3	42789019	42789149	E074	-11142
chr3	42789153	42789270	E074	-11021
chr3	42789412	42789462	E074	-10829
chr3	42789955	42790015	E074	-10276
chr3	42790187	42790280	E074	-10011
chr3	42791227	42791864	E074	-8427
chr3	42793158	42793269	E074	-7022
chr3	42793369	42793495	E074	-6796
chr3	42802890	42803277	E074	2599
chr3	42803621	42803752	E074	3330
chr3	42803782	42803898	E074	3491
chr3	42804579	42804793	E074	4288
chr3	42804902	42804958	E074	4611
chr3	42805287	42805337	E074	4996
chr3	42805451	42805501	E074	5160
chr3	42805704	42805863	E074	5413
chr3	42806057	42806145	E074	5766
chr3	42822048	42822246	E074	21757
chr3	42822279	42822930	E074	21988
chr3	42841464	42841603	E074	41173
chr3	42841873	42841953	E074	41582
chr3	42842694	42842794	E074	42403
chr3	42787336	42787449	E081	-12842
chr3	42787649	42787913	E081	-12378
chr3	42788030	42788394	E081	-11897
chr3	42788584	42788669	E081	-11622
chr3	42822279	42822930	E081	21988
chr3	42822942	42822993	E081	22651
chr3	42843603	42843653	E081	43312
chr3	42787158	42787302	E082	-12989
chr3	42787336	42787449	E082	-12842
chr3	42787649	42787913	E082	-12378
chr3	42788030	42788394	E082	-11897
chr3	42788584	42788669	E082	-11622
chr3	42788837	42788877	E082	-11414
chr3	42843603	42843653	E082	43312

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	42814014	42815164	E067	13723
chr3	42844583	42847184	E067	44292
chr3	42814014	42815164	E068	13723
chr3	42844583	42847184	E068	44292
chr3	42814014	42815164	E069	13723
chr3	42844583	42847184	E069	44292
chr3	42814014	42815164	E070	13723
chr3	42844583	42847184	E070	44292
chr3	42814014	42815164	E071	13723
chr3	42844583	42847184	E071	44292
chr3	42814014	42815164	E072	13723
chr3	42844583	42847184	E072	44292
chr3	42814014	42815164	E073	13723
chr3	42844583	42847184	E073	44292
chr3	42814014	42815164	E074	13723
chr3	42844583	42847184	E074	44292
chr3	42814014	42815164	E081	13723
chr3	42844583	42847184	E081	44292
chr3	42814014	42815164	E082	13723
chr3	42844583	42847184	E082	44292