rs17290977

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ST18 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0221 (6640/29958,GnomAD)
T=0239 (6981/29118,TOPMED)
T=0198 (993/5008,1000G)
T=0197 (758/3854,ALSPAC)
T=0195 (724/3708,TWINSUK)

Position: chr8:52156360 (GRCh38.p7) (8q11.23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 171 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.52156360C>T
GRCh37.p13 chr 8	NC_000008.10:g.53068920C>T

Gene: ST18, suppression of tumorigenicity 18, zinc finger(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ST18 transcript variant 1	NM_014682.2:c.	N/A	Intron Variant
ST18 transcript variant X9	XM_006716487.1:c.	N/A	Intron Variant
ST18 transcript variant X2	XM_011517629.1:c.	N/A	Intron Variant
ST18 transcript variant X12	XM_011517631.1:c.	N/A	Intron Variant
ST18 transcript variant X3	XM_011517632.1:c.	N/A	Intron Variant
ST18 transcript variant X4	XM_011517633.1:c.	N/A	Intron Variant
ST18 transcript variant X11	XM_011517634.1:c.	N/A	Intron Variant
ST18 transcript variant X2	XM_011517635.1:c.	N/A	Intron Variant
ST18 transcript variant X7	XM_011517636.2:c.	N/A	Intron Variant
ST18 transcript variant X5	XM_011517637.1:c.	N/A	Intron Variant
ST18 transcript variant X33	XM_011517638.2:c.	N/A	Intron Variant
ST18 transcript variant X6	XM_011517641.1:c.	N/A	Intron Variant
ST18 transcript variant X7	XM_011517642.1:c.	N/A	Intron Variant
ST18 transcript variant X1	XM_017014047.1:c.	N/A	Intron Variant
ST18 transcript variant X5	XM_017014048.1:c.	N/A	Intron Variant
ST18 transcript variant X6	XM_017014049.1:c.	N/A	Intron Variant
ST18 transcript variant X8	XM_017014050.1:c.	N/A	Intron Variant
ST18 transcript variant X10	XM_017014051.1:c.	N/A	Intron Variant
ST18 transcript variant X13	XM_017014052.1:c.	N/A	Intron Variant
ST18 transcript variant X14	XM_017014053.1:c.	N/A	Intron Variant
ST18 transcript variant X15	XM_017014054.1:c.	N/A	Intron Variant
ST18 transcript variant X16	XM_017014055.1:c.	N/A	Intron Variant
ST18 transcript variant X17	XM_017014056.1:c.	N/A	Intron Variant
ST18 transcript variant X18	XM_017014057.1:c.	N/A	Intron Variant
ST18 transcript variant X1	XM_017014058.1:c.	N/A	Intron Variant
ST18 transcript variant X20	XM_017014059.1:c.	N/A	Intron Variant
ST18 transcript variant X21	XM_017014060.1:c.	N/A	Intron Variant
ST18 transcript variant X22	XM_017014061.1:c.	N/A	Intron Variant
ST18 transcript variant X23	XM_017014062.1:c.	N/A	Intron Variant
ST18 transcript variant X24	XM_017014063.1:c.	N/A	Intron Variant
ST18 transcript variant X25	XM_017014064.1:c.	N/A	Intron Variant
ST18 transcript variant X27	XM_017014065.1:c.	N/A	Intron Variant
ST18 transcript variant X28	XM_017014066.1:c.	N/A	Intron Variant
ST18 transcript variant X29	XM_017014067.1:c.	N/A	Intron Variant
ST18 transcript variant X30	XM_017014068.1:c.	N/A	Intron Variant
ST18 transcript variant X32	XM_017014069.1:c.	N/A	Intron Variant
ST18 transcript variant X34	XM_017014070.1:c.	N/A	Intron Variant
ST18 transcript variant X35	XM_017014071.1:c.	N/A	Intron Variant
ST18 transcript variant X36	XM_017014072.1:c.	N/A	Intron Variant
ST18 transcript variant X37	XM_017014073.1:c.	N/A	Intron Variant
ST18 transcript variant X38	XM_017014074.1:c.	N/A	Intron Variant
ST18 transcript variant X40	XM_017014075.1:c.	N/A	Intron Variant
ST18 transcript variant X41	XM_017014076.1:c.	N/A	Intron Variant
ST18 transcript variant X42	XM_017014077.1:c.	N/A	Intron Variant
ST18 transcript variant X43	XM_017014078.1:c.	N/A	Intron Variant
ST18 transcript variant X44	XM_017014079.1:c.	N/A	Intron Variant
ST18 transcript variant X45	XM_017014080.1:c.	N/A	Intron Variant
ST18 transcript variant X47	XM_017014081.1:c.	N/A	Intron Variant
ST18 transcript variant X48	XM_017014082.1:c.	N/A	Intron Variant
ST18 transcript variant X49	XM_017014083.1:c.	N/A	Intron Variant
ST18 transcript variant X50	XM_017014084.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.698	T=0.302
1000Genomes	American	Sub	694	C=0.870	T=0.130
1000Genomes	East Asian	Sub	1008	C=0.887	T=0.113
1000Genomes	Europe	Sub	1006	C=0.809	T=0.191
1000Genomes	Global	Study-wide	5008	C=0.802	T=0.198
1000Genomes	South Asian	Sub	978	C=0.800	T=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.803	T=0.197
The Genome Aggregation Database	African	Sub	8716	C=0.709	T=0.291
The Genome Aggregation Database	American	Sub	838	C=0.880	T=0.120
The Genome Aggregation Database	East Asian	Sub	1616	C=0.867	T=0.133
The Genome Aggregation Database	Europe	Sub	18486	C=0.799	T=0.200
The Genome Aggregation Database	Global	Study-wide	29958	C=0.778	T=0.221
The Genome Aggregation Database	Other	Sub	302	C=0.730	T=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.760	T=0.239
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.805	T=0.195

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
rs17290977	0.00012	alcohol dependence	20201924

eQTL of rs17290977 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 rs17290977 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 )
chr8	53059302	53059786	E067	-9134
chr8	53059920	53060030	E067	-8890
chr8	53063086	53063276	E067	-5644
chr8	53063401	53063553	E067	-5367
chr8	53063592	53063812	E067	-5108
chr8	53063818	53064047	E067	-4873
chr8	53064111	53064283	E067	-4637
chr8	53064362	53064568	E067	-4352
chr8	53064640	53064832	E067	-4088
chr8	53064863	53064976	E067	-3944
chr8	53085983	53086111	E067	17063
chr8	53087780	53087831	E067	18860
chr8	53087922	53088001	E067	19002
chr8	53088158	53088198	E067	19238
chr8	53106798	53106904	E067	37878
chr8	53107057	53107107	E067	38137
chr8	53085983	53086111	E068	17063
chr8	53086224	53086718	E068	17304
chr8	53086891	53086945	E068	17971
chr8	53087026	53087268	E068	18106
chr8	53087308	53087466	E068	18388
chr8	53087780	53087831	E068	18860
chr8	53087922	53088001	E068	19002
chr8	53088158	53088198	E068	19238
chr8	53037398	53037448	E069	-31472
chr8	53037518	53037679	E069	-31241
chr8	53085983	53086111	E069	17063
chr8	53086224	53086718	E069	17304
chr8	53086891	53086945	E069	17971
chr8	53087026	53087268	E069	18106
chr8	53087308	53087466	E069	18388
chr8	53087780	53087831	E069	18860
chr8	53087922	53088001	E069	19002
chr8	53088158	53088198	E069	19238
chr8	53019609	53019663	E070	-49257
chr8	53024773	53025358	E070	-43562
chr8	53058260	53058310	E070	-10610
chr8	53058643	53058693	E070	-10227
chr8	53058723	53058792	E070	-10128
chr8	53058867	53059256	E070	-9664
chr8	53062899	53063077	E070	-5843
chr8	53063086	53063276	E070	-5644
chr8	53063401	53063553	E070	-5367
chr8	53063592	53063812	E070	-5108
chr8	53063818	53064047	E070	-4873
chr8	53064111	53064283	E070	-4637
chr8	53064362	53064568	E070	-4352
chr8	53064640	53064832	E070	-4088
chr8	53064863	53064976	E070	-3944
chr8	53080605	53080655	E070	11685
chr8	53080923	53080984	E070	12003
chr8	53081096	53081179	E070	12176
chr8	53083190	53083240	E070	14270
chr8	53085666	53085727	E070	16746
chr8	53086224	53086718	E070	17304
chr8	53087922	53088001	E070	19002
chr8	53088158	53088198	E070	19238
chr8	53096656	53096753	E070	27736
chr8	53109067	53109117	E070	40147
chr8	53109455	53109505	E070	40535
chr8	53109675	53109725	E070	40755
chr8	53110332	53110386	E070	41412
chr8	53111422	53111524	E070	42502
chr8	53058643	53058693	E071	-10227
chr8	53058723	53058792	E071	-10128
chr8	53062198	53062279	E071	-6641
chr8	53062357	53062423	E071	-6497
chr8	53062523	53062633	E071	-6287
chr8	53062899	53063077	E071	-5843
chr8	53063086	53063276	E071	-5644
chr8	53063401	53063553	E071	-5367
chr8	53063592	53063812	E071	-5108
chr8	53063818	53064047	E071	-4873
chr8	53064111	53064283	E071	-4637
chr8	53064362	53064568	E071	-4352
chr8	53064640	53064832	E071	-4088
chr8	53064863	53064976	E071	-3944
chr8	53085983	53086111	E071	17063
chr8	53086224	53086718	E071	17304
chr8	53086891	53086945	E071	17971
chr8	53087026	53087268	E071	18106
chr8	53087308	53087466	E071	18388
chr8	53087780	53087831	E071	18860
chr8	53087922	53088001	E071	19002
chr8	53088158	53088198	E071	19238
chr8	53019609	53019663	E072	-49257
chr8	53062523	53062633	E072	-6287
chr8	53062899	53063077	E072	-5843
chr8	53063086	53063276	E072	-5644
chr8	53063401	53063553	E072	-5367
chr8	53063592	53063812	E072	-5108
chr8	53063818	53064047	E072	-4873
chr8	53064111	53064283	E072	-4637
chr8	53064362	53064568	E072	-4352
chr8	53064640	53064832	E072	-4088
chr8	53064863	53064976	E072	-3944
chr8	53065794	53065854	E072	-3066
chr8	53065874	53065924	E072	-2996
chr8	53085983	53086111	E072	17063
chr8	53086224	53086718	E072	17304
chr8	53086891	53086945	E072	17971
chr8	53087026	53087268	E072	18106
chr8	53087308	53087466	E072	18388
chr8	53087780	53087831	E072	18860
chr8	53087922	53088001	E072	19002
chr8	53088158	53088198	E072	19238
chr8	53089089	53089139	E072	20169
chr8	53096656	53096753	E072	27736
chr8	53106798	53106904	E072	37878
chr8	53107057	53107107	E072	38137
chr8	53107310	53107383	E072	38390
chr8	53085983	53086111	E073	17063
chr8	53086224	53086718	E073	17304
chr8	53087780	53087831	E073	18860
chr8	53087922	53088001	E073	19002
chr8	53088158	53088198	E073	19238
chr8	53019609	53019663	E074	-49257
chr8	53020298	53020380	E074	-48540
chr8	53020597	53020669	E074	-48251
chr8	53058643	53058693	E074	-10227
chr8	53058723	53058792	E074	-10128
chr8	53060255	53060430	E074	-8490
chr8	53060618	53060727	E074	-8193
chr8	53060820	53060874	E074	-8046
chr8	53060999	53061049	E074	-7871
chr8	53061121	53061193	E074	-7727
chr8	53061331	53061381	E074	-7539
chr8	53061578	53062032	E074	-6888
chr8	53062198	53062279	E074	-6641
chr8	53062357	53062423	E074	-6497
chr8	53063086	53063276	E074	-5644
chr8	53063401	53063553	E074	-5367
chr8	53063592	53063812	E074	-5108
chr8	53063818	53064047	E074	-4873
chr8	53064111	53064283	E074	-4637
chr8	53064362	53064568	E074	-4352
chr8	53064640	53064832	E074	-4088
chr8	53064863	53064976	E074	-3944
chr8	53085983	53086111	E074	17063
chr8	53086224	53086718	E074	17304
chr8	53086891	53086945	E074	17971
chr8	53087026	53087268	E074	18106
chr8	53087308	53087466	E074	18388
chr8	53087780	53087831	E074	18860
chr8	53087922	53088001	E074	19002
chr8	53088158	53088198	E074	19238
chr8	53062899	53063077	E081	-5843
chr8	53063086	53063276	E081	-5644
chr8	53063401	53063553	E081	-5367
chr8	53063592	53063812	E081	-5108
chr8	53063818	53064047	E081	-4873
chr8	53064111	53064283	E081	-4637
chr8	53064362	53064568	E081	-4352
chr8	53064640	53064832	E081	-4088
chr8	53064863	53064976	E081	-3944
chr8	53066670	53066720	E081	-2200
chr8	53066770	53067130	E081	-1790
chr8	53069266	53069316	E081	346
chr8	53087780	53087831	E081	18860
chr8	53087922	53088001	E081	19002
chr8	53088158	53088198	E081	19238
chr8	53062523	53062633	E082	-6287
chr8	53063592	53063812	E082	-5108
chr8	53063818	53064047	E082	-4873
chr8	53064111	53064283	E082	-4637
chr8	53064362	53064568	E082	-4352
chr8	53064640	53064832	E082	-4088
chr8	53085983	53086111	E082	17063
chr8	53086224	53086718	E082	17304
chr8	53086891	53086945	E082	17971
chr8	53087026	53087268	E082	18106