rs12610873

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ZSWIM4 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0340 (10150/29802,GnomAD)
A=0328 (9555/29118,TOPMED)
A=0318 (1595/5008,1000G)
A=0345 (1331/3854,ALSPAC)
A=0335 (1242/3708,TWINSUK)

Position: chr19:13831773 (GRCh38.p7) (19p13.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 51 Enhancers around

Promoter: 42 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.13831773G>A
GRCh37.p13 chr 19	NC_000019.9:g.13942587G>A

Gene: ZSWIM4, zinc finger SWIM-type containing 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZSWIM4 transcript	NM_023072.2:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X1	XM_017027153.1:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X2	XM_005260023.3:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X3	XM_017027154.1:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X4	XM_017027155.1:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X6	XM_017027156.1:c.	N/A	3 Prime UTR Variant
ZSWIM4 transcript variant X7	XM_017027157.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.631	A=0.369
1000Genomes	American	Sub	694	G=0.670	A=0.330
1000Genomes	East Asian	Sub	1008	G=0.763	A=0.237
1000Genomes	Europe	Sub	1006	G=0.681	A=0.319
1000Genomes	Global	Study-wide	5008	G=0.682	A=0.318
1000Genomes	South Asian	Sub	978	G=0.680	A=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.655	A=0.345
The Genome Aggregation Database	African	Sub	8674	G=0.605	A=0.395
The Genome Aggregation Database	American	Sub	838	G=0.770	A=0.230
The Genome Aggregation Database	East Asian	Sub	1608	G=0.776	A=0.224
The Genome Aggregation Database	Europe	Sub	18380	G=0.668	A=0.331
The Genome Aggregation Database	Global	Study-wide	29802	G=0.659	A=0.340
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.671	A=0.328
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.665	A=0.335

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
26446360	Mendelian randomization studies of biomarkers and type 2 diabetes.	Abbasi A	Endocr Connect

P-Value

SNP ID	p-value	Traits	Study
rs12610873	0.00012	alcohol dependence	20201924

eQTL of rs12610873 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 rs12610873 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg17299615	chr19:13944571		0.00661471384753702	2.1230e-17

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 )
chr19	13895717	13896355	E067	-46232
chr19	13933749	13934897	E067	-7690
chr19	13957137	13960530	E067	14550
chr19	13960743	13962734	E067	18156
chr19	13895305	13895401	E068	-47186
chr19	13895503	13895609	E068	-46978
chr19	13895717	13896355	E068	-46232
chr19	13932872	13933545	E068	-9042
chr19	13933749	13934897	E068	-7690
chr19	13946331	13948618	E068	3744
chr19	13960743	13962734	E068	18156
chr19	13990491	13990629	E068	47904
chr19	13895717	13896355	E069	-46232
chr19	13908127	13908408	E069	-34179
chr19	13932872	13933545	E069	-9042
chr19	13960743	13962734	E069	18156
chr19	13979624	13979796	E069	37037
chr19	13990491	13990629	E069	47904
chr19	13904570	13905058	E070	-37529
chr19	13908127	13908408	E070	-34179
chr19	13977987	13978037	E070	35400
chr19	13899037	13899200	E071	-43387
chr19	13899204	13899544	E071	-43043
chr19	13904570	13905058	E071	-37529
chr19	13908127	13908408	E071	-34179
chr19	13933749	13934897	E071	-7690
chr19	13957137	13960530	E071	14550
chr19	13960743	13962734	E071	18156
chr19	13990491	13990629	E071	47904
chr19	13898074	13898155	E072	-44432
chr19	13960743	13962734	E072	18156
chr19	13904570	13905058	E073	-37529
chr19	13933749	13934897	E073	-7690
chr19	13946331	13948618	E073	3744
chr19	13990491	13990629	E073	47904
chr19	13895503	13895609	E074	-46978
chr19	13895717	13896355	E074	-46232
chr19	13933749	13934897	E074	-7690
chr19	13946331	13948618	E074	3744
chr19	13956584	13956958	E074	13997
chr19	13957004	13957068	E074	14417
chr19	13957137	13960530	E074	14550
chr19	13960743	13962734	E074	18156
chr19	13990491	13990629	E074	47904
chr19	13904570	13905058	E081	-37529
chr19	13908127	13908408	E081	-34179
chr19	13957137	13960530	E081	14550
chr19	13960743	13962734	E081	18156
chr19	13984750	13984822	E081	42163
chr19	13984875	13984984	E081	42288
chr19	13904570	13905058	E082	-37529

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	13905161	13906894	E067	-35693
chr19	13948988	13956211	E067	6401
chr19	13976088	13976221	E067	33501
chr19	13976239	13976286	E067	33652
chr19	13976327	13977724	E067	33740
chr19	13905161	13906894	E068	-35693
chr19	13948988	13956211	E068	6401
chr19	13976327	13977724	E068	33740
chr19	13905161	13906894	E069	-35693
chr19	13948988	13956211	E069	6401
chr19	13976088	13976221	E069	33501
chr19	13976239	13976286	E069	33652
chr19	13976327	13977724	E069	33740
chr19	13905161	13906894	E070	-35693
chr19	13948988	13956211	E070	6401
chr19	13976088	13976221	E070	33501
chr19	13976239	13976286	E070	33652
chr19	13976327	13977724	E070	33740
chr19	13905161	13906894	E071	-35693
chr19	13948988	13956211	E071	6401
chr19	13976088	13976221	E071	33501
chr19	13976239	13976286	E071	33652
chr19	13976327	13977724	E071	33740
chr19	13905161	13906894	E072	-35693
chr19	13948988	13956211	E072	6401
chr19	13976088	13976221	E072	33501
chr19	13976239	13976286	E072	33652
chr19	13976327	13977724	E072	33740
chr19	13905161	13906894	E073	-35693
chr19	13948988	13956211	E073	6401
chr19	13976239	13976286	E073	33652
chr19	13976327	13977724	E073	33740
chr19	13905161	13906894	E074	-35693
chr19	13948988	13956211	E074	6401
chr19	13976327	13977724	E074	33740
chr19	13905161	13906894	E081	-35693
chr19	13976327	13977724	E081	33740
chr19	13905161	13906894	E082	-35693
chr19	13976088	13976221	E082	33501
chr19	13976239	13976286	E082	33652
chr19	13976327	13977724	E082	33740
chr19	13983221	13984529	E082	40634