rs10848190

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RIMBP2 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0347 (10413/29930,GnomAD)
T=0337 (9830/29118,TOPMED)
T=0338 (1693/5008,1000G)
T=0376 (1450/3854,ALSPAC)
T=0380 (1408/3708,TWINSUK)

Position: chr12:130717490 (GRCh38.p7) (12q24.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 77 Enhancers around

Promoter: 46 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.130717490C>T
GRCh37.p13 chr 12	NC_000012.11:g.131202035C>T

Gene: RIMBP2, RIMS binding protein 2(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
RIMBP2 transcript	NM_015347.4:c.	N/A	N/A
RIMBP2 transcript variant X3	XM_011538104.2:c.	N/A	Upstream Transcript Variant
RIMBP2 transcript variant X8	XM_017019107.1:c.	N/A	Upstream Transcript Variant
RIMBP2 transcript variant X11	XM_017019110.1:c.	N/A	Upstream Transcript Variant
RIMBP2 transcript variant X12	XM_017019111.1:c.	N/A	Upstream Transcript Variant
RIMBP2 transcript variant X1	XM_011538102.1:c.	N/A	N/A
RIMBP2 transcript variant X2	XM_011538103.2:c.	N/A	N/A
RIMBP2 transcript variant X5	XM_011538105.2:c.	N/A	N/A
RIMBP2 transcript variant X6	XM_011538106.2:c.	N/A	N/A
RIMBP2 transcript variant X13	XM_011538107.2:c.	N/A	N/A
RIMBP2 transcript variant X14	XM_011538108.2:c.	N/A	N/A
RIMBP2 transcript variant X4	XM_017019105.1:c.	N/A	N/A
RIMBP2 transcript variant X7	XM_017019106.1:c.	N/A	N/A
RIMBP2 transcript variant X9	XM_017019108.1:c.	N/A	N/A
RIMBP2 transcript variant X10	XM_017019109.1:c.	N/A	N/A
RIMBP2 transcript variant X15	XM_017019112.1:c.	N/A	N/A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.722	T=0.278
1000Genomes	American	Sub	694	C=0.670	T=0.330
1000Genomes	East Asian	Sub	1008	C=0.601	T=0.399
1000Genomes	Europe	Sub	1006	C=0.617	T=0.383
1000Genomes	Global	Study-wide	5008	C=0.662	T=0.338
1000Genomes	South Asian	Sub	978	C=0.690	T=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.624	T=0.376
The Genome Aggregation Database	African	Sub	8722	C=0.716	T=0.284
The Genome Aggregation Database	American	Sub	838	C=0.700	T=0.300
The Genome Aggregation Database	East Asian	Sub	1606	C=0.616	T=0.384
The Genome Aggregation Database	Europe	Sub	18462	C=0.624	T=0.375
The Genome Aggregation Database	Global	Study-wide	29930	C=0.652	T=0.347
The Genome Aggregation Database	Other	Sub	302	C=0.560	T=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.662	T=0.337
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.620	T=0.380

PMID	Title	Author	Journal
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs10848190	5.43E-06	alcohol dependence	23691058

eQTL of rs10848190 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 rs10848190 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 )
chr12	131186144	131186212	E067	-15823
chr12	131186573	131186644	E067	-15391
chr12	131232445	131233003	E067	30410
chr12	131155991	131156041	E069	-45994
chr12	131156163	131156345	E069	-45690
chr12	131155749	131155831	E070	-46204
chr12	131155991	131156041	E070	-45994
chr12	131156163	131156345	E070	-45690
chr12	131156418	131157537	E070	-44498
chr12	131157686	131158037	E070	-43998
chr12	131172179	131172256	E070	-29779
chr12	131176666	131176716	E070	-25319
chr12	131190184	131190348	E070	-11687
chr12	131190403	131190488	E070	-11547
chr12	131190588	131190642	E070	-11393
chr12	131246083	131246234	E070	44048
chr12	131246254	131246927	E070	44219
chr12	131246939	131247023	E071	44904
chr12	131156418	131157537	E072	-44498
chr12	131157686	131158037	E072	-43998
chr12	131232445	131233003	E072	30410
chr12	131246083	131246234	E072	44048
chr12	131246254	131246927	E072	44219
chr12	131189674	131189786	E073	-12249
chr12	131189852	131189927	E073	-12108
chr12	131189991	131190088	E073	-11947
chr12	131190184	131190348	E073	-11687
chr12	131197676	131197726	E073	-4309
chr12	131152067	131152204	E081	-49831
chr12	131152308	131152358	E081	-49677
chr12	131153462	131153516	E081	-48519
chr12	131153735	131153785	E081	-48250
chr12	131155585	131155635	E081	-46400
chr12	131155749	131155831	E081	-46204
chr12	131155991	131156041	E081	-45994
chr12	131156163	131156345	E081	-45690
chr12	131156418	131157537	E081	-44498
chr12	131157686	131158037	E081	-43998
chr12	131165022	131165076	E081	-36959
chr12	131165095	131165178	E081	-36857
chr12	131165346	131165396	E081	-36639
chr12	131165622	131165723	E081	-36312
chr12	131169978	131170054	E081	-31981
chr12	131170120	131170228	E081	-31807
chr12	131170282	131170322	E081	-31713
chr12	131170355	131170415	E081	-31620
chr12	131170455	131170505	E081	-31530
chr12	131172179	131172256	E081	-29779
chr12	131172363	131172573	E081	-29462
chr12	131173429	131173535	E081	-28500
chr12	131186144	131186212	E081	-15823
chr12	131187988	131188053	E081	-13982
chr12	131188124	131188250	E081	-13785
chr12	131188284	131188358	E081	-13677
chr12	131189852	131189927	E081	-12108
chr12	131189991	131190088	E081	-11947
chr12	131190184	131190348	E081	-11687
chr12	131190403	131190488	E081	-11547
chr12	131190588	131190642	E081	-11393
chr12	131191223	131191284	E081	-10751
chr12	131191361	131191424	E081	-10611
chr12	131197367	131197466	E081	-4569
chr12	131197676	131197726	E081	-4309
chr12	131214383	131214433	E081	12348
chr12	131214601	131214694	E081	12566
chr12	131214706	131214804	E081	12671
chr12	131155991	131156041	E082	-45994
chr12	131156163	131156345	E082	-45690
chr12	131156418	131157537	E082	-44498
chr12	131157686	131158037	E082	-43998
chr12	131170120	131170228	E082	-31807
chr12	131170282	131170322	E082	-31713
chr12	131170355	131170415	E082	-31620
chr12	131170455	131170505	E082	-31530
chr12	131172179	131172256	E082	-29779
chr12	131172363	131172573	E082	-29462
chr12	131174335	131174394	E082	-27641

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	131197967	131198945	E067	-3090
chr12	131198946	131199027	E067	-3008
chr12	131199304	131199731	E067	-2304
chr12	131199745	131199771	E067	-2264
chr12	131199780	131199845	E067	-2190
chr12	131199860	131200341	E067	-1694
chr12	131200350	131200461	E067	-1574
chr12	131200476	131201798	E067	-237
chr12	131197967	131198945	E068	-3090
chr12	131198946	131199027	E068	-3008
chr12	131199304	131199731	E068	-2304
chr12	131199745	131199771	E068	-2264
chr12	131199780	131199845	E068	-2190
chr12	131199860	131200341	E068	-1694
chr12	131200350	131200461	E068	-1574
chr12	131200476	131201798	E068	-237
chr12	131197967	131198945	E069	-3090
chr12	131198946	131199027	E069	-3008
chr12	131200350	131200461	E069	-1574
chr12	131200476	131201798	E069	-237
chr12	131197967	131198945	E071	-3090
chr12	131197967	131198945	E072	-3090
chr12	131198946	131199027	E072	-3008
chr12	131199304	131199731	E072	-2304
chr12	131199745	131199771	E072	-2264
chr12	131199780	131199845	E072	-2190
chr12	131199860	131200341	E072	-1694
chr12	131200350	131200461	E072	-1574
chr12	131200476	131201798	E072	-237
chr12	131197967	131198945	E073	-3090
chr12	131198946	131199027	E073	-3008
chr12	131199304	131199731	E073	-2304
chr12	131199745	131199771	E073	-2264
chr12	131199780	131199845	E073	-2190
chr12	131199860	131200341	E073	-1694
chr12	131200350	131200461	E073	-1574
chr12	131200476	131201798	E073	-237
chr12	131199860	131200341	E074	-1694
chr12	131200350	131200461	E074	-1574
chr12	131200476	131201798	E074	-237
chr12	131200350	131200461	E081	-1574
chr12	131200476	131201798	E081	-237
chr12	131198946	131199027	E082	-3008
chr12	131199860	131200341	E082	-1694
chr12	131200350	131200461	E082	-1574
chr12	131200476	131201798	E082	-237