rs13362120

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CAST : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0251 (7544/29966,GnomAD)
C=0245 (7138/29118,TOPMED)
C=0191 (956/5008,1000G)
C=0333 (1282/3854,ALSPAC)
C=0334 (1237/3708,TWINSUK)

Position: chr5:96735490 (GRCh38.p7) (5q15)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 78 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.96735490T>C
GRCh37.p13 chr 5	NC_000005.9:g.96071194T>C
CAST RefSeqGene	NG_029490.1:g.78454T>C

Gene: CAST, calpastatin(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAST transcript variant 6	NM_001042440.3:c.	N/A	Intron Variant
CAST transcript variant 16	NM_001190442.1:c.	N/A	Intron Variant
CAST transcript variant 13	NM_001284212.2:c.	N/A	Intron Variant
CAST transcript variant 14	NM_001284213.2:c.	N/A	Intron Variant
CAST transcript variant 2	NM_173060.3:c.	N/A	Intron Variant
CAST transcript variant 15	NR_104285.1:n.	N/A	Genic Upstream Transcript Variant
CAST transcript variant X1	XM_006714696.3:c.	N/A	Intron Variant
CAST transcript variant X2	XM_006714697.3:c.	N/A	Intron Variant
CAST transcript variant X3	XM_006714698.3:c.	N/A	Intron Variant
CAST transcript variant X6	XM_006714699.3:c.	N/A	Intron Variant
CAST transcript variant X7	XM_006714700.3:c.	N/A	Intron Variant
CAST transcript variant X10	XM_006714701.3:c.	N/A	Intron Variant
CAST transcript variant X17	XM_006714702.3:c.	N/A	Intron Variant
CAST transcript variant X18	XM_006714703.3:c.	N/A	Intron Variant
CAST transcript variant X19	XM_006714704.3:c.	N/A	Intron Variant
CAST transcript variant X21	XM_006714705.3:c.	N/A	Intron Variant
CAST transcript variant X27	XM_006714706.3:c.	N/A	Intron Variant
CAST transcript variant X32	XM_006714707.3:c.	N/A	Intron Variant
CAST transcript variant X34	XM_006714708.3:c.	N/A	Intron Variant
CAST transcript variant X36	XM_006714709.3:c.	N/A	Intron Variant
CAST transcript variant X39	XM_006714710.3:c.	N/A	Intron Variant
CAST transcript variant X41	XM_006714711.3:c.	N/A	Intron Variant
CAST transcript variant X43	XM_006714712.3:c.	N/A	Intron Variant
CAST transcript variant X13	XM_011543654.2:c.	N/A	Intron Variant
CAST transcript variant X15	XM_011543655.2:c.	N/A	Intron Variant
CAST transcript variant X22	XM_011543656.2:c.	N/A	Intron Variant
CAST transcript variant X29	XM_011543657.2:c.	N/A	Intron Variant
CAST transcript variant X42	XM_011543658.2:c.	N/A	Intron Variant
CAST transcript variant X4	XM_017009911.1:c.	N/A	Intron Variant
CAST transcript variant X5	XM_017009912.1:c.	N/A	Intron Variant
CAST transcript variant X8	XM_017009913.1:c.	N/A	Intron Variant
CAST transcript variant X9	XM_017009914.1:c.	N/A	Intron Variant
CAST transcript variant X11	XM_017009915.1:c.	N/A	Intron Variant
CAST transcript variant X12	XM_017009916.1:c.	N/A	Intron Variant
CAST transcript variant X14	XM_017009917.1:c.	N/A	Intron Variant
CAST transcript variant X16	XM_017009918.1:c.	N/A	Intron Variant
CAST transcript variant X20	XM_017009919.1:c.	N/A	Intron Variant
CAST transcript variant X23	XM_017009920.1:c.	N/A	Intron Variant
CAST transcript variant X24	XM_017009921.1:c.	N/A	Intron Variant
CAST transcript variant X25	XM_017009922.1:c.	N/A	Intron Variant
CAST transcript variant X26	XM_017009923.1:c.	N/A	Intron Variant
CAST transcript variant X28	XM_017009924.1:c.	N/A	Intron Variant
CAST transcript variant X30	XM_017009925.1:c.	N/A	Intron Variant
CAST transcript variant X31	XM_017009926.1:c.	N/A	Intron Variant
CAST transcript variant X33	XM_017009927.1:c.	N/A	Intron Variant
CAST transcript variant X35	XM_017009928.1:c.	N/A	Intron Variant
CAST transcript variant X37	XM_017009929.1:c.	N/A	Intron Variant
CAST transcript variant X38	XM_017009930.1:c.	N/A	Intron Variant
CAST transcript variant X40	XM_017009931.1:c.	N/A	Intron Variant
CAST transcript variant X44	XM_017009932.1:c.	N/A	Intron Variant
CAST transcript variant X45	XM_006714713.3:c.	N/A	Genic Upstream Transcript Variant
CAST transcript variant X46	XM_006714714.3:c.	N/A	Genic Upstream Transcript Variant
CAST transcript variant X47	XM_006714715.3:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.874	C=0.126
1000Genomes	American	Sub	694	T=0.770	C=0.230
1000Genomes	East Asian	Sub	1008	T=0.908	C=0.092
1000Genomes	Europe	Sub	1006	T=0.659	C=0.341
1000Genomes	Global	Study-wide	5008	T=0.809	C=0.191
1000Genomes	South Asian	Sub	978	T=0.800	C=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.667	C=0.333
The Genome Aggregation Database	African	Sub	8722	T=0.835	C=0.165
The Genome Aggregation Database	American	Sub	838	T=0.800	C=0.200
The Genome Aggregation Database	East Asian	Sub	1622	T=0.938	C=0.062
The Genome Aggregation Database	Europe	Sub	18484	T=0.689	C=0.310
The Genome Aggregation Database	Global	Study-wide	29966	T=0.748	C=0.251
The Genome Aggregation Database	Other	Sub	300	T=0.680	C=0.320
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.754	C=0.245
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.666	C=0.334

PMID	Title	Author	Journal
19680542	Tissue effect on genetic control of transcript isoform variation.	Kwan T	PLoS Genet
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry
20127884	SNPs in CAST are associated with Parkinson disease: a confirmation study.	Allen AS	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs13362120	9.65E-06	alcohol dependence	19581569

eQTL of rs13362120 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	2.2003e-7	-72609	Cerebellum
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	9.0222e-10	-72609	Hypothalamus
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	8.4153e-17	-72609	Cortex
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	3.7415e-13	-72609	Caudate_basal_ganglia
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	2.8458e-8	-72609	Brain_Spinal_cord_cervical
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	2.2688e-9	-72609	Hippocampus
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	6.0046e-11	-72609	Putamen_basal_ganglia
Chr5:96071194	ERAP1	ENSG00000164307.8	T>C	3.3654e-8	-72609	Amygdala

meQTL of rs13362120 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 )
chr5	96035202	96035657	E067	-35537
chr5	96047814	96048016	E067	-23178
chr5	96054311	96054811	E067	-16383
chr5	96057168	96057396	E067	-13798
chr5	96057486	96057616	E067	-13578
chr5	96062541	96062834	E067	-8360
chr5	96107308	96107358	E067	36114
chr5	96112149	96112193	E067	40955
chr5	96112320	96112697	E067	41126
chr5	96112777	96112843	E067	41583
chr5	96049884	96051216	E068	-19978
chr5	96051219	96051340	E068	-19854
chr5	96051381	96051510	E068	-19684
chr5	96051520	96051676	E068	-19518
chr5	96054311	96054811	E068	-16383
chr5	96057486	96057616	E068	-13578
chr5	96062541	96062834	E068	-8360
chr5	96087969	96088235	E068	16775
chr5	96088291	96088436	E068	17097
chr5	96107308	96107358	E068	36114
chr5	96108912	96108991	E068	37718
chr5	96111488	96111601	E068	40294
chr5	96112149	96112193	E068	40955
chr5	96035202	96035657	E069	-35537
chr5	96037654	96037838	E069	-33356
chr5	96047814	96048016	E069	-23178
chr5	96048118	96048172	E069	-23022
chr5	96048546	96048696	E069	-22498
chr5	96049884	96051216	E069	-19978
chr5	96051219	96051340	E069	-19854
chr5	96051381	96051510	E069	-19684
chr5	96051520	96051676	E069	-19518
chr5	96054311	96054811	E069	-16383
chr5	96112320	96112697	E069	41126
chr5	96112777	96112843	E069	41583
chr5	96112857	96112907	E069	41663
chr5	96035033	96035157	E071	-36037
chr5	96035202	96035657	E071	-35537
chr5	96040219	96040437	E071	-30757
chr5	96049884	96051216	E071	-19978
chr5	96051219	96051340	E071	-19854
chr5	96051381	96051510	E071	-19684
chr5	96054025	96054294	E071	-16900
chr5	96057168	96057396	E071	-13798
chr5	96057486	96057616	E071	-13578
chr5	96087021	96087370	E071	15827
chr5	96087396	96087474	E071	16202
chr5	96111488	96111601	E071	40294
chr5	96112149	96112193	E071	40955
chr5	96112320	96112697	E071	41126
chr5	96112777	96112843	E071	41583
chr5	96112857	96112907	E071	41663
chr5	96035202	96035657	E072	-35537
chr5	96047814	96048016	E072	-23178
chr5	96048118	96048172	E072	-23022
chr5	96049884	96051216	E072	-19978
chr5	96053660	96053968	E072	-17226
chr5	96054025	96054294	E072	-16900
chr5	96057168	96057396	E072	-13798
chr5	96057486	96057616	E072	-13578
chr5	96108912	96108991	E072	37718
chr5	96109134	96109207	E072	37940
chr5	96049884	96051216	E073	-19978
chr5	96057168	96057396	E073	-13798
chr5	96057486	96057616	E073	-13578
chr5	96035202	96035657	E074	-35537
chr5	96049884	96051216	E074	-19978
chr5	96051219	96051340	E074	-19854
chr5	96051381	96051510	E074	-19684
chr5	96051520	96051676	E074	-19518
chr5	96054025	96054294	E074	-16900
chr5	96054311	96054811	E074	-16383
chr5	96062541	96062834	E074	-8360
chr5	96112320	96112697	E074	41126
chr5	96112777	96112843	E074	41583
chr5	96112857	96112907	E074	41663
chr5	96114217	96114509	E074	43023
chr5	96114569	96114613	E074	43375

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	96038021	96040057	E067	-31137
chr5	96038021	96040057	E068	-31137
chr5	96038021	96040057	E069	-31137
chr5	96038021	96040057	E070	-31137
chr5	96038021	96040057	E071	-31137
chr5	96038021	96040057	E072	-31137
chr5	96038021	96040057	E073	-31137
chr5	96038021	96040057	E074	-31137
chr5	96038021	96040057	E082	-31137