rs4240530

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CHIA : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0320 (9605/29938,GnomAD)
C==0328 (9575/29118,TOPMED)
C==0314 (1573/5008,1000G)
C==0299 (1154/3854,ALSPAC)
C==0292 (1083/3708,TWINSUK)

Position: chr1:111310959 (GRCh38.p7) (1p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.111310959C>T
GRCh37.p13 chr 1	NC_000001.10:g.111853581C>T

Gene: CHIA, chitinase, acidic(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHIA transcript variant 3	NM_001040623.2:c.	N/A	Intron Variant
CHIA transcript variant 5	NM_001258001.1:c.	N/A	Intron Variant
CHIA transcript variant 6	NM_001258002.1:c.	N/A	Intron Variant
CHIA transcript variant 7	NM_001258003.1:c.	N/A	Intron Variant
CHIA transcript variant 8	NM_001258004.1:c.	N/A	Intron Variant
CHIA transcript variant 9	NM_001258005.1:c.	N/A	Intron Variant
CHIA transcript variant 2	NM_021797.3:c.	N/A	Intron Variant
CHIA transcript variant 4	NM_201653.3:c.	N/A	Intron Variant
CHIA transcript variant X1	XM_006710577.3:c.	N/A	Intron Variant
CHIA transcript variant X3	XM_017001048.1:c.	N/A	Intron Variant
CHIA transcript variant X2	XM_017001047.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.449	T=0.551
1000Genomes	American	Sub	694	C=0.190	T=0.810
1000Genomes	East Asian	Sub	1008	C=0.156	T=0.844
1000Genomes	Europe	Sub	1006	C=0.320	T=0.680
1000Genomes	Global	Study-wide	5008	C=0.314	T=0.686
1000Genomes	South Asian	Sub	978	C=0.380	T=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.299	T=0.701
The Genome Aggregation Database	African	Sub	8706	C=0.416	T=0.584
The Genome Aggregation Database	American	Sub	836	C=0.190	T=0.810
The Genome Aggregation Database	East Asian	Sub	1620	C=0.161	T=0.839
The Genome Aggregation Database	Europe	Sub	18474	C=0.296	T=0.703
The Genome Aggregation Database	Global	Study-wide	29938	C=0.320	T=0.679
The Genome Aggregation Database	Other	Sub	302	C=0.320	T=0.680
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.328	T=0.671
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.292	T=0.708

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
20226308	Polymorphisms of chitinases are not associated with asthma.	Wu AC	J Allergy Clin Immunol
23180006	Power of a reproducing kernel-based method for testing the joint effect of a set of single-nucleotide polymorphisms.	He H	Genetica
20538957	Fungal exposure modulates the effect of polymorphisms of chitinases on emergency department visits and hospitalizations.	Wu AC	Am J Respir Crit Care Med

P-Value

SNP ID	p-value	Traits	Study
rs4240530	0.00084	alcohol dependence	20201924

eQTL of rs4240530 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 rs4240530 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 )
chr1	111817394	111817664	E068	-35917
chr1	111817762	111818087	E068	-35494
chr1	111814880	111814951	E070	-38630
chr1	111817394	111817664	E071	-35917
chr1	111817762	111818087	E071	-35494
chr1	111817394	111817664	E072	-35917
chr1	111817394	111817664	E074	-35917
chr1	111817762	111818087	E074	-35494

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111888671	111889542	E067	35090
chr1	111889571	111889663	E067	35990
chr1	111888671	111889542	E068	35090
chr1	111889571	111889663	E068	35990
chr1	111888671	111889542	E069	35090
chr1	111889571	111889663	E069	35990
chr1	111888671	111889542	E070	35090
chr1	111889571	111889663	E070	35990
chr1	111888671	111889542	E071	35090
chr1	111889571	111889663	E071	35990
chr1	111888671	111889542	E072	35090
chr1	111889571	111889663	E072	35990
chr1	111888671	111889542	E073	35090
chr1	111889571	111889663	E073	35990
chr1	111888671	111889542	E074	35090
chr1	111889571	111889663	E074	35990
chr1	111888671	111889542	E082	35090