rs4839122

Homo sapiens
T>C
CHIA : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0318 (9515/29910,GnomAD)
T==0328 (9570/29118,TOPMED)
T==0313 (1569/5008,1000G)
T==0298 (1150/3854,ALSPAC)
T==0292 (1081/3708,TWINSUK)
chr1:111311585 (GRCh38.p7) (1p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.111311585T>C
GRCh37.p13 chr 1NC_000001.10:g.111854207T>C

Gene: CHIA, chitinase, acidic(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CHIA transcript variant 3NM_001040623.2:c.N/AIntron Variant
CHIA transcript variant 5NM_001258001.1:c.N/AIntron Variant
CHIA transcript variant 6NM_001258002.1:c.N/AIntron Variant
CHIA transcript variant 7NM_001258003.1:c.N/AIntron Variant
CHIA transcript variant 8NM_001258004.1:c.N/AIntron Variant
CHIA transcript variant 9NM_001258005.1:c.N/AIntron Variant
CHIA transcript variant 2NM_021797.3:c.N/AIntron Variant
CHIA transcript variant 4NM_201653.3:c.N/AIntron Variant
CHIA transcript variant X1XM_006710577.3:c.N/AIntron Variant
CHIA transcript variant X3XM_017001048.1:c.N/AIntron Variant
CHIA transcript variant X2XM_017001047.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.448C=0.552
1000GenomesAmericanSub694T=0.190C=0.810
1000GenomesEast AsianSub1008T=0.156C=0.844
1000GenomesEuropeSub1006T=0.317C=0.683
1000GenomesGlobalStudy-wide5008T=0.313C=0.687
1000GenomesSouth AsianSub978T=0.380C=0.620
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.298C=0.702
The Genome Aggregation DatabaseAfricanSub8692T=0.415C=0.585
The Genome Aggregation DatabaseAmericanSub838T=0.180C=0.820
The Genome Aggregation DatabaseEast AsianSub1614T=0.159C=0.841
The Genome Aggregation DatabaseEuropeSub18464T=0.292C=0.707
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.318C=0.681
The Genome Aggregation DatabaseOtherSub302T=0.320C=0.680
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.328C=0.671
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.292C=0.708
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs48391220.000505alcohol dependence21314694

eQTL of rs4839122 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 rs4839122 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 )
chr1111817394111817664E068-36543
chr1111817762111818087E068-36120
chr1111814880111814951E070-39256
chr1111817394111817664E071-36543
chr1111817762111818087E071-36120
chr1111817394111817664E072-36543
chr1111817394111817664E074-36543
chr1111817762111818087E074-36120





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1111888671111889542E06734464
chr1111889571111889663E06735364
chr1111888671111889542E06834464
chr1111889571111889663E06835364
chr1111888671111889542E06934464
chr1111889571111889663E06935364
chr1111888671111889542E07034464
chr1111889571111889663E07035364
chr1111888671111889542E07134464
chr1111889571111889663E07135364
chr1111888671111889542E07234464
chr1111889571111889663E07235364
chr1111888671111889542E07334464
chr1111889571111889663E07335364
chr1111888671111889542E07434464
chr1111889571111889663E07435364
chr1111888671111889542E08234464