rs2595248

Homo sapiens
T>C
SCHIP1 : Intron Variant
IQCJ-SCHIP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0440 (13152/29890,GnomAD)
C=0465 (13549/29118,TOPMED)
C=0394 (1974/5008,1000G)
C=0441 (1698/3854,ALSPAC)
C=0449 (1666/3708,TWINSUK)
chr3:159300738 (GRCh38.p7) (3q25.33)
ND
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.159300738T>C
GRCh37.p13 chr 3NC_000003.11:g.159018527T>C

Gene: SCHIP1, schwannomin interacting protein 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SCHIP1 transcript variant 2NM_001197107.1:c.N/AIntron Variant
SCHIP1 transcript variant 3NM_001197108.1:c.N/AIntron Variant
SCHIP1 transcript variant 1NM_014575.3:c.N/AIntron Variant
SCHIP1 transcript variant 4NM_001197109.1:c.N/AGenic Upstream Transcript Variant

Gene: IQCJ-SCHIP1, IQCJ-SCHIP1 readthrough(plus strand)

Molecule type Change Amino acid[Codon] SO Term
IQCJ-SCHIP1 transcript variant 1NM_001197113.1:c.N/AIntron Variant
IQCJ-SCHIP1 transcript variant 2NM_001197114.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.486C=0.514
1000GenomesAmericanSub694T=0.650C=0.350
1000GenomesEast AsianSub1008T=0.603C=0.397
1000GenomesEuropeSub1006T=0.570C=0.430
1000GenomesGlobalStudy-wide5008T=0.606C=0.394
1000GenomesSouth AsianSub978T=0.780C=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.559C=0.441
The Genome Aggregation DatabaseAfricanSub8702T=0.484C=0.516
The Genome Aggregation DatabaseAmericanSub838T=0.630C=0.370
The Genome Aggregation DatabaseEast AsianSub1604T=0.559C=0.441
The Genome Aggregation DatabaseEuropeSub18444T=0.593C=0.406
The Genome Aggregation DatabaseGlobalStudy-wide29890T=0.560C=0.440
The Genome Aggregation DatabaseOtherSub302T=0.530C=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.534C=0.465
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.551C=0.449
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs25952489.29E-05nicotine dependence (smoking)22377092

eQTL of rs2595248 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 rs2595248 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 )
chr3158981667158981810E067-36717
chr3158982128158982216E067-36311
chr3158997961158998029E069-20498
chr3158998227158999031E069-19496
chr3158997961158998029E070-20498
chr3158998227158999031E070-19496
chr3158998227158999031E073-19496
chr3159036907159037410E07418380
chr3158981667158981810E081-36717
chr3158982128158982216E081-36311
chr3158997961158998029E081-20498
chr3158998227158999031E081-19496
chr3159022252159022568E0813725
chr3159064027159065021E08145500
chr3159065584159065902E08147057
chr3158997961158998029E082-20498
chr3158998227158999031E082-19496
chr3159064027159065021E08245500







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3158990955158991133E067-27394
chr3158991411158991473E067-27054
chr3158991542158991682E067-26845
chr3158993466158994210E067-24317
chr3158991411158991473E071-27054
chr3158991542158991682E071-26845
chr3158990955158991133E072-27394
chr3158991411158991473E072-27054
chr3158991542158991682E072-26845
chr3158991411158991473E073-27054
chr3158991542158991682E073-26845
chr3158990955158991133E082-27394
chr3158991411158991473E082-27054
chr3158991542158991682E082-26845
chr3158993466158994210E082-24317
chr3158995036158995086E082-23441