rs7031588

Homo sapiens
C>T
COL15A1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0261 (7817/29856,GnomAD)
T=0298 (8686/29118,TOPMED)
T=0390 (1954/5008,1000G)
C==0260 (1188/4566,GO-ESP)
T=0206 (792/3854,ALSPAC)
T=0199 (739/3708,TWINSUK)
chr9:99060020 (GRCh38.p7) (9q22.33)
ND
GWASdb2
1   publication(s)
See rs on genome
44 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.99060020C>T
GRCh37.p13 chr 9NC_000009.11:g.101822302C>T

Gene: COL15A1, collagen type XV alpha 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
COL15A1 transcriptNM_001855.4:c.N/AIntron Variant
COL15A1 transcript variant X1XM_011518214.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.593T=0.407
1000GenomesAmericanSub694C=0.660T=0.340
1000GenomesEast AsianSub1008C=0.429T=0.571
1000GenomesEuropeSub1006C=0.805T=0.195
1000GenomesGlobalStudy-wide5008C=0.610T=0.390
1000GenomesSouth AsianSub978C=0.580T=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.794T=0.206
The Genome Aggregation DatabaseAfricanSub8692C=0.615T=0.385
The Genome Aggregation DatabaseAmericanSub828C=0.610T=0.390
The Genome Aggregation DatabaseEast AsianSub1618C=0.452T=0.548
The Genome Aggregation DatabaseEuropeSub18416C=0.825T=0.174
The Genome Aggregation DatabaseGlobalStudy-wide29856C=0.738T=0.261
The Genome Aggregation DatabaseOtherSub302C=0.820T=0.180
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.701T=0.298
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.801T=0.199
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs70315880.000941nicotine dependence17158188

eQTL of rs7031588 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 rs7031588 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 )
chr9101869823101870290E06747521
chr9101782942101782996E068-39306
chr9101786057101786525E068-35777
chr9101788565101788712E068-33590
chr9101788731101788826E068-33476
chr9101788991101789188E068-33114
chr9101808494101808624E068-13678
chr9101808627101808719E068-13583
chr9101808838101809056E068-13246
chr9101809071101809125E068-13177
chr9101809134101809385E068-12917
chr9101869823101870290E06847521
chr9101870337101870391E06848035
chr9101803997101804168E069-18134
chr9101848409101848907E06926107
chr9101849383101849521E06927081
chr9101869823101870290E06947521
chr9101870337101870391E06948035
chr9101800293101801143E070-21159
chr9101869823101870290E07047521
chr9101854947101854987E07132645
chr9101802970101803937E072-18365
chr9101869823101870290E07447521
chr9101870337101870391E07448035
chr9101799283101799333E081-22969
chr9101799384101799444E081-22858
chr9101799565101799615E081-22687
chr9101800075101800281E081-22021
chr9101800293101801143E081-21159
chr9101801741101801791E081-20511
chr9101801874101802380E081-19922
chr9101802412101802565E081-19737
chr9101802634101802885E081-19417
chr9101869823101870290E08147521
chr9101870337101870391E08148035
chr9101870529101871084E08148227
chr9101799283101799333E082-22969
chr9101799384101799444E082-22858
chr9101799565101799615E082-22687
chr9101800075101800281E082-22021
chr9101801741101801791E082-20511
chr9101801874101802380E082-19922
chr9101802412101802565E082-19737
chr9101870337101870391E08248035









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr9101865368101868773E06743066
chr9101865368101868773E06843066
chr9101865368101868773E06943066
chr9101865368101868773E07043066
chr9101865368101868773E07143066
chr9101865368101868773E07243066
chr9101865368101868773E07343066
chr9101865368101868773E07443066
chr9101865368101868773E08143066
chr9101865368101868773E08243066