rs12440459

Homo sapiens
C>T
CGNL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0091 (2729/29970,GnomAD)
T=0106 (532/5008,1000G)
T=0095 (367/3854,ALSPAC)
T=0094 (348/3708,TWINSUK)
chr15:57402740 (GRCh38.p7) (15q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
162 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.57402740C>T
GRCh37.p13 chr 15NC_000015.9:g.57694938C>T
CGNL1 RefSeqGeneNG_030584.1:g.31236C>T

Gene: CGNL1, cingulin-like 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CGNL1 transcript variant 1NM_001252335.1:c.N/AIntron Variant
CGNL1 transcript variant 2NM_032866.4:c.N/AIntron Variant
CGNL1 transcript variant X4XM_005254726.3:c.N/AIntron Variant
CGNL1 transcript variant X2XM_005254727.4:c.N/AIntron Variant
CGNL1 transcript variant X4XM_011522120.1:c.N/AIntron Variant
CGNL1 transcript variant X5XM_011522121.1:c.N/AIntron Variant
CGNL1 transcript variant X1XM_017022685.1:c.N/AGenic Upstream Transcript Variant
CGNL1 transcript variant X6XM_017022686.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.908T=0.092
1000GenomesAmericanSub694C=0.830T=0.170
1000GenomesEast AsianSub1008C=0.968T=0.032
1000GenomesEuropeSub1006C=0.902T=0.098
1000GenomesGlobalStudy-wide5008C=0.894T=0.106
1000GenomesSouth AsianSub978C=0.830T=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.905T=0.095
The Genome Aggregation DatabaseAfricanSub8724C=0.919T=0.081
The Genome Aggregation DatabaseAmericanSub836C=0.850T=0.150
The Genome Aggregation DatabaseEast AsianSub1620C=0.960T=0.040
The Genome Aggregation DatabaseEuropeSub18488C=0.901T=0.098
The Genome Aggregation DatabaseGlobalStudy-wide29970C=0.908T=0.091
The Genome Aggregation DatabaseOtherSub302C=0.930T=0.070
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.906T=0.094
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
rs124404596.76E-05alcohol dependence21314694

eQTL of rs12440459 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 rs12440459 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 )
chr155772020957720529E06725271
chr155772056257720769E06725624
chr155772079657720871E06725858
chr155772088457720999E06725946
chr155772118357721259E06726245
chr155772129557721371E06726357
chr155772423757725116E06729299
chr155773161857731978E06736680
chr155773198057732078E06737042
chr155773235957732446E06737421
chr155773247257732755E06737534
chr155767110157671393E068-23545
chr155767633857676513E068-18425
chr155767670857676794E068-18144
chr155767687957677051E068-17887
chr155767705457677335E068-17603
chr155767741357677524E068-17414
chr155767757957677651E068-17287
chr155767767057677869E068-17069
chr155767809257678603E068-16335
chr155767872557679058E068-15880
chr155768747057687873E068-7065
chr155768796557688058E068-6880
chr155770860357708802E06813665
chr155770885657708906E06813918
chr155770899557709217E06814057
chr155771360157713644E06818663
chr155771372357713773E06818785
chr155771382257714115E06818884
chr155771418857714371E06819250
chr155771443957714821E06819501
chr155771919057719433E06824252
chr155771948757720159E06824549
chr155772020957720529E06825271
chr155772056257720769E06825624
chr155772079657720871E06825858
chr155772088457720999E06825946
chr155772118357721259E06826245
chr155772129557721371E06826357
chr155772141957721501E06826481
chr155772164257721753E06826704
chr155772423757725116E06829299
chr155773198057732078E06837042
chr155773235957732446E06837421
chr155773247257732755E06837534
chr155773293857733538E06838000
chr155767924357679732E069-15206
chr155767974857681328E069-13610
chr155768283657683265E069-11673
chr155768747057687873E069-7065
chr155768796557688058E069-6880
chr155771895157719132E06924013
chr155771919057719433E06924252
chr155771948757720159E06924549
chr155772020957720529E06925271
chr155772056257720769E06925624
chr155772079657720871E06925858
chr155772088457720999E06925946
chr155772118357721259E06926245
chr155772129557721371E06926357
chr155772141957721501E06926481
chr155772164257721753E06926704
chr155772343157724174E06928493
chr155772423757725116E06929299
chr155773235957732446E06937421
chr155773247257732755E06937534
chr155773734157737868E06942403
chr155773787757737971E06942939
chr155772020957720529E07025271
chr155772056257720769E07025624
chr155772079657720871E07025858
chr155772088457720999E07025946
chr155772343157724174E07028493
chr155772423757725116E07029299
chr155772513457725258E07030196
chr155772531657725686E07030378
chr155772576457725878E07030826
chr155772590957726021E07030971
chr155772604057726214E07031102
chr155765644157657370E071-37568
chr155769663657696686E0711698
chr155769696257697044E0712024
chr155769730557697410E0712367
chr155771602157716405E07121083
chr155771662057716680E07121682
chr155771675357716856E07121815
chr155771919057719433E07124252
chr155771948757720159E07124549
chr155772020957720529E07125271
chr155772056257720769E07125624
chr155772079657720871E07125858
chr155772088457720999E07125946
chr155772118357721259E07126245
chr155772129557721371E07126357
chr155772141957721501E07126481
chr155772164257721753E07126704
chr155772343157724174E07128493
chr155772423757725116E07129299
chr155772513457725258E07130196
chr155773161857731978E07136680
chr155773198057732078E07137042
chr155773235957732446E07137421
chr155773247257732755E07137534
chr155771360157713644E07218663
chr155771372357713773E07218785
chr155771382257714115E07218884
chr155771418857714371E07219250
chr155771443957714821E07219501
chr155771919057719433E07224252
chr155771948757720159E07224549
chr155772020957720529E07225271
chr155772056257720769E07225624
chr155772079657720871E07225858
chr155772088457720999E07225946
chr155772118357721259E07226245
chr155772129557721371E07226357
chr155772141957721501E07226481
chr155772164257721753E07226704
chr155772423757725116E07229299
chr155773734157737868E07242403
chr155773787757737971E07242939
chr155767872557679058E073-15880
chr155767908857679219E073-15719
chr155767924357679732E073-15206
chr155768283657683265E073-11673
chr155769508257696496E073144
chr155770860357708802E07313665
chr155770885657708906E07313918
chr155770899557709217E07314057
chr155771948757720159E07324549
chr155772020957720529E07325271
chr155772056257720769E07325624
chr155772079657720871E07325858
chr155772088457720999E07325946
chr155772118357721259E07326245
chr155772129557721371E07326357
chr155772141957721501E07326481
chr155772423757725116E07329299
chr155773247257732755E07337534
chr155773787757737971E07342939
chr155767443857675135E074-19803
chr155767872557679058E074-15880
chr155768466957684812E074-10126
chr155771382257714115E07418884
chr155771418857714371E07419250
chr155771501657715066E07420078
chr155771509557715179E07420157
chr155771948757720159E07424549
chr155772020957720529E07425271
chr155772056257720769E07425624
chr155772079657720871E07425858
chr155772088457720999E07425946
chr155772118357721259E07426245
chr155772129557721371E07426357
chr155772141957721501E07426481
chr155772343157724174E07428493
chr155773235957732446E07437421
chr155773247257732755E07437534
chr155773734157737868E07442403
chr155773787757737971E07442939
chr155772343157724174E08128493
chr155772423757725116E08129299









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr155766797857670059E067-24879
chr155766797857670059E068-24879
chr155766797857670059E069-24879
chr155766797857670059E071-24879
chr155766797857670059E072-24879
chr155766797857670059E073-24879
chr155766797857670059E074-24879
chr155766797857670059E082-24879