rs419382

Homo sapiens
T>C
CDH13 : Intron Variant
LOC105371366 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0191 (5749/29960,GnomAD)
T==0207 (6029/29118,TOPMED)
T==0171 (855/5008,1000G)
T==0187 (721/3854,ALSPAC)
T==0181 (673/3708,TWINSUK)
chr16:83725484 (GRCh38.p7) (16q23.3)
ND
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.83725484T>C
GRCh37.p13 chr 16NC_000016.9:g.83759089T>C

Gene: CDH13, cadherin 13(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH13 transcript variant 2NM_001220488.1:c.N/AIntron Variant
CDH13 transcript variant 3NM_001220489.1:c.N/AIntron Variant
CDH13 transcript variant 4NM_001220490.1:c.N/AIntron Variant
CDH13 transcript variant 1NM_001257.4:c.N/AIntron Variant
CDH13 transcript variant 5NM_001220491.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant 6NM_001220492.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant X1XM_011522804.2:c.N/AIntron Variant
CDH13 transcript variant X2XM_017022848.1:c.N/AGenic Downstream Transcript Variant
CDH13 transcript variant X3XM_017022849.1:c.N/AGenic Downstream Transcript Variant

Gene: LOC105371366, uncharacterized LOC105371366(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105371366 transcript variant X1XR_001752382.1:n....XR_001752382.1:n.237A>GA>GNon Coding Transcript Variant
LOC105371366 transcript variant X3XR_933801.2:n.237A>GA>GNon Coding Transcript Variant
LOC105371366 transcript variant X4XR_001752383.1:n.N/AGenic Upstream Transcript Variant
LOC105371366 transcript variant X5XR_001752384.1:n.N/AGenic Upstream Transcript Variant
LOC105371366 transcript variant X6XR_001752385.1:n.N/AGenic Upstream Transcript Variant
LOC105371366 transcript variant X2XR_933802.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.262C=0.738
1000GenomesAmericanSub694T=0.150C=0.850
1000GenomesEast AsianSub1008T=0.071C=0.929
1000GenomesEuropeSub1006T=0.199C=0.801
1000GenomesGlobalStudy-wide5008T=0.171C=0.829
1000GenomesSouth AsianSub978T=0.140C=0.860
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.187C=0.813
The Genome Aggregation DatabaseAfricanSub8716T=0.232C=0.768
The Genome Aggregation DatabaseAmericanSub838T=0.120C=0.880
The Genome Aggregation DatabaseEast AsianSub1616T=0.056C=0.944
The Genome Aggregation DatabaseEuropeSub18488T=0.188C=0.811
The Genome Aggregation DatabaseGlobalStudy-wide29960T=0.191C=0.808
The Genome Aggregation DatabaseOtherSub302T=0.190C=0.810
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.207C=0.792
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.181C=0.819
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs4193820.000103nicotine smoking19268276

eQTL of rs419382 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 rs419382 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 )
chr168375096783751185E067-7904
chr168375146283751720E067-7369
chr168377544083775534E06716351
chr168377752383777615E06718434
chr168377772183777775E06718632
chr168377784983777910E06718760
chr168377794483778613E06718855
chr168377890883778958E06719819
chr168379518183795288E06736092
chr168379565983796849E06736570
chr168379753483797628E06738445
chr168379766583797789E06738576
chr168380430583804365E06745216
chr168380438083804430E06745291
chr168380458183804641E06745492
chr168380469383804743E06745604
chr168380665683806988E06747567
chr168380702883807108E06747939
chr168374798883748129E068-10960
chr168374823883748386E068-10703
chr168374852483748590E068-10499
chr168375096783751185E068-7904
chr168375124683751357E068-7732
chr168375146283751720E068-7369
chr168377752383777615E06818434
chr168377772183777775E06818632
chr168377794483778613E06818855
chr168377890883778958E06819819
chr168378246783782507E06823378
chr168378268483782753E06823595
chr168379565983796849E06836570
chr168380265183803758E06843562
chr168380381483804108E06844725
chr168380430583804365E06845216
chr168380438083804430E06845291
chr168380665683806988E06847567
chr168380702883807108E06847939
chr168380781783807956E06848728
chr168375096783751185E069-7904
chr168375124683751357E069-7732
chr168375146283751720E069-7369
chr168377425983774362E06915170
chr168377544083775534E06916351
chr168377752383777615E06918434
chr168377772183777775E06918632
chr168377784983777910E06918760
chr168377794483778613E06918855
chr168377890883778958E06919819
chr168378071683780766E06921627
chr168378133683781389E06922247
chr168378167183781891E06922582
chr168378220783782261E06923118
chr168378246783782507E06923378
chr168379473583794815E06935646
chr168379518183795288E06936092
chr168379565983796849E06936570
chr168379753483797628E06938445
chr168379766583797789E06938576
chr168380265183803758E06943562
chr168380381483804108E06944725
chr168380430583804365E06945216
chr168380438083804430E06945291
chr168380458183804641E06945492
chr168380469383804743E06945604
chr168380665683806988E06947567
chr168380702883807108E06947939
chr168371541983715499E070-43590
chr168371562783715691E070-43398
chr168371582083715991E070-43098
chr168371610883716158E070-42931
chr168371625883716446E070-42643
chr168371652483716743E070-42346
chr168377576783776142E07016678
chr168374763483747684E071-11405
chr168374798883748129E071-10960
chr168374823883748386E071-10703
chr168374852483748590E071-10499
chr168375096783751185E071-7904
chr168375146283751720E071-7369
chr168377425983774362E07115170
chr168377752383777615E07118434
chr168377772183777775E07118632
chr168377890883778958E07119819
chr168378167183781891E07122582
chr168378220783782261E07123118
chr168378246783782507E07123378
chr168378268483782753E07123595
chr168379473583794815E07135646
chr168379518183795288E07136092
chr168379753483797628E07138445
chr168379766583797789E07138576
chr168379840583798455E07139316
chr168379880683798856E07139717
chr168379937083799675E07140281
chr168379980283799842E07140713
chr168380006783800133E07140978
chr168380039283800491E07141303
chr168380236083802418E07143271
chr168380265183803758E07143562
chr168380665683806988E07147567
chr168380702883807108E07147939
chr168380781783807956E07148728
chr168380879383808853E07149704
chr168372294483723374E072-35715
chr168372343083723502E072-35587
chr168375096783751185E072-7904
chr168377576783776142E07216678
chr168377624283776363E07217153
chr168377752383777615E07218434
chr168377772183777775E07218632
chr168377890883778958E07219819
chr168378246783782507E07223378
chr168378268483782753E07223595
chr168379473583794815E07235646
chr168379518183795288E07236092
chr168379565983796849E07236570
chr168380265183803758E07243562
chr168380381483804108E07244725
chr168380665683806988E07247567
chr168380702883807108E07247939
chr168380781783807956E07248728
chr168377544083775534E07316351
chr168377752383777615E07318434
chr168377772183777775E07318632
chr168377784983777910E07318760
chr168377794483778613E07318855
chr168377890883778958E07319819
chr168379565983796849E07336570
chr168380265183803758E07343562
chr168380438083804430E07345291
chr168380458183804641E07345492
chr168380469383804743E07345604
chr168380879383808853E07349704
chr168375096783751185E074-7904
chr168375124683751357E074-7732
chr168375146283751720E074-7369
chr168377544083775534E07416351
chr168377576783776142E07416678
chr168377624283776363E07417153
chr168377691783777276E07417828
chr168377752383777615E07418434
chr168377772183777775E07418632
chr168377784983777910E07418760
chr168377794483778613E07418855
chr168377890883778958E07419819
chr168378167183781891E07422582
chr168378220783782261E07423118
chr168378246783782507E07423378
chr168378268483782753E07423595
chr168379473583794815E07435646
chr168379518183795288E07436092
chr168379753483797628E07438445
chr168379766583797789E07438576
chr168379840583798455E07439316
chr168379937083799675E07440281
chr168379980283799842E07440713
chr168380006783800133E07440978
chr168380265183803758E07443562
chr168380430583804365E07445216
chr168380438083804430E07445291
chr168380665683806988E07447567
chr168380702883807108E07447939
chr168380781783807956E07448728
chr168370967983710051E081-49038
chr168371009483710168E081-48921
chr168377544083775534E08116351
chr168377576783776142E08116678
chr168377624283776363E08117153
chr168377691783777276E08117828
chr168377752383777615E08118434
chr168377772183777775E08118632
chr168377784983777910E08118760
chr168377794483778613E08118855
chr168377890883778958E08119819
chr168370967983710051E082-49038
chr168371009483710168E082-48921
chr168372294483723374E082-35715
chr168374823883748386E082-10703
chr168374852483748590E082-10499
chr168377155983771609E08212470
chr168377170683771934E08212617
chr168377544083775534E08216351
chr168377576783776142E08216678
chr168377624283776363E08217153
chr168377691783777276E08217828










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr168380522483805465E06746135
chr168380565983805739E06746570
chr168380594083806111E06746851
chr168380615083806200E06747061
chr168380653383806640E06747444
chr168380522483805465E06846135
chr168380565983805739E06846570
chr168380594083806111E06846851
chr168380615083806200E06847061
chr168380653383806640E06847444
chr168380522483805465E06946135
chr168380565983805739E06946570
chr168380594083806111E06946851
chr168380615083806200E06947061
chr168380653383806640E06947444
chr168380522483805465E07146135
chr168380565983805739E07146570
chr168380594083806111E07146851
chr168380615083806200E07147061
chr168380653383806640E07147444
chr168380522483805465E07246135
chr168380565983805739E07246570
chr168380594083806111E07246851
chr168380615083806200E07247061
chr168380522483805465E07346135
chr168380565983805739E07346570
chr168380594083806111E07346851
chr168380615083806200E07347061
chr168380522483805465E07446135
chr168380565983805739E07446570
chr168380594083806111E07446851
chr168380615083806200E07447061
chr168380653383806640E07447444