rs10869409

Homo sapiens
T>C
RORB : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0288 (8627/29870,GnomAD)
C=0291 (8479/29118,TOPMED)
C=0232 (1164/5008,1000G)
C=0340 (1312/3854,ALSPAC)
C=0329 (1221/3708,TWINSUK)
chr9:74508473 (GRCh38.p7) (9q21.13)
ND
GWASdb2
1   publication(s)
See rs on genome
105 Enhancers around
64 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.74508473T>C
GRCh37.p13 chr 9NC_000009.11:g.77123389T>C
RORB RefSeqGeneNG_046926.1:g.16138T>C

Gene: RORB, RAR related orphan receptor B(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RORB transcriptNM_006914.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.763C=0.237
1000GenomesAmericanSub694T=0.560C=0.440
1000GenomesEast AsianSub1008T=0.938C=0.062
1000GenomesEuropeSub1006T=0.695C=0.305
1000GenomesGlobalStudy-wide5008T=0.768C=0.232
1000GenomesSouth AsianSub978T=0.820C=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.660C=0.340
The Genome Aggregation DatabaseAfricanSub8718T=0.760C=0.240
The Genome Aggregation DatabaseAmericanSub834T=0.550C=0.450
The Genome Aggregation DatabaseEast AsianSub1606T=0.919C=0.081
The Genome Aggregation DatabaseEuropeSub18410T=0.676C=0.323
The Genome Aggregation DatabaseGlobalStudy-wide29870T=0.711C=0.288
The Genome Aggregation DatabaseOtherSub302T=0.740C=0.260
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.708C=0.291
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.671C=0.329
PMID Title Author Journal
18227835Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking.Berrettini WMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs108694095.53E-05nicotine dependence18227835

eQTL of rs10869409 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 rs10869409 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 )
chr97713080177130881E0677412
chr97713098077131030E0677591
chr97714065877140724E06717269
chr97715783077157880E06734441
chr97715798777158133E06734598
chr97715819677158339E06734807
chr97715875477158804E06735365
chr97715889277158972E06735503
chr97715915277159378E06735763
chr97716905177169111E06745662
chr97716915677169216E06745767
chr97716921777169285E06745828
chr97716931277169360E06745923
chr97713609777136238E06812708
chr97715783077157880E06834441
chr97715798777158133E06834598
chr97715819677158339E06834807
chr97715875477158804E06835365
chr97715889277158972E06835503
chr97715915277159378E06835763
chr97716905177169111E06845662
chr97716915677169216E06845767
chr97716921777169285E06845828
chr97716931277169360E06845923
chr97717136277171985E06847973
chr97717200577172113E06848616
chr97715783077157880E06934441
chr97715798777158133E06934598
chr97715819677158339E06934807
chr97715875477158804E06935365
chr97715889277158972E06935503
chr97715915277159378E06935763
chr97716971777169802E06946328
chr97717001677170291E06946627
chr97717047377170541E06947084
chr97717057077170690E06947181
chr97717200577172113E06948616
chr97717229977172405E06948910
chr97711812677118237E070-5152
chr97711840877118467E070-4922
chr97711852077118570E070-4819
chr97714960177149651E07026212
chr97714979877150040E07026409
chr97716915677169216E07045767
chr97716921777169285E07045828
chr97716931277169360E07045923
chr97717047377170541E07047084
chr97717057077170690E07047181
chr97717095877171012E07047569
chr97717118177171240E07047792
chr97715783077157880E07134441
chr97715798777158133E07134598
chr97715819677158339E07134807
chr97715875477158804E07135365
chr97715889277158972E07135503
chr97715915277159378E07135763
chr97716915677169216E07145767
chr97716921777169285E07145828
chr97716931277169360E07145923
chr97717047377170541E07147084
chr97717057077170690E07147181
chr97717095877171012E07147569
chr97717118177171240E07147792
chr97712146077121576E072-1813
chr97712157977121629E072-1760
chr97712204177122091E072-1298
chr97714960177149651E07226212
chr97714979877150040E07226409
chr97715783077157880E07234441
chr97715798777158133E07234598
chr97715819677158339E07234807
chr97715875477158804E07235365
chr97715889277158972E07235503
chr97715915277159378E07235763
chr97716971777169802E07246328
chr97716991277170007E07246523
chr97717047377170541E07247084
chr97717057077170690E07247181
chr97717095877171012E07247569
chr97717118177171240E07247792
chr97717136277171985E07247973
chr97715798777158133E07334598
chr97715819677158339E07334807
chr97715875477158804E07335365
chr97715889277158972E07335503
chr97715915277159378E07335763
chr97716915677169216E07345767
chr97716921777169285E07345828
chr97716931277169360E07345923
chr97716971777169802E07346328
chr97716991277170007E07346523
chr97714145177141623E07418062
chr97714168977141750E07418300
chr97715798777158133E07434598
chr97715819677158339E07434807
chr97715875477158804E07435365
chr97715889277158972E07435503
chr97715915277159378E07435763
chr97716971777169802E07446328
chr97714960177149651E08126212
chr97714979877150040E08126409
chr97715025977150309E08126870
chr97716971777169802E08146328
chr97716991277170007E08146523
chr97717001677170291E08146627









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr97711143977111623E067-11766
chr97711163477115990E067-7399
chr97711600877116173E067-7216
chr97711624077116294E067-7095
chr97714077877140862E06717389
chr97714099977141069E06717610
chr97714117177141361E06717782
chr97711096177111020E068-12369
chr97711114577111195E068-12194
chr97711130877111393E068-11996
chr97711143977111623E068-11766
chr97711163477115990E068-7399
chr97711600877116173E068-7216
chr97714077877140862E06817389
chr97714099977141069E06817610
chr97714117177141361E06817782
chr97711096177111020E069-12369
chr97711114577111195E069-12194
chr97711130877111393E069-11996
chr97711143977111623E069-11766
chr97711163477115990E069-7399
chr97711600877116173E069-7216
chr97714077877140862E06917389
chr97714099977141069E06917610
chr97714117177141361E06917782
chr97711143977111623E070-11766
chr97711624077116294E070-7095
chr97711096177111020E071-12369
chr97711114577111195E071-12194
chr97711130877111393E071-11996
chr97711143977111623E071-11766
chr97711163477115990E071-7399
chr97714077877140862E07117389
chr97714099977141069E07117610
chr97714117177141361E07117782
chr97711096177111020E072-12369
chr97711114577111195E072-12194
chr97711130877111393E072-11996
chr97711143977111623E072-11766
chr97711163477115990E072-7399
chr97711600877116173E072-7216
chr97711624077116294E072-7095
chr97714077877140862E07217389
chr97714099977141069E07217610
chr97714117177141361E07217782
chr97711096177111020E073-12369
chr97711114577111195E073-12194
chr97711130877111393E073-11996
chr97711143977111623E073-11766
chr97711163477115990E073-7399
chr97711600877116173E073-7216
chr97711624077116294E073-7095
chr97714077877140862E07317389
chr97714099977141069E07317610
chr97714117177141361E07317782
chr97711143977111623E074-11766
chr97711163477115990E074-7399
chr97714077877140862E07417389
chr97714099977141069E07417610
chr97714117177141361E07417782
chr97711163477115990E081-7399
chr97711143977111623E082-11766
chr97711163477115990E082-7399
chr97711624077116294E082-7095