rs2411109

Homo sapiens
G>A
SEPT9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0376 (11225/29846,GnomAD)
A=0342 (9957/29118,TOPMED)
A=0384 (1921/5008,1000G)
A=0449 (1732/3854,ALSPAC)
A=0449 (1666/3708,TWINSUK)
chr17:77336374 (GRCh38.p7) (17q25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
196 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.77336374G>A
GRCh37.p13 chr 17NC_000017.10:g.75332456G>A
SEPT9 RefSeqGeneNG_011683.1:g.59965G>A

Gene: SEPT9, septin 9(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SEPT9 transcript variant 1NM_001113491.1:c.N/AIntron Variant
SEPT9 transcript variant 5NM_001113492.1:c.N/AIntron Variant
SEPT9 transcript variant 8NM_001293695.1:c.N/AIntron Variant
SEPT9 transcript variant 3NM_006640.4:c.N/AIntron Variant
SEPT9 transcript variant 2NM_001113493.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 6NM_001113494.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 4NM_001113495.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 7NM_001113496.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 9NM_001293696.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 10NM_001293697.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant 11NM_001293698.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X3XM_006721643.2:c.N/AIntron Variant
SEPT9 transcript variant X1XM_011524204.1:c.N/AIntron Variant
SEPT9 transcript variant X9XM_005256962.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X6XM_006721644.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X2XM_011524206.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X4XM_011524207.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X8XM_011524208.2:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X5XM_017024031.1:c.N/AGenic Upstream Transcript Variant
SEPT9 transcript variant X7XM_017024032.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.877A=0.123
1000GenomesAmericanSub694G=0.500A=0.500
1000GenomesEast AsianSub1008G=0.496A=0.504
1000GenomesEuropeSub1006G=0.528A=0.472
1000GenomesGlobalStudy-wide5008G=0.616A=0.384
1000GenomesSouth AsianSub978G=0.560A=0.440
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.551A=0.449
The Genome Aggregation DatabaseAfricanSub8698G=0.838A=0.162
The Genome Aggregation DatabaseAmericanSub838G=0.450A=0.550
The Genome Aggregation DatabaseEast AsianSub1612G=0.543A=0.457
The Genome Aggregation DatabaseEuropeSub18396G=0.539A=0.461
The Genome Aggregation DatabaseGlobalStudy-wide29846G=0.623A=0.376
The Genome Aggregation DatabaseOtherSub302G=0.560A=0.440
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.658A=0.342
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.551A=0.449
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
rs24111090.000269alcohol dependence21314694

eQTL of rs2411109 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 rs2411109 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 )
chr177530088375300962E067-31494
chr177531192175312019E067-20437
chr177531202175313058E067-19398
chr177531774275320512E067-11944
chr177535499275355289E06722536
chr177535541875355613E06722962
chr177535977175360410E06727315
chr177536094875361075E06728492
chr177536109575361377E06728639
chr177536149675361561E06729040
chr177536165175362651E06729195
chr177536266775363281E06730211
chr177537415475374270E06741698
chr177537434875374432E06741892
chr177537447475374732E06742018
chr177537491075375055E06742454
chr177537510875375266E06742652
chr177537528175375358E06742825
chr177537540775375472E06742951
chr177537552275375730E06743066
chr177537574575376451E06743289
chr177537654875376880E06744092
chr177537971975379808E06747263
chr177537993775380316E06747481
chr177531202175313058E068-19398
chr177531764875317692E068-14764
chr177531774275320512E068-11944
chr177534634175348217E06813885
chr177535977175360410E06827315
chr177536042775360815E06827971
chr177536094875361075E06828492
chr177536109575361377E06828639
chr177536149675361561E06829040
chr177536165175362651E06829195
chr177536266775363281E06830211
chr177537415475374270E06841698
chr177537540775375472E06842951
chr177537552275375730E06843066
chr177537574575376451E06843289
chr177537654875376880E06844092
chr177537688375376937E06844427
chr177537703775377106E06844581
chr177537715775377270E06844701
chr177537729775377913E06844841
chr177537793175378017E06845475
chr177537838475379658E06845928
chr177537971975379808E06847263
chr177537993775380316E06847481
chr177530088375300962E069-31494
chr177530489775305814E069-26642
chr177531192175312019E069-20437
chr177531774275320512E069-11944
chr177535977175360410E06927315
chr177536042775360815E06927971
chr177536165175362651E06929195
chr177537415475374270E06941698
chr177537434875374432E06941892
chr177537447475374732E06942018
chr177537491075375055E06942454
chr177537510875375266E06942652
chr177537528175375358E06942825
chr177537540775375472E06942951
chr177537552275375730E06943066
chr177537654875376880E06944092
chr177537688375376937E06944427
chr177537703775377106E06944581
chr177537715775377270E06944701
chr177537729775377913E06944841
chr177537793175378017E06945475
chr177530018875300790E070-31666
chr177530088375300962E070-31494
chr177537415475374270E07041698
chr177537434875374432E07041892
chr177530088375300962E071-31494
chr177530114875301521E071-30935
chr177531764875317692E071-14764
chr177531774275320512E071-11944
chr177535977175360410E07127315
chr177536042775360815E07127971
chr177536094875361075E07128492
chr177536109575361377E07128639
chr177536149675361561E07129040
chr177536165175362651E07129195
chr177536266775363281E07130211
chr177537415475374270E07141698
chr177537434875374432E07141892
chr177537447475374732E07142018
chr177537491075375055E07142454
chr177537510875375266E07142652
chr177537528175375358E07142825
chr177537540775375472E07142951
chr177537552275375730E07143066
chr177537654875376880E07144092
chr177537688375376937E07144427
chr177537703775377106E07144581
chr177537715775377270E07144701
chr177537729775377913E07144841
chr177537838475379658E07145928
chr177537971975379808E07147263
chr177537993775380316E07147481
chr177538032375380719E07147867
chr177538075375380928E07148297
chr177538096375381204E07148507
chr177538138075381486E07148924
chr177538149675381591E07149040
chr177538169875381754E07149242
chr177531166375311882E072-20574
chr177531192175312019E072-20437
chr177531774275320512E072-11944
chr177532692875327104E072-5352
chr177532715175327212E072-5244
chr177532729775329639E072-2817
chr177535499275355289E07222536
chr177535977175360410E07227315
chr177536042775360815E07227971
chr177536149675361561E07229040
chr177536165175362651E07229195
chr177536266775363281E07230211
chr177537415475374270E07241698
chr177537434875374432E07241892
chr177537447475374732E07242018
chr177537491075375055E07242454
chr177537510875375266E07242652
chr177537528175375358E07242825
chr177537540775375472E07242951
chr177537552275375730E07243066
chr177537654875376880E07244092
chr177537688375376937E07244427
chr177537703775377106E07244581
chr177537715775377270E07244701
chr177537971975379808E07247263
chr177537993775380316E07247481
chr177538032375380719E07247867
chr177538169875381754E07249242
chr177530489775305814E073-26642
chr177530989475309987E073-22469
chr177532060575320800E073-11656
chr177532729775329639E073-2817
chr177535499275355289E07322536
chr177535541875355613E07322962
chr177535977175360410E07327315
chr177536042775360815E07327971
chr177536165175362651E07329195
chr177536266775363281E07330211
chr177537415475374270E07341698
chr177537434875374432E07341892
chr177537447475374732E07342018
chr177537491075375055E07342454
chr177537510875375266E07342652
chr177537528175375358E07342825
chr177537540775375472E07342951
chr177537552275375730E07343066
chr177537729775377913E07344841
chr177537793175378017E07345475
chr177537838475379658E07345928
chr177537971975379808E07347263
chr177537993775380316E07347481
chr177531774275320512E074-11944
chr177536149675361561E07429040
chr177536165175362651E07429195
chr177536266775363281E07430211
chr177536341675363574E07430960
chr177537447475374732E07442018
chr177537491075375055E07442454
chr177537510875375266E07442652
chr177537528175375358E07442825
chr177537540775375472E07442951
chr177537552275375730E07443066
chr177537971975379808E07447263
chr177537993775380316E07447481
chr177538032375380719E07447867
chr177538075375380928E07448297
chr177538096375381204E07448507
chr177538138075381486E07448924
chr177538149675381591E07449040
chr177538169875381754E07449242
chr177529981875300152E081-32304
chr177530018875300790E081-31666
chr177530088375300962E081-31494
chr177530114875301521E081-30935
chr177530154075301785E081-30671
chr177530469375304878E081-27578
chr177530489775305814E081-26642
chr177530589575306063E081-26393
chr177531764875317692E081-14764
chr177531774275320512E081-11944
chr177534634175348217E08113885
chr177537415475374270E08141698
chr177537434875374432E08141892
chr177537447475374732E08142018
chr177529981875300152E082-32304
chr177530018875300790E082-31666
chr177530088375300962E082-31494
chr177530114875301521E082-30935
chr177530489775305814E082-26642
chr177531774275320512E082-11944