rs6955604

Homo sapiens
G>C
GLI3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0380 (11394/29918,GnomAD)
C=0305 (8907/29118,TOPMED)
C=0391 (1960/5008,1000G)
C=0433 (1668/3854,ALSPAC)
C=0427 (1584/3708,TWINSUK)
chr7:42217285 (GRCh38.p7) (7p14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
66 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.42217285G>C
GRCh37.p13 chr 7NC_000007.13:g.42256884G>C
GLI3 RefSeqGeneNG_008434.1:g.24735C>G

Gene: GLI3, GLI family zinc finger 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GLI3 transcriptNM_000168.5:c.N/AIntron Variant
GLI3 transcript variant X2XM_011515274.2:c.N/AGenic Upstream Transcript Variant
GLI3 transcript variant X1XM_017011997.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.929C=0.071
1000GenomesAmericanSub694G=0.590C=0.410
1000GenomesEast AsianSub1008G=0.317C=0.683
1000GenomesEuropeSub1006G=0.584C=0.416
1000GenomesGlobalStudy-wide5008G=0.609C=0.391
1000GenomesSouth AsianSub978G=0.520C=0.480
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.567C=0.433
The Genome Aggregation DatabaseAfricanSub8718G=0.869C=0.131
The Genome Aggregation DatabaseAmericanSub836G=0.560C=0.440
The Genome Aggregation DatabaseEast AsianSub1618G=0.256C=0.744
The Genome Aggregation DatabaseEuropeSub18444G=0.535C=0.464
The Genome Aggregation DatabaseGlobalStudy-wide29918G=0.619C=0.380
The Genome Aggregation DatabaseOtherSub302G=0.620C=0.380
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.694C=0.305
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.573C=0.427
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
rs69556040.000173nicotine smoking19268276

eQTL of rs6955604 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 rs6955604 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 )
chr74221400342214530E068-42354
chr74221553642215815E068-41069
chr74221584842216342E068-40542
chr74221647442216591E068-40293
chr74221668042216777E068-40107
chr74221678742216884E068-40000
chr74222522942225303E068-31581
chr74222538142225530E068-31354
chr74222562742225707E068-31177
chr74222588842226033E068-30851
chr74228682942287558E06829945
chr74221400342214530E069-42354
chr74221455842214744E069-42140
chr74223209442232307E069-24577
chr74223230942233876E069-23008
chr74221584842216342E070-40542
chr74221647442216591E070-40293
chr74221668042216777E070-40107
chr74221678742216884E070-40000
chr74225290642253042E070-3842
chr74225305942253109E070-3775
chr74225313842253182E070-3702
chr74226003142260608E0703147
chr74230209742302299E07045213
chr74230246942302961E07045585
chr74230333942303514E07046455
chr74230358042303703E07046696
chr74221584842216342E071-40542
chr74223230942233876E071-23008
chr74223388942234251E071-22633
chr74224490242244988E072-11896
chr74224826942248471E072-8413
chr74221455842214744E074-42140
chr74221668042216777E074-40107
chr74221678742216884E074-40000
chr74221702642217227E074-39657
chr74221729742217375E074-39509
chr74221738642217442E074-39442
chr74223230942233876E074-23008
chr74221317142213351E081-43533
chr74221348142213558E081-43326
chr74221361242213661E081-43223
chr74221374842213841E081-43043
chr74221400342214530E081-42354
chr74221455842214744E081-42140
chr74221584842216342E081-40542
chr74221647442216591E081-40293
chr74222963242229703E081-27181
chr74223774442238449E081-18435
chr74223867742238902E081-17982
chr74223890542239251E081-17633
chr74223928242239342E081-17542
chr74224678742246876E081-10008
chr74225469742254778E081-2106
chr74225496842255022E081-1862
chr74226003142260608E0813147
chr74226061542260895E0813731
chr74226092842261182E0814044
chr74226154642262898E0814662
chr74227340342273984E08116519
chr74230246942302961E08145585
chr74221584842216342E082-40542
chr74221647442216591E082-40293
chr74221668042216777E082-40107
chr74221678742216884E082-40000
chr74223867742238902E082-17982








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr74227472542279419E06717841
chr74227472542279419E06817841
chr74227472542279419E06917841
chr74227472542279419E07017841
chr74227472542279419E07117841
chr74227472542279419E07217841
chr74227472542279419E07317841
chr74227472542279419E07417841
chr74227472542279419E08217841