rs716703

Homo sapiens
C>T
BCL9 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0066 (1998/29944,GnomAD)
T=0090 (2640/29118,TOPMED)
T=0062 (308/5008,1000G)
T=0023 (87/3854,ALSPAC)
T=0022 (82/3708,TWINSUK)
chr1:147549375 (GRCh38.p7) (1q21.2)
ND
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.147549375C>T
GRCh37.p13 chr 1 fix patch HG1287_PATCHNW_003871055.3:g.4364788C>T
GRCh37.p13 chr 1NC_000001.10:g.147021148C>T

Gene: BCL9, B-cell CLL/lymphoma 9(plus strand)

Molecule type Change Amino acid[Codon] SO Term
BCL9 transcriptNM_004326.3:c.N/AIntron Variant
BCL9 transcript variant X2XM_005277417.3:c.N/AIntron Variant
BCL9 transcript variant X3XM_005277418.3:c.N/AIntron Variant
BCL9 transcript variant X1XM_005272971.4:c.N/AGenic Upstream Transcript Variant
BCL9 transcript variant X4XM_017002026.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.809T=0.191
1000GenomesAmericanSub694C=0.980T=0.020
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=0.965T=0.035
1000GenomesGlobalStudy-wide5008C=0.938T=0.062
1000GenomesSouth AsianSub978C=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.977T=0.023
The Genome Aggregation DatabaseAfricanSub8710C=0.828T=0.172
The Genome Aggregation DatabaseAmericanSub836C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1616C=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18480C=0.974T=0.025
The Genome Aggregation DatabaseGlobalStudy-wide29944C=0.933T=0.066
The Genome Aggregation DatabaseOtherSub302C=0.970T=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.909T=0.090
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.978T=0.022
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs7167030.000539nicotine dependence17158188

eQTL of rs716703 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 rs716703 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 )
chr143269434327027E069-37761
chr143670344367088E0692246
chr143269434327027E070-37761
chr143272714327328E070-37460
chr143275614327792E070-36996
chr144051934405289E07040405
chr144059794406023E07041191
chr143676024367657E0712814
chr143228894323358E081-41430
chr143296564329758E081-35030
chr143306134330782E081-34006
chr143307944331107E081-33681
chr143313794331448E081-33340
chr143782344378397E08113446
chr143794804379551E08114692
chr143796074379900E08114819
chr143818214382075E08117033
chr143296564329758E082-35030
chr143638454363914E082-874
chr143794804379551E08214692
chr143796074379900E08214819
chr143818214382075E08217033