rs6960379

Homo sapiens
T>C
LOC105375323 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0149 (4461/29922,GnomAD)
C=0205 (5983/29118,TOPMED)
C=0136 (682/5008,1000G)
C=0052 (201/3854,ALSPAC)
C=0055 (205/3708,TWINSUK)
chr7:64290139 (GRCh38.p7) (7q11.21)
ND
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
64 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.64290139T>C
GRCh37.p13 chr 7NC_000007.13:g.63750517T>C

Gene: LOC105375323, uncharacterized LOC105375323(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105375323 transcript variant X3XR_001745021.1:n....XR_001745021.1:n.52A>GA>GNon Coding Transcript Variant
LOC105375323 transcript variant X4XR_927595.2:n.N/AIntron Variant
LOC105375323 transcript variant X1XR_927597.2:n.N/AIntron Variant
LOC105375323 transcript variant X2XR_001745020.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.557C=0.443
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=0.998C=0.002
1000GenomesEuropeSub1006T=0.952C=0.048
1000GenomesGlobalStudy-wide5008T=0.864C=0.136
1000GenomesSouth AsianSub978T=0.990C=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.948C=0.052
The Genome Aggregation DatabaseAfricanSub8698T=0.599C=0.401
The Genome Aggregation DatabaseAmericanSub838T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1622T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18462T=0.952C=0.047
The Genome Aggregation DatabaseGlobalStudy-wide29922T=0.850C=0.149
The Genome Aggregation DatabaseOtherSub302T=0.880C=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.794C=0.205
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.945C=0.055
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
rs69603796.58E-05nicotine smoking19268276

eQTL of rs6960379 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 rs6960379 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 )
chr76377654563776640E06726028
chr76377377563773836E06823258
chr76376629263766527E06915775
chr76376659363766667E06916076
chr76376670563766762E06916188
chr76377331863773475E07022801
chr76377357463773624E07023057
chr76377377563773836E07023258
chr76377664963776713E07126132
chr76376629263766527E07215775
chr76376659363766667E07216076
chr76377377563773836E07223258
chr76377357463773624E08123057
chr76377377563773836E08123258
chr76377654563776640E08126028







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr76376681263767292E06716295
chr76376738363767445E06716866
chr76376753563768684E06717018
chr76377396463774930E06723447
chr76377499063775597E06724473
chr76377580763775873E06725290
chr76377593763775989E06725420
chr76376681263767292E06816295
chr76376738363767445E06816866
chr76376753563768684E06817018
chr76377396463774930E06823447
chr76377499063775597E06824473
chr76377580763775873E06825290
chr76377593763775989E06825420
chr76376681263767292E06916295
chr76376738363767445E06916866
chr76376753563768684E06917018
chr76377396463774930E06923447
chr76377499063775597E06924473
chr76377580763775873E06925290
chr76377593763775989E06925420
chr76376681263767292E07016295
chr76376738363767445E07016866
chr76376753563768684E07017018
chr76377396463774930E07023447
chr76377499063775597E07024473
chr76377580763775873E07025290
chr76377593763775989E07025420
chr76376681263767292E07116295
chr76376738363767445E07116866
chr76376753563768684E07117018
chr76377396463774930E07123447
chr76377499063775597E07124473
chr76377580763775873E07125290
chr76377593763775989E07125420
chr76376681263767292E07216295
chr76376738363767445E07216866
chr76376753563768684E07217018
chr76377396463774930E07223447
chr76377499063775597E07224473
chr76377580763775873E07225290
chr76377593763775989E07225420
chr76376681263767292E07316295
chr76376738363767445E07316866
chr76376753563768684E07317018
chr76377396463774930E07323447
chr76377499063775597E07324473
chr76377580763775873E07325290
chr76377593763775989E07325420
chr76376681263767292E07416295
chr76376738363767445E07416866
chr76376753563768684E07417018
chr76377396463774930E07423447
chr76377499063775597E07424473
chr76376738363767445E08116866
chr76376753563768684E08117018
chr76377499063775597E08124473
chr76376681263767292E08216295
chr76376738363767445E08216866
chr76376753563768684E08217018
chr76377396463774930E08223447
chr76377499063775597E08224473
chr76377580763775873E08225290
chr76377593763775989E08225420