rs6661946

Homo sapiens
C>T
HEATR1 : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0079 (9648/121284,ExAC)
T=0120 (3600/29956,GnomAD)
C==0133 (1736/13006,GO-ESP)
T=0172 (860/5008,1000G)
T=0036 (138/3854,ALSPAC)
T=0031 (114/3708,TWINSUK)
chr1:236559808 (GRCh38.p7) (1q43)
ND
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.236559808C>T
GRCh37.p13 chr 1NC_000001.10:g.236723108C>T

Gene: HEATR1, HEAT repeat containing 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
HEATR1 transcriptNM_018072.5:c.467...NM_018072.5:c.4676G>AS [AGT]> N [AAT]Coding Sequence Variant
HEAT repeat-containing protein 1NP_060542.4:p.Ser...NP_060542.4:p.Ser1559AsnS [Ser]> N [Asn]Missense Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.632T=0.368
1000GenomesAmericanSub694C=0.860T=0.140
1000GenomesEast AsianSub1008C=0.823T=0.177
1000GenomesEuropeSub1006C=0.967T=0.033
1000GenomesGlobalStudy-wide5008C=0.828T=0.172
1000GenomesSouth AsianSub978C=0.930T=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.964T=0.036
The Exome Aggregation ConsortiumAmericanSub21956C=0.780T=0.219
The Exome Aggregation ConsortiumAsianSub25134C=0.907T=0.093
The Exome Aggregation ConsortiumEuropeSub73286C=0.966T=0.033
The Exome Aggregation ConsortiumGlobalStudy-wide121284C=0.920T=0.079
The Exome Aggregation ConsortiumOtherSub908C=0.930T=0.070
The Genome Aggregation DatabaseAfricanSub8700C=0.683T=0.317
The Genome Aggregation DatabaseAmericanSub838C=0.870T=0.130
The Genome Aggregation DatabaseEast AsianSub1616C=0.876T=0.124
The Genome Aggregation DatabaseEuropeSub18500C=0.972T=0.027
The Genome Aggregation DatabaseGlobalStudy-wide29956C=0.879T=0.120
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.969T=0.031
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
rs66619464.11E-06nicotine smoking19268276

eQTL of rs6661946 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 rs6661946 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 )
chr1236699210236699398E067-23710
chr1236699210236699398E069-23710
chr1236738259236738320E06915151
chr1236738941236739087E06915833
chr1236739422236739564E06916314
chr1236699871236700086E070-23022
chr1236699210236699398E071-23710
chr1236699871236700086E071-23022
chr1236738070236738185E07114962
chr1236738259236738320E07115151
chr1236738941236739087E07115833
chr1236699210236699398E072-23710
chr1236699871236700086E072-23022
chr1236741177236741241E08118069
chr1236752344236752444E08129236
chr1236752876236753202E08129768
chr1236753228236753496E08130120
chr1236765574236765662E08242466







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1236686087236688427E067-34681
chr1236767227236768577E06744119
chr1236686087236688427E068-34681
chr1236767227236768577E06844119
chr1236686087236688427E069-34681
chr1236767227236768577E06944119
chr1236686087236688427E070-34681
chr1236767227236768577E07044119
chr1236686087236688427E071-34681
chr1236767227236768577E07144119
chr1236686087236688427E072-34681
chr1236767227236768577E07244119
chr1236686087236688427E073-34681
chr1236767227236768577E07344119
chr1236686087236688427E074-34681
chr1236767227236768577E07444119
chr1236686087236688427E081-34681
chr1236686087236688427E082-34681
chr1236767227236768577E08244119