rs17079029

Homo sapiens
C>T
RAET1G : Synonymous Variant
RAET1E-AS1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0173 (20924/120826,ExAC)
T=0146 (4388/29952,GnomAD)
T=0123 (3595/29118,TOPMED)
C==0124 (1620/13006,GO-ESP)
T=0227 (1137/5008,1000G)
T=0122 (470/3854,ALSPAC)
T=0132 (489/3708,TWINSUK)
chr6:149918194 (GRCh38.p7) (6q25.1)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
44 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.149918194C>T
GRCh37.p13 chr 6NC_000006.11:g.150239330C>T

Gene: RAET1G, retinoic acid early transcript 1G(minus strand)

Molecule type Change Amino acid[Codon] SO Term
RAET1G transcript variant 1NM_001001788.3:c....NM_001001788.3:c.822G>AR [AGG]> R [AGA]Coding Sequence Variant
UL-16 binding protein 5 preproproteinNP_001001788.2:p....NP_001001788.2:p.Arg274=R [Arg]> R [Arg]Synonymous Variant
RAET1G transcript variant 2NR_130110.1:n.864G>AG>ANon Coding Transcript Variant
RAET1G transcript variant X1XM_017010831.1:c....XM_017010831.1:c.822G>AR [AGG]> R [AGA]Coding Sequence Variant
UL-16 binding protein 5 isoform X1XP_016866320.1:p....XP_016866320.1:p.Arg274=R [Arg]> R [Arg]Synonymous Variant
RAET1G transcript variant X2XM_011535800.2:c....XM_011535800.2:c.822G>AR [AGG]> R [AGA]Coding Sequence Variant
UL-16 binding protein 5 isoform X2XP_011534102.1:p....XP_011534102.1:p.Arg274=R [Arg]> R [Arg]Synonymous Variant

Gene: RAET1E-AS1, RAET1E antisense RNA 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RAET1E-AS1 transcript variant 1NR_045126.1:n.N/AIntron Variant
RAET1E-AS1 transcript variant 2NR_045127.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.898T=0.102
1000GenomesAmericanSub694C=0.890T=0.110
1000GenomesEast AsianSub1008C=0.463T=0.537
1000GenomesEuropeSub1006C=0.849T=0.151
1000GenomesGlobalStudy-wide5008C=0.773T=0.227
1000GenomesSouth AsianSub978C=0.760T=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.878T=0.122
The Exome Aggregation ConsortiumAmericanSub21866C=0.911T=0.088
The Exome Aggregation ConsortiumAsianSub25056C=0.662T=0.337
The Exome Aggregation ConsortiumEuropeSub73014C=0.857T=0.142
The Exome Aggregation ConsortiumGlobalStudy-wide120826C=0.826T=0.173
The Exome Aggregation ConsortiumOtherSub890C=0.820T=0.180
The Genome Aggregation DatabaseAfricanSub8720C=0.881T=0.119
The Genome Aggregation DatabaseAmericanSub836C=0.910T=0.090
The Genome Aggregation DatabaseEast AsianSub1610C=0.455T=0.545
The Genome Aggregation DatabaseEuropeSub18484C=0.872T=0.127
The Genome Aggregation DatabaseGlobalStudy-wide29952C=0.853T=0.146
The Genome Aggregation DatabaseOtherSub302C=0.880T=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.876T=0.123
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.868T=0.132
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
rs170790290.000743alcohol dependence21314694

eQTL of rs17079029 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 rs17079029 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 )
chr6150247950150248068E0678620
chr6150217009150217553E068-21777
chr6150217563150218115E068-21215
chr6150218926150219005E068-20325
chr6150219112150219358E068-19972
chr6150219387150219493E068-19837
chr6150216861150216944E069-22386
chr6150217009150217553E069-21777
chr6150217563150218115E069-21215
chr6150218926150219005E069-20325
chr6150216861150216944E071-22386
chr6150217009150217553E071-21777
chr6150217563150218115E071-21215
chr6150218926150219005E071-20325
chr6150219112150219358E071-19972
chr6150217563150218115E072-21215
chr6150218926150219005E072-20325
chr6150219112150219358E072-19972
chr6150217009150217553E074-21777
chr6150217563150218115E074-21215
chr6150263807150263950E08124477
chr6150263985150264035E08124655







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr6150243601150244880E0674271
chr6150246411150247078E0677081
chr6150247155150247789E0677825
chr6150262492150262613E06723162
chr6150262682150263779E06723352
chr6150284203150286955E06744873
chr6150246411150247078E0687081
chr6150247155150247789E0687825
chr6150262492150262613E06823162
chr6150262682150263779E06823352
chr6150243601150244880E0694271
chr6150246411150247078E0697081
chr6150247155150247789E0697825
chr6150262492150262613E06923162
chr6150262682150263779E06923352
chr6150284203150286955E06944873
chr6150262492150262613E07023162
chr6150262682150263779E07023352
chr6150246411150247078E0717081
chr6150247155150247789E0717825
chr6150262492150262613E07123162
chr6150262682150263779E07123352
chr6150284203150286955E07144873
chr6150246411150247078E0727081
chr6150247155150247789E0727825
chr6150262492150262613E07223162
chr6150262682150263779E07223352
chr6150243601150244880E0734271
chr6150246411150247078E0737081
chr6150247155150247789E0737825
chr6150259365150260839E07320035
chr6150262492150262613E07323162
chr6150262682150263779E07323352
chr6150284203150286955E07344873
chr6150243601150244880E0744271
chr6150246411150247078E0747081
chr6150247155150247789E0747825
chr6150262492150262613E07423162
chr6150262682150263779E07423352
chr6150284203150286955E07444873
chr6150246411150247078E0827081
chr6150247155150247789E0827825
chr6150262492150262613E08223162
chr6150262682150263779E08223352