rs1053407

Homo sapiens
C>T
ILDR2 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0427 (12776/29900,GnomAD)
T=0411 (11990/29118,TOPMED)
T=0484 (2423/5008,1000G)
T=0423 (1631/3854,ALSPAC)
T=0410 (1521/3708,TWINSUK)
chr1:166913500 (GRCh38.p7) (1q24.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.166913500C>T
GRCh37.p13 chr 1NC_000001.10:g.166882737C>T

Gene: ILDR2, immunoglobulin like domain containing receptor 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ILDR2 transcriptNM_199351.2:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X1XM_017001252.1:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X2XM_017001253.1:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X3XM_017001254.1:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X4XM_017001255.1:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X5XM_017001256.1:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X8XM_006711314.3:c.N/A3 Prime UTR Variant
ILDR2 transcript variant X6XM_017001257.1:c.N/AGenic Downstream Transcript Variant
ILDR2 transcript variant X7XM_017001258.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.626T=0.374
1000GenomesAmericanSub694C=0.620T=0.380
1000GenomesEast AsianSub1008C=0.306T=0.694
1000GenomesEuropeSub1006C=0.538T=0.462
1000GenomesGlobalStudy-wide5008C=0.516T=0.484
1000GenomesSouth AsianSub978C=0.490T=0.510
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.577T=0.423
The Genome Aggregation DatabaseAfricanSub8694C=0.641T=0.359
The Genome Aggregation DatabaseAmericanSub838C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1610C=0.315T=0.685
The Genome Aggregation DatabaseEuropeSub18456C=0.559T=0.440
The Genome Aggregation DatabaseGlobalStudy-wide29900C=0.572T=0.427
The Genome Aggregation DatabaseOtherSub302C=0.520T=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.588T=0.411
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.590T=0.410
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs10534070.000624alcohol consumption (maxi-drinks)24277619

eQTL of rs1053407 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:166882737DUTP6ENSG00000225171.2C>T5.7008e-744752Cerebellum
Chr1:166882737DUTP6ENSG00000225171.2C>T5.4909e-444752Frontal_Cortex_BA9
Chr1:166882737RP4-782G3.1ENSG00000237096.1C>T1.7479e-55420Frontal_Cortex_BA9
Chr1:166882737MAELENSG00000143194.8C>T8.4953e-14-75609Frontal_Cortex_BA9
Chr1:166882737RP4-782G3.1ENSG00000237096.1C>T9.8236e-65420Cortex
Chr1:166882737MAELENSG00000143194.8C>T2.1392e-14-75609Cortex
Chr1:166882737DUTP6ENSG00000225171.2C>T3.8295e-1144752Cerebellar_Hemisphere
Chr1:166882737DUTP6ENSG00000225171.2C>T3.5796e-1144752Caudate_basal_ganglia
Chr1:166882737MAELENSG00000143194.8C>T1.1825e-5-75609Caudate_basal_ganglia
Chr1:166882737MAELENSG00000143194.8C>T1.9878e-11-75609Hippocampus
Chr1:166882737MAELENSG00000143194.8C>T1.1440e-4-75609Putamen_basal_ganglia
Chr1:166882737MAELENSG00000143194.8C>T1.2128e-13-75609Anterior_cingulate_cortex
Chr1:166882737DUTP6ENSG00000225171.2C>T1.0270e-444752Nucleus_accumbens_basal_ganglia
Chr1:166882737MAELENSG00000143194.8C>T1.3509e-9-75609Nucleus_accumbens_basal_ganglia
Chr1:166882737MAELENSG00000143194.8C>T2.9462e-4-75609Amygdala

meQTL of rs1053407 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 )
chr1166841359166841523E067-41214
chr1166842627166842713E067-40024
chr1166843894166843990E067-38747
chr1166844346166844396E067-38341
chr1166913758166913820E06731021
chr1166913942166914201E06731205
chr1166914411166914489E06731674
chr1166919300166919359E06736563
chr1166919473166919697E06736736
chr1166921382166921631E06738645
chr1166921730166921956E06738993
chr1166841359166841523E068-41214
chr1166841951166842001E068-40736
chr1166842196166842282E068-40455
chr1166843894166843990E068-38747
chr1166844346166844396E068-38341
chr1166906544166906985E06823807
chr1166908038166908088E06825301
chr1166913942166914201E06831205
chr1166914411166914489E06831674
chr1166919300166919359E06836563
chr1166919473166919697E06836736
chr1166921217166921277E06838480
chr1166841359166841523E069-41214
chr1166841951166842001E069-40736
chr1166842196166842282E069-40455
chr1166842540166842580E069-40157
chr1166842627166842713E069-40024
chr1166843894166843990E069-38747
chr1166858084166858258E069-24479
chr1166908038166908088E06925301
chr1166913758166913820E06931021
chr1166913942166914201E06931205
chr1166919300166919359E06936563
chr1166919473166919697E06936736
chr1166842540166842580E070-40157
chr1166842627166842713E070-40024
chr1166858084166858258E070-24479
chr1166858332166858427E070-24310
chr1166899310166899479E07016573
chr1166912969166913066E07030232
chr1166913758166913820E07031021
chr1166913942166914201E07031205
chr1166914411166914489E07031674
chr1166919300166919359E07036563
chr1166919473166919697E07036736
chr1166920194166920270E07037457
chr1166920568166920645E07037831
chr1166921217166921277E07038480
chr1166921382166921631E07038645
chr1166921730166921956E07038993
chr1166838124166838184E071-44553
chr1166841359166841523E071-41214
chr1166841951166842001E071-40736
chr1166842196166842282E071-40455
chr1166842540166842580E071-40157
chr1166842627166842713E071-40024
chr1166843894166843990E071-38747
chr1166879386166879451E071-3286
chr1166908038166908088E07125301
chr1166913942166914201E07131205
chr1166914411166914489E07131674
chr1166919300166919359E07136563
chr1166835253166835447E072-47290
chr1166841359166841523E072-41214
chr1166841951166842001E072-40736
chr1166842196166842282E072-40455
chr1166842540166842580E072-40157
chr1166842627166842713E072-40024
chr1166843894166843990E072-38747
chr1166844346166844396E072-38341
chr1166908038166908088E07225301
chr1166913942166914201E07231205
chr1166914411166914489E07231674
chr1166920194166920270E07237457
chr1166920568166920645E07237831
chr1166921217166921277E07238480
chr1166838124166838184E073-44553
chr1166841359166841523E073-41214
chr1166841951166842001E073-40736
chr1166842196166842282E073-40455
chr1166844346166844396E073-38341
chr1166919300166919359E07336563
chr1166919473166919697E07336736
chr1166920194166920270E07337457
chr1166921217166921277E07338480
chr1166921382166921631E07338645
chr1166841359166841523E074-41214
chr1166842627166842713E074-40024
chr1166843894166843990E074-38747
chr1166844346166844396E074-38341
chr1166908038166908088E07425301
chr1166913942166914201E07431205
chr1166914411166914489E07431674
chr1166919300166919359E07436563
chr1166919473166919697E07436736
chr1166843894166843990E081-38747
chr1166844346166844396E081-38341
chr1166858084166858258E081-24479
chr1166858332166858427E081-24310
chr1166894615166894802E08111878
chr1166894861166894986E08112124
chr1166895091166895452E08112354
chr1166908924166909584E08126187
chr1166913758166913820E08131021
chr1166913942166914201E08131205
chr1166919300166919359E08136563
chr1166919473166919697E08136736
chr1166920194166920270E08137457
chr1166921217166921277E08138480
chr1166921382166921631E08138645
chr1166858084166858258E082-24479
chr1166858332166858427E082-24310
chr1166913942166914201E08231205
chr1166919300166919359E08236563
chr1166919473166919697E08236736
chr1166920194166920270E08237457
chr1166921382166921631E08238645
chr1166921730166921956E08238993










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1166844623166846078E067-36659
chr1166846160166846229E067-36508
chr1166853411166853837E067-28900
chr1166889825166890966E0677088
chr1166916414166917455E06733677
chr1166844623166846078E068-36659
chr1166846160166846229E068-36508
chr1166853411166853837E068-28900
chr1166889576166889778E0686839
chr1166889825166890966E0687088
chr1166916414166917455E06833677
chr1166844623166846078E069-36659
chr1166846160166846229E069-36508
chr1166853411166853837E069-28900
chr1166889825166890966E0697088
chr1166916414166917455E06933677
chr1166844623166846078E070-36659
chr1166846160166846229E070-36508
chr1166853411166853837E070-28900
chr1166889825166890966E0707088
chr1166916414166917455E07033677
chr1166844623166846078E071-36659
chr1166846160166846229E071-36508
chr1166853411166853837E071-28900
chr1166889576166889778E0716839
chr1166889825166890966E0717088
chr1166916414166917455E07133677
chr1166844623166846078E072-36659
chr1166853411166853837E072-28900
chr1166889576166889778E0726839
chr1166889825166890966E0727088
chr1166916414166917455E07233677
chr1166844623166846078E073-36659
chr1166846160166846229E073-36508
chr1166853411166853837E073-28900
chr1166889825166890966E0737088
chr1166916414166917455E07333677
chr1166844623166846078E074-36659
chr1166846160166846229E074-36508
chr1166916414166917455E07433677
chr1166844623166846078E082-36659
chr1166846160166846229E082-36508
chr1166889825166890966E0827088
chr1166916414166917455E08233677