rs17552189

Homo sapiens
C>T
LINC01122 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0302 (9020/29832,GnomAD)
T=0267 (7778/29116,TOPMED)
T=0217 (1086/5008,1000G)
T=0390 (1504/3854,ALSPAC)
T=0395 (1465/3708,TWINSUK)
chr2:58845834 (GRCh38.p7) (2p16.1)
AD
GWASdb2
2   publication(s)
See rs on genome
27 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.58845834C>T
GRCh37.p13 chr 2NC_000002.11:g.59072969C>T

Gene: LINC01122, long intergenic non-protein coding RNA 1122(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01122 transcriptNR_033873.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.871T=0.129
1000GenomesAmericanSub694C=0.740T=0.260
1000GenomesEast AsianSub1008C=0.860T=0.140
1000GenomesEuropeSub1006C=0.607T=0.393
1000GenomesGlobalStudy-wide5008C=0.783T=0.217
1000GenomesSouth AsianSub978C=0.790T=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.610T=0.390
The Genome Aggregation DatabaseAfricanSub8708C=0.819T=0.181
The Genome Aggregation DatabaseAmericanSub832C=0.760T=0.240
The Genome Aggregation DatabaseEast AsianSub1564C=0.859T=0.141
The Genome Aggregation DatabaseEuropeSub18426C=0.622T=0.377
The Genome Aggregation DatabaseGlobalStudy-wide29832C=0.697T=0.302
The Genome Aggregation DatabaseOtherSub302C=0.780T=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.732T=0.267
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.605T=0.395
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
21668797A genome-wide association study of DSM-IV cannabis dependence.Agrawal AAddict Biol

P-Value

SNP ID p-value Traits Study
rs175521890.0000846alcoholismpha002892
rs175521890.000085alcohol dependence20201924

eQTL of rs17552189 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 rs17552189 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 )
chr25912075259121537E07047783
chr25902572159025784E081-47185
chr25902597259026053E081-46916
chr25902607659026198E081-46771
chr25902623859026332E081-46637
chr25902640459026636E081-46333
chr25908676559087312E08113796
chr25908741559087491E08114446
chr25908749659087550E08114527
chr25910239959103165E08129430
chr25910324259103510E08130273
chr25910352359103619E08130554
chr25910397259104038E08131003
chr25912041259120647E08147443
chr25912075259121537E08147783
chr25902354459023664E082-49305
chr25902371459023883E082-49086
chr25902572159025784E082-47185
chr25902597259026053E082-46916
chr25902607659026198E082-46771
chr25903969859039770E082-33199
chr25903978859039838E082-33131
chr25908068859080770E0827719
chr25910239959103165E08229430
chr25910324259103510E08230273
chr25910352359103619E08230554
chr25910397259104038E08231003