BDgene

SNP Report

Basic Info
Name rs2251219 dbSNP Ensembl
Location chr3:52550771 - 52550771(1)
Variant Alleles T/C
Ancestral Allele T
Minor Allele C
Minor Allele Frequence 0.323083
Functional Annotation 3_prime_UTR_variant; downstream_gene_variant; intron_variant; NMD_transcript_variant; synonymous_variant.
Consequence to Transcript 3_prime_UTR_variant(ENST00000412587); downstream_gene_variant(ENST00000423351, ENST00000516959); intron_variant(ENST00000476842); NMD_transcript_variant(ENST00000412587); synonymous_variant(ENST00000296302, ENST00000337303, ENST00000356770, ENST00000394830, ENST00000409057, ENST00000409114, ENST00000409767, ENST00000410007)
No. of Studies 5 (Positive: 5; Negative: 0; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 5)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
McMahon, F. J., 2010 P-value = 3.63E-8, odds ratio = 0.87, 95% confidence interva...... P-value = 3.63E-8, odds ratio = 0.87, 95% confidence interval=0.83-0.92 for all major mood disorders. The C allele was consistently less common in cases than controls (P-value = 1.12E-8). More... rs2251219 was significantly associated with major mood disor...... rs2251219 was significantly associated with major mood disorder. The findings were more robust in bipolar disorder than in MDD.The result is replicable in replication samples. We did not find a significant association signal at any of these loci after genome-wide correction for multiple testing. Our genetic association results provide support for the previous epidemiologic evidence of genetic overlap between bipolar disorder and MDD. More... Positive
Chen, D. T.,2011 T Meta-analysis results by ancestry: European and Asian-ancest...... Meta-analysis results by ancestry: European and Asian-ancestry phase I samples: Fixed effects P-value = 6.35E-07, Random effects P-value = 5.63E-07, I2=0, Q test=2.82, Q test P-value = 0.421; European and Asian-ancestry phase I & phase II samples: Fixed effects P-value = 1.84E-07, Random effects P-value = 1.63E-07, I2=32.9, Q test=7.45, Q test P-value = 0.189; European-ancestry phase I samples: Fixed effects P-value = 2.81E-07, Random effects P-value = 2.36E-07, I2=0, Q test=0.69, Q test P-value = 0.708; European-ancestry phase I and phase II samples: Fixed effects P-value = 1.03E-07, Random effects P-value = 8.39E-08, I2=29.5, Q test=5.67, Q test P-value = 0.225 More... The results suggest novel association findings. The results suggest novel association findings. Positive
Major Depressive Disorder Working Group of the Psychiatric, G. C., 2013 P-value=0.0000000438, OR=1.149 for BIP, P-value=0.0000000191...... P-value=0.0000000438, OR=1.149 for BIP, P-value=0.00000001913, OR=1.1 for combined sample More... In the combined analysis of these 819 SNPs, 15 exceeded geno...... In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.2. More... Positive
Kondo, K.,2013 A/G P-value = 0.011,OR= 1.17;P-value = 0.042,P-vorrection = 0.08...... P-value = 0.011,OR= 1.17;P-value = 0.042,P-vorrection = 0.085,OR = 1.11 for replication. More... Significant association was observed. Significant association was observed. Positive
Vassos, E.,2012 T/C T Case-control study OR= 0.89, P-value = 0 .003; meta-analysis...... Case-control study OR= 0.89, P-value = 0 .003; meta-analysis OR=0.875, P-value = 2.68E-9 More... rs2251219 was associated with BP rs2251219 was associated with BP Positive

SNP related genes (count: 3)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
RNU6-856P RNA, U6 small nuclear 856, pseudogene 3p21.1 Mapped by Literature SNP
SMIM4 small integral membrane protein 4 3p21.1 Mapped by Literature SNP
PBRM1 polybromo 1 3p21 5(4/0/1)

SNPs in LD with rs2251219 (count: 94) View in gBrowse (chr3:52502498..52747523 )
The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r2<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 94)


Overlap with SZ from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Vassos, E.,2012 Association analysis:allele P-value = 0.21, OR=0.97 No significant association was observed in SZ. Negative
Kondo, K.,2013 P-value = 0.0018,OR= 1.21;P-value = 0.0051,P-vorrection = 0.01,OR = 1.13 for replication. Significant association was observed. Positive

Overlap with MDD from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Major Depressive Disorder Working Group of the Psychiatric, G. C., 2013 P-value=0.008059, OR=1.062 for MDD, P-value=0.00000001913, OR=1.1 for combined sample In the combined analysis of these 819 SNPs, 15 exceeded genome-wide significance and all were in a 248 kb interval of high LD on 3p21.2. Positive
McMahon, F. J., 2010 rs2251219 was significantly associated with major mood disorder. The findings were more robust in bipolar disorder than in MDD.The result is replicable in replication samples. We did not find a significant association signal at any of these loci after genome-wide correction for multiple testing. Our genetic association results provide support for the previous epidemiologic evidence of genetic overlap between bipolar disorder and MDD. Positive

Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback Acknowledgements
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Last update: March 31, 2016