BDgene

SNP Report

Basic Info
Name rs6313 dbSNP Ensembl
Location chr13:46895805 - 46895805(1)
Variant Alleles G/A
Ancestral Allele G
Minor Allele A
Minor Allele Frequence 0.441294
Functional Annotation intron_variant; synonymous_variant.
Consequence to Transcript intron_variant(ENST00000543956); synonymous_variant(ENST00000378688, ENST00000542664, ENST00000612998)
No. of Studies 4 (Positive: 0; Negative: 4; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? YES

SNP related studies (count: 4)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Tan J., 2014 T/C Overall: T vs. C (Allele frequency): OR=0.987, 95%CI=0.908-1...... Overall: T vs. C (Allele frequency): OR=0.987, 95%CI=0.908-1.073, P-value=0.761; TT + TC vs. CC (Dominant): OR=0.972, 95%CI=0.838-1.128, P-value=0.708; TT vs. TC + CC (Recessive): OR=1.064, 95%CI=0.913-1.240, P-value=0.428; TT vs. TC (Codominant1): OR=1.073, 95%CI=0.912-1.263, P-value=0.394; TC vs. CC (Codominant2): OR=0.957, 95%CI=0.818-1.120, P-value=0.581; TT vs. CC (Homozygote): OR=1.004, 95%CI=0.831-1.214, P-value=0.964. Caucasian: T vs. C (Allele frequency): OR=0.904, 95%CI=0.806-1.014, P-value=0.086; TT + TC vs. CC (Dominant): OR=0.920, 95%CI=0.759-1.116, P-value=0.399; TT vs. TC + CC (Recessive): OR=0.915, 95%CI=0.728-1.150, P-value=0.446; TT vs. TC (Codominant1): OR=0.936, 95%CI=0.736-1.192, P-value=0.592; TC vs. CC (Codominant2): OR=0.942, 95%CI=0.768-1.156, P-value=0.568; TT vs. CC (Homozygote): OR=0.869, 95%CI=0.668-1.130, P-value=0.294. Asian: T vs. C (Allele frequency): OR=1.089, 95%CI=0.964-1.230, P-value=0.169; TT + TC vs. CC (Dominant): OR=1.052, 95%CI=0.834-1.326, P-value=0.669; TT vs. TC + CC (Recessive): OR=1.205, 95%CI=0.979-1.482, P-value=0.078; TT vs. TC (Codominant1): OR=1.203, 95%CI=0.965-1.500, P-value=0.1; TC vs. CC (Codominant2): OR=0.978, 95%CI=0.764-1.252, P-value=0.861; TT vs. CC (Homozygote): OR=1.175, 95%CI=0.894-1.545, P-value=0.248. Chinese: T vs. C (Allele frequency): OR=1.037, 95%CI=0.799-1.346, P-value=0.784; TT + TC vs. CC (Dominant): OR=0.933, 95%CI=0.570-1.526, P-value=0.782; TT vs. TC + CC (Recessive): OR=1.128, 95%CI=0.771-1.651, P-value=0.535; TT vs. TC (Codominant1): OR=1.166, 95%CI=0.780-1.743, P-value=0.454; TC vs. CC (Codominant2): OR=0.867, 95%CI=0.515-1.460, P-value=0.592; TT vs. CC (Homozygote): OR=1.030, 95%CI=0.595-1.783, P-value=0.915 More... The results of our study indicate that theT102C polymorphism...... The results of our study indicate that theT102C polymorphism is not associates with increased susceptibility to BPD. More... Negative
Yosifova, A.,2009 A/G Allelic association: P-value = 0.071 Allelic association: P-value = 0.071 No significant association was observed No significant association was observed Negative
Kishi, T.,2009(b) T/C chi-square test: 1.total samples: P-value = 0.172(Genotype),...... chi-square test: 1.total samples: P-value = 0.172(Genotype), P-value = 0.104(Allele) in BP 2. male samples: P-value = 0.533(Genotype), P-value = 0.324(Allele) in BP 3. female samples: P-value = 0.0643(Genotype), P-value = 0.208(Allele) in BP More... No significant association was observed No significant association was observed Negative
McAuley, E. Z.,2009 single marker association: Asymptotic P-value = 0.46, Empiri...... single marker association: Asymptotic P-value = 0.46, Empirical P-value = 0.49, Odds ratio=0.9 More... No significant allelic association with BP was found No significant allelic association with BP was found Negative

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
HTR2A 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled 13q14-q21 22(7/15/0)

SNPs in LD with rs6313 (count: 22) View in gBrowse (chr13:46865236..46949489 )
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: 22)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Tan J., 2014 Overall: T vs. C (Allele frequency): OR=0.970, 95%CI=0.914-1.030, P-value=0.316; TT + TC vs. CC (Dominant): OR=0.970, 95%CI=0.888-1.059, P-value=0.495; TT vs. TC + CC (Recessive): OR=0.965, 95%CI=0.885-1.053, P-value=0.428; TT vs. TC (Codominant1): OR=0.982, 95%CI=0.921-1.047, P-value=0.578; TC vs. CC (Codominant2): OR=1.010, 95%CI=0.949-1.074, P-value=0.761; TT vs. CC (Homozygote): OR=0.948, 95%CI=0.838-1.073, P-value=0.397. Caucasian: T vs. C (Allele frequency): OR=0.994, 95%CI=0.903-1.093, P-value=0.894; TT + TC vs. CC (Dominant): OR=0.989, 95%CI=0.887-1.102, P-value=0.84; TT vs. TC + CC (Recessive): OR=0.989, 95%CI=0.838-1.167, P-value=0.895; TT vs. TC (Codominant1): OR=1.011, 95%CI=0.919-1.112, P-value=0.824; TC vs. CC (Codominant2): OR=1.018, 95%CI=0.940-1.102, P-value=0.664; TT vs. CC (Homozygote): OR=0.968, 95%CI=0.796-1.178, P-value=0.747. Asian: T vs. C (Allele frequency): OR=0.952, 95%CI=0.879-1.032, P-value=0.232; TT + TC vs. CC (Dominant): OR=0.956, 95%CI=0.822-1.113, P-value=0.564; TT vs. TC + CC (Recessive): OR=0.949, 95%CI=0.867-1.040, P-value=0.265; TT vs. TC (Codominant1): OR=0.951, 95%CI=0.870-1.038, P-value=0.261; TC vs. CC (Codominant2): OR=1.016, 95%CI=0.917-1.126, P-value=0.761; TT vs. CC (Homozygote): OR=0.933, 95%CI=0.786-1.106, P-value=0.423. Other/Mixed: T vs. C (Allele frequency): OR=0.929, 95%CI=0.742-1.164, P-value=0.523; TT + TC vs. CC (Dominant): OR=0.834, 95%CI=0.521-1.333, P-value=0.447; TT vs. TC + CC (Recessive): OR=1.034, 95%CI=0.719-1.486, P-value=0.856; TT vs. TC (Codominant1): OR=1.142, 95%CI=0.772-1.69, P-value=0.505; TC vs. CC (Codominant2): OR=0.769, 95%CI=0.525-1.128, P-value=0.179; TT vs. CC (Homozygote): OR=0.882, 95%CI=0.572-1.360, P-value=0.57. Chinese: T vs. C (Allele frequency): OR=0.990, 95%CI=0.925-1.059, P-value=0.77; TT + TC vs. CC (Dominant): OR=1.017, 95%CI=0.899-1.150, P-value=0.793; TT vs. TC + CC (Recessive): OR=0.967, 95%CI=0.875-1.069, P-value=0.516; TT vs. TC (Codominant1): OR=0.957, 95%CI=0.861-1.064, P-value=0.419; TC vs. CC (Codominant2): OR=1.032, 95%CI=0.905-1.176, P-value=0.64; TT vs. CC (Homozygote): OR=1.004, 95%CI=0.872-1.154, P-value=0.961 The results of our study indicate that theT102C polymorphism is not associates with increased susceptibility to SCZ. Negative

Overlap with MDD from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Tan J., 2014 Overall: T vs. C (Allele frequency): OR=1.006, 95%CI=0.914-1.107, P-value=0.908; TT + TC vs. CC (Dominant): OR=0.999, 95%CI=0.845-1.181, P-value=0.994; TT vs. TC + CC (Recessive): OR=1.033, 95%CI=0.919-1.161, P-value=0.592; TT vs. TC (Codominant1): OR=1.022, 95%CI=0.903-1.158, P-value=0.73; TC vs. CC (Codominant2): OR=1.012, 95%CI=0.891-1.148, P-value=0.856; TT vs. CC (Homozygote): OR=0.993, 95%CI=0.807-1.222, P-value=0.949. Caucasian: T vs. C (Allele frequency): OR=1.055, 95%CI=0.894-1.246, P-value=0.528; TT + TC vs. CC (Dominant): OR=1.085, 95%CI=0.806-1.461, P-value=0.689; TT vs. TC + CC (Recessive): OR=1.068, 95%CI=0.852-1.339, P-value=0.568; TT vs. TC (Codominant1): OR=1.028, 95%CI=0.809-1.306, P-value=0.824; TC vs. CC (Codominant2): OR=1.085, 95%CI=0.878-1.342, P-value=0.449; TT vs. CC (Homozygote): OR=1.092, 95%CI=0.781-1.527, P-value=0.607. Asian: T vs. C (Allele frequency): OR=0.980, 95%CI=0.868-1.106, P-value=0.743; TT + TC vs. CC (Dominant): OR=0.950, 95%CI=0.772-1.169, P-value=0.629; TT vs. TC + CC (Recessive): OR=1.020, 95%CI=0.890-1.169, P-value=0.778; TT vs. TC (Codominant1): OR=1.020, 95%CI=0.882-1.180, P-value=0.788; TC vs. CC (Codominant2): OR=0.973, 95%CI=0.831-1.139, P-value=0.737; TT vs. CC (Homozygote): OR=0.936, 95%CI=0.713-1.229, P-value=0.635. Chinese: T vs. C (Allele frequency): OR=1.008, 95%CI=0.864-1.177, P-value=0.917; TT + TC vs. CC (Dominant): OR=1.034, 95%CI=0.850-1.259, P-value=0.736; TT vs. TC + CC (Recessive): OR=1.042, 95%CI=0.877-1.238, P-value=0.637; TT vs. TC (Codominant1): OR=1.021, 95%CI=0.851-1.225, P-value=0.823; TC vs. CC (Codominant2): OR=1.026, 95%CI=0.833-1.264, P-value=0.81; TT vs. CC (Homozygote): OR=0.977, 95%CI=0.664-1.436, P-value=0.905 The results of our study indicate that theT102C polymorphism is not associates with increased susceptibility to MDD. Negative
Kishi, T.,2009(b) chi-square test: 1.total samples:P-value = 0.430(Genotype), P-value = 0.254(Allele) in Mood disorders;P-value = 0.883(Genotype), P-value = 0.656(Allele) in MDD 2. male samples: P-value = 0.424(Genotype), P-value = 0.240(Allele) in Mood disorders;P-value = 0.616(Genotype), P-value = 0.361(Allele) in MDD 3. female samples: P-value = 0.310(Genotype), P-value = 0.731(Allele) in Mood disorders;P-value = 0.763(Genotype), P-value = 0.732(Allele) in MDD we did not detect any significant association of HTR2A with MDD or BP in allele/genotype-wise analysis. Negative

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