BDgene

SNP Report

Basic Info
Name rs3738401 dbSNP Ensembl
Location chr1:231694549 - 231694549(1)
Variant Alleles G/A
Ancestral Allele G
Minor Allele A
Minor Allele Frequence 0.232228
Functional Annotation 3_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Polyphen Annotation: benign(ENST00000295051, ENST00000317586, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000622252, ENST00000628350); unknown(ENST00000620189)
SIFT Annotation: tolerated(ENST00000295051, ENST00000317586, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000622252, ENST00000628350, ENST00000620189)
Consequence to Transcript 3_prime_UTR_variant(ENST00000422590, ENST00000602567, ENST00000602634, ENST00000602885, ENST00000602956, ENST00000602962); downstream_gene_variant(ENST00000602600); intron_variant(ENST00000602873); missense_variant(ENST00000295051, ENST00000317586, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000622252, ENST00000628350, ENST00000620189); NMD_transcript_variant(ENST00000295051, ENST00000366632, ENST00000535944, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000422590, ENST00000602567, ENST00000602634, ENST00000602885, ENST00000602956, ENST00000602962); non_coding_transcript_exon_variant(ENST00000468399); non_coding_transcript_variant(ENST00000468399)
No. of Studies 5 (Positive: 0; Negative: 5; 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
Maeda, K., 2006 Arg/Gln data not shown data not shown Analysis of the individual markers identified no significant...... Analysis of the individual markers identified no significant association with BP disorder. More... Negative
Ram Murthy, A., 2012 BPAD patients: P-value=0.368, P-value=0.443 for females, P-v...... BPAD patients: P-value=0.368, P-value=0.443 for females, P-value=0.0614 for males; BPAD&SCZ: P-value=0.520, P-value=0.875 for females, P-value=0.529 for males More... Negative
Schosser, A., 2010 A/G genotypic/allelic test P-value = 0.25/0.49 genotypic/allelic test P-value = 0.25/0.49 Marker rs3738401 was excluded from further analyses, as the ...... Marker rs3738401 was excluded from further analyses, as the controls were out of the HWE and the percentage of missing data was > 10%. More... Negative
Thomson, P. A.,2005(a) Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.83 More... No significant association was observed. No significant association was observed. Negative
Palo, O. M., 2007 G/A P-value = 0.888 in all patients, P-value = 0.281 in males, P...... P-value = 0.888 in all patients, P-value = 0.281 in males, P-value = 0.862 in females, with bipolar spectrum disorder More... With psychotic disorder as an outcome, the analysis of indiv...... With psychotic disorder as an outcome, the analysis of individual SNPs in the complete sample provided only evidence of a trend for an association with rs3738401 in exon 2 (P=0.051, Pseudomarker). More... Negative

SNP related genes (count: 2)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
TSNAX translin-associated factor X 1q42.2 4(3/1/0)
DISC1 disrupted in schizophrenia 1 1q42.1 18(10/7/1)

SNPs in LD with rs3738401 (count: 28) View in gBrowse (chr1:231684331..231723435 )
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: 28)


Overlap with SZ from cross-disorder studies (count: 2)
Reference Statistical Result Description Result Category
Ram Murthy, A., 2012 SZ patients: P-value=0.794, P-value=0.473 for females, P-value=0.427 for males; BPAD&SCZ: P-value=0.520, P-value=0.875 for females, P-value=0.529 for males Negative
Thomson, P. A.,2005(a) Single-Marker Analysis:allele frequency, for SZ, P-value = 0.15 No significant association was observed. Negative

Overlap with MDD from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Schosser, A., 2010 genotypic/allelic test P-value: 0.77/0.59 No significant genotypic or allelic association was observed. Negative

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