BDgene

SNP Report

Basic Info
Name rs1538979 dbSNP Ensembl
Location chr1:231761122 - 231761122(1)
Variant Alleles C/T
Ancestral Allele C
Minor Allele T
Minor Allele Frequence 0.236022
Functional Annotation intron_variant; NMD_transcript_variant.
Consequence to Transcript intron_variant(ENST00000295051, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000422590, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602873, ENST00000602885, ENST00000602956, ENST00000602962, ENST00000620189, ENST00000622252, ENST00000628350); NMD_transcript_variant(ENST00000295051, ENST00000366632, ENST00000422590, ENST00000535944, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602885, ENST00000602956, ENST00000602962)
No. of Studies 2 (Positive: 1; Negative: 1; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 2)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Hennah, W.,2009 In the Finnish cohorts, uncorrected P-value = 0.00020; cor...... In the Finnish cohorts, uncorrected P-value = 0.00020; corrected P-value = 0.016; odds ratio=2.73, 95%, confidence interval (CI) 1.42-5.27 More... Significant associations were found . Significant associations were found . Positive
Chakirova, G.,2011 C/T T (CC+CT)>CC: for BD, P-value > 0.05 (CC+CT)>CC: for BD, P-value > 0.05 No significant association was observed. No significant association was observed. Negative

SNP related genes (count: 1)
Approved Symbol Approved Name Location No. of Studies (Positive/Negative/Trend)
DISC1 disrupted in schizophrenia 1 1q42.1 18(10/7/1)

SNPs in LD with rs1538979 (count: 5) View in gBrowse (chr1:231761122..231773009 )
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: 5)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Chakirova, G.,2011 (CC+CT)>CC:for SZ, in the left postcentral gyrus (P-value corrected=0.001, z=4.39) for the sentence completion versus baseline. The schizophrenia group activation was significantly increased in those carrying the risk allele of rs1538979 compared to non-carriers in the left postcentral gyrus for the sentence completion versus baseline. Positive

Overlap with MDD from cross-disorder studies (count: 0)

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