BDgene

SNP Report

Basic Info
Name rs1954175 dbSNP Ensembl
Location chr1:231719664 - 231719664(1)
Variant Alleles T/C
Ancestral Allele C
Minor Allele C
Minor Allele Frequence 0.280152
Functional Annotation intron_variant; NMD_transcript_variant.
Consequence to Transcript intron_variant(ENST00000295051, ENST00000317586, 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 3 (Positive: 0; Negative: 3; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 3)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Thomson, P. A.,2005(a) Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.69 More... No significant association was observed. No significant association was observed. Negative
Xiao, Y.,2011 C/T C Allelic permutated P-value = 1, genotypic permutated P-valu...... Allelic permutated P-value = 1, genotypic permutated P-value = 0.674 More... No significant association was observed in BD. No significant association was observed in BD. Negative
Maeda, K., 2006 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

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 rs1954175 (count: 30) View in gBrowse (chr1:231684331..231727458 )
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: 30)


Overlap with SZ from cross-disorder studies (count: 1)
Reference Statistical Result Description Result Category
Thomson, P. A.,2005(a) Single-Marker Analysis:allele frequency, for SZ, P-value = 0.093 No significant association was observed. Negative

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