BDgene

SNP Report

Basic Info
Name rs821616 dbSNP Ensembl
Location chr1:232008852 - 232008852(1)
Variant Alleles A/T
Ancestral Allele A
Minor Allele T
Minor Allele Frequence 0.2502
Functional Annotation 3_prime_UTR_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant.
Polyphen Annotation: possibly damaging(ENST00000366637, ENST00000439617); unknown(ENST00000535983); probably damaging(ENST00000620189)
SIFT Annotation: deleterious(ENST00000366637, ENST00000439617, ENST00000620189)
Consequence to Transcript 3_prime_UTR_variant(ENST00000422590, ENST00000622252); missense_variant(ENST00000366637, ENST00000439617, ENST00000620189, ENST00000535983); NMD_transcript_variant(ENST00000422590); non_coding_transcript_exon_variant(ENST00000427560); non_coding_transcript_variant(ENST00000427560)
No. of Studies 6 (Positive: 1; Negative: 5; Trend: 0)
Source Literature
Overlap with SZ? YES
Overlap with MDD? NO

SNP related studies (count: 6)
Reference Allele Change Risk Allele Statistical Values Author Comments Result Category
Ram Murthy, A., 2012 BPAD patients: P-value=0.035, P-value=0.175 for females, P-v...... BPAD patients: P-value=0.035, P-value=0.175 for females, P-value=0.112 for males; BPAD&SCZ: P-value=0.04, P-value=0.138 for females, P-value=0.183 for males More... One SNP (rs821616) showed moderate significant association w...... One SNP (rs821616) showed moderate significant association with cases compared with controls in regression analysis More... Positive
Green, E. K.,2011 A/T the Cochran-Armitage trend test: genotype P-value = 0.870; a...... the Cochran-Armitage trend test: genotype P-value = 0.870; allele P-value = 0.79, OR(95%CI)=1.02(0.87-1.21) More... No significant association was observed. No significant association was observed. Negative
Prata, D. P.,2011 Ser/Cys Ser In both the prefrontal ROI, and across the whole brain, ther...... In both the prefrontal ROI, and across the whole brain, there were no significant genotype effects in either patient group, or in both combined, and no significant genotype by diagnosis interaction between BD group and control group (all FWE P>0.05). More... No significant association was observed. No significant association was observed. Negative
Maeda, K., 2006 Ser/Cys 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
Palo, O. M., 2007 A/T P-value = 0.218 in all patients, P-value = 0.256 in males, P...... P-value = 0.218 in all patients, P-value = 0.256 in males, P-value = 0.221 in females, with bipolar spectrum disorder 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 = 0.31 More... No significant association was observed. No significant association was observed. 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 rs821616 (count: 36) View in gBrowse (chr1:231958513..232011822 )
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: 36)


Overlap with SZ from cross-disorder studies (count: 3)
Reference Statistical Result Description Result Category
Thomson, P. A.,2005(a) Single-Marker Analysis:allele frequency, for SZ, P-value = 0.5 No significant association was observed. Negative
Ram Murthy, A., 2012 SZ patients: P-value=0.179, P-value=0.213 for females, P-value=0.579 for males; BPAD&SCZ: P-value=0.04, P-value=0.138 for females, P-value=0.183 for males One SNP (rs821616) showed moderate significant association with cases compared with controls in regression analysis Positive
Prata, D. P.,2011 In the left middle/superior frontal gyral ROI (P = 0.002 after FWE small volume correction). There was an interaction between controls and patients with schizophrenia. Positive

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