SNP Report

Basic Info

Name	rs1938526 dbSNP Ensembl
Location	chr10:60540625 - 60540625(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.147165
Functional Annotation	intron_variant; NMD_transcript_variant; non_coding_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000373827, ENST00000503366, ENST00000510382, ENST00000622427); NMD_transcript_variant(ENST00000622427); non_coding_transcript_variant(ENST00000510382)
No. of Studies	5 (Positive: 3; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 5)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Lim C.H., 2014	T/C	C	All ethnicities: OR=0.92, 95%CI =0.72-1.17, P-value=0.483; M...... All ethnicities: OR=0.92, 95%CI =0.72-1.17, P-value=0.483; Malay: OR=0.47, 95%CI =0.30-0.74, P-value=0.001; Chinese: OR=0.92, 95%CI =0.64-1.32, P-value=0.646; Indian: OR=2.03, 95%CI =1.15-3.58, P-value=0.015 More...	ANK3 rs1938526 was associated with BPD in Indians (P = 0.015...... ANK3 rs1938526 was associated with BPD in Indians (P = 0.015). More...	Positive
Ferreira, M. A.,2008		G	Genotyped P value=1.3E-08, OR=1.395 in the combined analysis...... Genotyped P value=1.3E-08, OR=1.395 in the combined analysis of WTCCC, STEP-UCL and ED-DUB-STEP2 datasets. Genotyped P value=0.0014 in the WTCCC. Genotyped P value=0.0008 in the STEP-UCL. Genotyped P value=0.0002 in the ED-DUB-STEP2 dataset. More...		Positive
Tesli, M.,2011	G/A		SCOPE sample: MAF=0.072, Cochrane-Mantel-Haenszel test P-val...... SCOPE sample: MAF=0.072, Cochrane-Mantel-Haenszel test P-value = 0.75, Bonferroni corrected P-value = 1, OR (95%CI)=1.04(0.83-1.30); Icelandic sample: MAF(affected)=0.07, MAF(unaffected)=0.058, allelic P-value = 0.32, Bonferroni corrected P-value = 0.96, OR (95%CI)=1.23(0.93-1.61) More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Dedman, A.,2012	G/A		Association analysis: for UCL1 sample, P-value = 0.008, OR=1...... Association analysis: for UCL1 sample, P-value = 0.008, OR=1.65; for UCL2 sample, P-value = 0.39, OR=1.17; for UCL1+UCL2 sample, P-value = 0.0095, OR=1.4 More...	Significant association was observed in BD. Significant association was observed in BD.	Positive
Takata, A.,2011(b)	A/G	G	chi-square test: allele P-value = 0.31, OR(95%CI)=1.12(0.90-...... chi-square test: allele P-value = 0.31, OR(95%CI)=1.12(0.90-1.38) for Korean sample; allele P-value = 0.359, OR(95%CI)=1.06(0.93-1.22) for Japanese sample; allele P-value = 0.13, OR(95%CI)=1.11(0.97-1.27) for Taiwan sample More...	No significant association was observed in BD. No significant association was observed in BD.	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
ANK3	ankyrin 3, node of Ranvier (ankyrin G)	10q21	17(13/3/1)

SNPs in LD with rs1938526 (count: 8) View in gBrowse (chr10:60493544..60566929 )

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: 8)

rs_ID	Functional Annotation	r²[population]
rs2154393	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.906[JPT]
rs2393641	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.907[JPT]
rs12412135	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.866[CEU]; 1.0[CHB]; 0.907[JPT]
rs10994384	intron_variant; NMD_transcript_variant	0.834[CHB]
rs10821789	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.866[CEU]; 1.0[CHB]; 0.907[JPT]
rs10994404	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.866[CEU]; 1.0[CHB]; 0.904[JPT]
rs2393640	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.815[CHD]
rs9633553	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.825[CHB]; 0.859[JPT]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Lim C.H., 2014	All ethnicities: OR=0.86, 95%CI =0.71-1.04, P-value=0.123; Malay: OR=0.60, 95%CI =0.41-0.89, P-value=0.012; Chinese: OR=0.87, 95%CI =0.66-1.15, P-value=0.334; Indian: OR=1.21, 95%CI =0.79-1.83, P-value=0.384	rs1938526 was found to be significantly associated with BPD and SZ.	Positive
Tesli, M.,2011	SCOPE sample:MAF=0.073, Cochrane-Mantel-Haenszel test P-value = 0.95, Bonferroni corrected P-value = 1, OR (95%CI)=0.99(0.81-1.22);Icelandic sample:MAF(affected)=0.06, MAF(unaffected)=0.058, allelic P-value = 0.32, Bonferroni corrected P-value = 0.96, OR (95%CI)=1.03(0.81-1.31)	No significant association was observed.	Negative

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