SNP Report

Basic Info

Name	rs6010260 dbSNP Ensembl
Location	chr22:50077414 - 50077414(1)
Variant Alleles	C/A
Ancestral Allele	C
Minor Allele	A
Minor Allele Frequence	0.121605
Functional Annotation	missense_variant; upstream_gene_variant. Polyphen Annotation: possibly damaging(ENST00000311597, ENST00000395876, ENST00000442311) SIFT Annotation: deleterious - low confidence(ENST00000311597, ENST00000395876); tolerated - low confidence(ENST00000442311)
Consequence to Transcript	missense_variant(ENST00000311597, ENST00000395876, ENST00000442311); upstream_gene_variant(ENST00000470008, ENST00000483836)
No. of Studies	2 (Positive: 0; Negative: 2; 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
Verma, R.,2005(b)	G/T		Case-control association: for BPAD, Fisher exact test, allel...... Case-control association: for BPAD, Fisher exact test, allele P-value > 0.05; chi-square test, genotype P-value(additive)>0.05, P-value(dominant)>0.05, P-value(recessive)>0.05 ; Family-Based Association: for BPAD, TDT, P-value > 0.05 More...	No significant association was observed. No significant association was observed.	Negative
Severinsen, J. E., 2006 (b)	G/T		P-value = 0.4011 in BD, P-value = 0.1631 in BD and SZ P-value = 0.4011 in BD, P-value = 0.1631 in BD and SZ		Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
MLC1	megalencephalic leukoencephalopathy with subcortical cysts 1	22q13.33	5(1/4/0)

SNPs in LD with rs6010260 (count: 9) View in gBrowse (chr22:50062852..50179849 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs5771143	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.929[CEU]; 1.0[CHB]; 1.0[JPT]
rs2076130	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.874[CEU]; 1.0[CHB]; 1.0[JPT]
rs6010152	3_prime_UTR_variant; downstream_gene_variant	1.0[CHB]
rs6010165	synonymous_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs2294387	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.874[CEU]; 1.0[CHB]; 1.0[JPT]
rs3817809	intron_variant; non_coding_transcript_variant	0.867[CEU]; 1.0[JPT]
rs3817808	intron_variant; non_coding_transcript_variant	0.874[CEU]
rs3817810	intron_variant; non_coding_transcript_variant	1.0[JPT]
rs17247883	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.81[JPT]

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

Reference	Statistical Result	Description	Result Category
Severinsen, J. E., 2006 (b)	P-value = 0.0823 in SZ, P-value = 0.1631 in BD and SZ		Negative
Verma, R.,2005(b)	Case-control association:for SCZ, Fisher exact test, allele P-value > 0.05; chi-square test, genotype P-value(additive)>0.05, P-value(dominant)>0.05, P-value(recessive)>0.05 ;Family-Based Association:for SCZ, TDT, P-value > 0.05	No significant association was observed.	Negative

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