SNP Report

Basic Info

Name	rs6198 dbSNP Ensembl
Location	chr5:143278056 - 143278056(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.0838658
Functional Annotation	3_prime_UTR_variant; downstream_gene_variant.
Consequence to Transcript	3_prime_UTR_variant(ENST00000343796, ENST00000394464, ENST00000415690); downstream_gene_variant(ENST00000231509, ENST00000394466, ENST00000424646, ENST00000503201, ENST00000504572)
No. of Studies	4 (Positive: 0; Negative: 4; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	YES

SNP related studies (count: 4)

Reference	Allele Change	Statistical Values	Author Comments	Result Category
Leszczynska-Rodziewicz, A., 2012	C/T	genotypic P-value = 0.69 genotypic P-value = 0.69	There were no significant differences for other polymorphism...... There were no significant differences for other polymorphisms in the studied group in comparison to the control group. More...	Negative
Szczepankiewicz, A.,2011	C/T	For BD, X² test: allele, P-value > 0.05; the Fish...... For BD, X² test: allele, P-value > 0.05; the Fisher exact test: genotype, P-value > 0.05; for the course of bipolar disorder: genotype P-value = 0.028 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Spijker, A. T.,2009	A/G	Genotypic association: OR = 0.76, 95% CI: 0.5-1.0, P-value =...... Genotypic association: OR = 0.76, 95% CI: 0.5-1.0, P-value = 0.14, corrected for age and gender; for age: OR = 1.04, 95% CI: 1.02-1.05, P-value = 0.000; for male gender: OR = 0.52, 95% CI: 0.37-0.72, P-value < 0.0001 More...	We found a nonsignificant trend for a lower frequency of the...... We found a nonsignificant trend for a lower frequency of the A ?G or G ?G variation in exon 9beta in the patient group versus the control group. More...	Negative
Leszczynska-Rodziewicz A, 2013	C/T	P-value=0.65 P-value=0.65	Neither genotypes nor alleles were significantly associated ...... Neither genotypes nor alleles were significantly associated with melancholic depression. More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
NR3C1	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	5q31-q32	5(2/3/0)

SNPs in LD with rs6198 (count: 6) View in gBrowse (chr5:143277456..143382248 )

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]
rs11740792	intron_variant; non_coding_transcript_variant	1.0[CEU]; 0.969[TSI]
rs4128428	intron_variant; non_coding_transcript_variant	1.0[CEU]; 0.969[TSI]
rs17339831	intron_variant; non_coding_transcript_variant	1.0[CEU]
rs17287758	downstream_gene_variant	1.0[CEU]; 0.969[TSI]
rs10482642	intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]
rs10515521	intron_variant; non_coding_transcript_variant	1.0[CEU]; 0.969[TSI]

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

Overlap with MDD from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Szczepankiewicz, A.,2011	X² test:allele, P-value > 0.05;the Fisher exact test:genotype, P-value = 0.018, df=2, X²=7.964, OR=0.950, 95% CI: 0.693-1.303.	Significant association was found.	Positive