SNP Report

Basic Info

Name	rs28932171 dbSNP Ensembl
Location	chr10:60071532 - 60071532(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.0315495
Functional Annotation	intron_variant; missense_variant; NMD_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000621739, ENST00000280772) SIFT Annotation: tolerated(ENST00000621739); tolerated - low confidence(ENST00000280772)
Consequence to Transcript	intron_variant(ENST00000355288, ENST00000373820, ENST00000373827, ENST00000503366, ENST00000511043, ENST00000610321, ENST00000616444); missense_variant(ENST00000621739, ENST00000280772); NMD_transcript_variant(ENST00000621739); upstream_gene_variant(ENST00000610901, ENST00000613207)
No. of Studies	2 (Positive: 0; Negative: 2; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Fiorentino A., 2014	T/C		eurMLP=0.07 eurMLP=0.07	No significant association was observed. No significant association was observed.	Negative
Dedman, A.,2012			Association analysis: for UCL1 sample, chi square=0.542, P-v...... Association analysis: for UCL1 sample, chi square=0.542, P-value = 0.46, OR=1.11; for UCL2 sample, chi square=0.387, P-value = 0.53, OR=0.92; for UCL1+UCL2 sample, chi square=0.201, P-value = 0.65, OR=1.01 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 rs28932171 (count: 8) View in gBrowse (chr10:60057722..60078822 )

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]
rs11593609	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]
rs17802208	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs17802184	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]
rs17208576	intron_variant; synonymous_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs17208611	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]
rs2393610	downstream_gene_variant; intron_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]
rs11593500	downstream_gene_variant; intron_variant; upstream_gene_variant	0.877[CEU]
rs17207897	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]

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

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