SNP Report

Basic Info

Name	rs2249060 dbSNP Ensembl
Location	chr21:46353263 - 46353263(1)
Variant Alleles	C/T
Ancestral Allele	C
Minor Allele	T
Minor Allele Frequence	0.159345
Functional Annotation	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant. Polyphen Annotation: benign(ENST00000359568) SIFT Annotation: tolerated(ENST00000359568)
Consequence to Transcript	downstream_gene_variant(ENST00000490468); missense_variant(ENST00000359568); non_coding_transcript_exon_variant(ENST00000466474, ENST00000480896, ENST00000483844); non_coding_transcript_variant(ENST00000466474, ENST00000480896, ENST00000483844)
No. of Studies	1 (Positive: 0; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Anitha, A., 2008	C/T		Genotypic P-value = 0.472, allelic P-value = 0.386 for BD wh...... Genotypic P-value = 0.472, allelic P-value = 0.386 for BD when compared with controls. More...	none of the SNPs analyzed in our study showed a significant ...... none of the SNPs analyzed in our study showed a significant association with bipolar disorder More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PCNT	pericentrin	21q22.3	1(0/1/0)

SNPs in LD with rs2249060 (count: 36) View in gBrowse (chr21:46337878..46548394 )

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)

rs_ID	Functional Annotation	r²[population]
rs2839235	intron_variant; non_coding_transcript_variant	0.931[CHB]; 0.89[CHD]; 0.814[JPT]
rs2839267	intron_variant; non_coding_transcript_variant	0.863[CHB]
rs17371795	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.863[CHB]
rs11701286	intron_variant; non_coding_transcript_variant	0.801[CHB]
rs9637222	intron_variant; non_coding_transcript_variant	0.852[CHB]
rs4818837	intron_variant; non_coding_transcript_variant	0.927[CHB]
rs2839271	downstream_gene_variant; intron_variant	0.856[CHB]
rs2839232	intron_variant; non_coding_transcript_variant	0.863[CHB]; 0.89[CHD]; 0.814[JPT]
rs3788261	intron_variant; non_coding_transcript_variant	0.863[CHB]; 0.814[JPT]
rs9983528	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs4143362	intron_variant	0.863[CHB]
rs9979962	downstream_gene_variant; intron_variant; upstream_gene_variant	0.802[CHB]
rs9979185	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.81[JPT]
rs7279193	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.881[JPT]
rs2839274	intron_variant	0.863[CHB]
rs762251	intron_variant; non_coding_transcript_variant	0.863[CHB]
rs7279052	intron_variant; non_coding_transcript_variant	0.931[CHB]; 0.817[CHD]
rs2839283	intron_variant	0.863[CHB]
rs2839234	intron_variant; non_coding_transcript_variant	0.931[CHB]; 0.89[CHD]; 0.814[JPT]
rs11089076	intron_variant; non_coding_transcript_variant	0.861[CHB]
rs2839226	intron_variant; non_coding_transcript_variant; splice_region_variant	1.0[CHB]; 1.0[CHD]; 0.881[JPT]
rs1010111		0.863[CHB]
rs2839273	intron_variant	0.862[CHB]
rs2839292	intron_variant	0.863[CHB]
rs4819241	intron_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs8134832	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.863[CHB]
rs8134014	intron_variant	0.863[CHB]
rs9306152	intron_variant; non_coding_transcript_variant	0.929[CHB]; 0.813[JPT]
rs2330591	intron_variant; non_coding_transcript_variant	0.863[CHB]
rs2032110	intron_variant	0.863[CHB]
rs2078203	intron_variant; upstream_gene_variant	0.863[CHB]
rs7282296	intron_variant	0.863[CHB]
rs8132320	intron_variant; non_coding_transcript_variant	0.863[CHB]
rs4819239	intron_variant; non_coding_transcript_variant	0.874[CHB]
rs2839240	intron_variant; non_coding_transcript_variant	0.931[CHB]; 0.89[CHD]
rs2839228	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	0.931[CHB]; 0.881[JPT]

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

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