SNP Report

Basic Info

Name	rs1050565 dbSNP Ensembl
Location	chr17:30249058 - 30249058(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.253794
Functional Annotation	3_prime_UTR_variant; intron_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant. Polyphen Annotation: benign(ENST00000261714) SIFT Annotation: tolerated(ENST00000261714)
Consequence to Transcript	3_prime_UTR_variant(ENST00000578090); intron_variant(ENST00000577420); missense_variant(ENST00000261714); NMD_transcript_variant(ENST00000578090); non_coding_transcript_exon_variant(ENST00000578795); non_coding_transcript_variant(ENST00000577420, ENST00000578795); upstream_gene_variant(ENST00000516303)
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
Ikeda, M., 2006			allelic P-value = 0.389, genotypic P-value = 0.377, Power ca...... allelic P-value = 0.389, genotypic P-value = 0.377, Power calculation GRR=1.67 More...	No associations of 'tagging' marker with BP was found. No associations of 'tagging' marker with BP was found.	Negative
Alaerts, M.,2009	A/G		Allelic association P-value = 0.71; Genotypic association P-...... Allelic association P-value = 0.71; Genotypic association P-value = 0.72 More...	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
BLMH	bleomycin hydrolase	17q11.2	Mapped by Literature SNP
SLC6A4	solute carrier family 6 (neurotransmitter transporter), member 4	17q11.2	44(18/26/0)

SNPs in LD with rs1050565 (count: 31) View in gBrowse (chr17:30244910..30331992 )

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: 31)

rs_ID	Functional Annotation	r²[population]
rs3764449	upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 0.924[CHB]; 0.944[CHD]; 1.0[JPT]
rs17767256	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.955[CEU]; 1.0[TSI]; 0.857[CHB]; 0.944[CHD]; 1.0[JPT]
rs11867581	upstream_gene_variant	0.804[CHD]; 0.939[JPT]
rs6505165	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.846[CHD]; 0.939[JPT]
rs13341611		0.937[JPT]
rs33980254	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CEU]; 1.0[TSI]; 0.924[CHB]; 0.944[CHD]; 1.0[JPT]
rs7342921	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	1.0[CEU]; 0.924[CHB]; 1.0[JPT]
rs12945042	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs7342929	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.939[JPT]
rs7214991	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.836[CEU]; 0.804[CHD]; 0.939[JPT]
rs12939390		1.0[CEU]; 1.0[TSI]; 0.924[CHB]; 0.944[CHD]; 1.0[JPT]
rs3103306	intron_variant	0.857[CHB]; 0.884[JPT]
rs8073378		0.804[CHD]; 0.939[JPT]
rs7210085	intron_variant; NMD_transcript_variant	0.804[CHD]; 0.939[JPT]
rs6505171		0.939[JPT]
rs3794806	intron_variant; NMD_transcript_variant	1.0[CEU]; 0.857[CHB]; 1.0[JPT]
rs7223821	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 0.857[CHB]; 0.944[CHD]; 1.0[JPT]
rs3110454	intron_variant	0.857[CHB]; 0.884[JPT]
rs2321705	intron_variant	0.833[JPT]
rs3110095	intron_variant	0.884[JPT]
rs3110061	intron_variant	0.857[CHB]; 0.884[JPT]
rs7214014	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.804[CHD]; 0.939[JPT]
rs2321706	intron_variant	0.857[CHB]; 0.884[JPT]
rs7208052	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.924[CHB]; 1.0[JPT]
rs12949747	intron_variant; NMD_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs8072345	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.804[CHD]; 0.939[JPT]
rs3110452	intron_variant	0.857[CHB]; 1.0[JPT]
rs6505173	intron_variant	0.804[CHD]; 0.939[JPT]
rs1487971	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.836[CEU]; 0.846[CHD]; 0.939[JPT]
rs6505169	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.804[CHD]; 0.939[JPT]
rs7214248	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.953[CEU]; 1.0[TSI]; 1.0[CHB]; 0.944[CHD]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Ikeda, M., 2006	allelic P-value = 0.343, genotypic P-value = 0.139, Power calculation GRR=1.47	No associations of 'tagging' marker with SCZ was found.	Negative

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