SNP Report

Basic Info

Name	rs3813034 dbSNP Ensembl
Location	chr17:30197786 - 30197786(1)
Variant Alleles	A/C
Ancestral Allele	A
Minor Allele	C
Minor Allele Frequence	0.483427
Functional Annotation	3_prime_UTR_variant; downstream_gene_variant.
Consequence to Transcript	3_prime_UTR_variant(ENST00000261707, ENST00000401766); downstream_gene_variant(ENST00000394821, ENST00000578609, ENST00000579221)
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 = 0.509, genotypic P-value = 0.42, Power cal...... allelic P-value = 0.509, genotypic P-value = 0.42, Power calculation GRR=1.68 More...	No associations of 'tagging' marker with BP was found. No associations of 'tagging' marker with BP was found.	Negative
Alaerts, M.,2009	A/C		Allelic association P-value = 0.33; Genotypic association P-...... Allelic association P-value = 0.33; Genotypic association P-value = 0.31 More...	No significant association was observed No significant association was observed	Negative

SNP related genes (count: 1)

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

SNPs in LD with rs3813034 (count: 80) View in gBrowse (chr17:30001801..30204995 )

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: 80)

rs_ID	Functional Annotation	r²[population]
rs9902453	intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs4581755	intron_variant; non_coding_transcript_variant	0.961[CEU]; 0.977[TSI]; 0.931[CHB]; 0.956[CHD]; 0.85[JPT]
rs7207021	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs4575590	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.96[CEU]
rs8080343	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]; 1.0[CHB]; 1.0[CHD]; 0.915[JPT]
rs12948898	intron_variant; upstream_gene_variant	0.889[CEU]
rs4470197	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs9896012	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.924[CEU]; 0.808[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4239227	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]
rs1906451	downstream_gene_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs17825877	downstream_gene_variant	1.0[CEU]; 0.977[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1979572	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs11653805	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.887[CEU]
rs9912741	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 0.954[TSI]
rs8071742	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 0.954[TSI]
rs12939344	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.889[CEU]
rs11080115	intron_variant	0.889[CEU]
rs12449783	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[JPT]
rs2054847	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.857[CHB]; 0.92[JPT]
rs2054846	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs11080121	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7217638	intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs4795529	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.889[CEU]; 0.803[TSI]; 0.931[CHB]; 0.956[CHD]; 0.85[JPT]
rs9303628	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.924[CEU]; 0.808[TSI]; 1.0[CHB]; 0.956[CHD]; 1.0[JPT]
rs8065059	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.961[CEU]; 0.977[TSI]; 0.931[CHB]; 0.956[CHD]
rs8082175	intron_variant; non_coding_transcript_variant	0.961[CEU]; 0.977[TSI]; 0.931[CHB]; 0.956[CHD]; 0.85[JPT]
rs7217961	downstream_gene_variant; intron_variant	0.889[CEU]
rs7220004	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.889[CEU]
rs7213076	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.887[CEU]; 0.803[TSI]; 0.931[CHB]; 0.956[CHD]
rs9906340	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs10853136	downstream_gene_variant; intron_variant	0.902[CEU]
rs4528633	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.889[CEU]
rs9890205	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]
rs7219456	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.889[CEU]
rs9896062	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]
rs4465650	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.931[TSI]
rs4427857	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.924[CEU]; 1.0[CHB]; 1.0[JPT]
rs7212497	intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs7216631	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.896[JPT]
rs8074028	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 0.954[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4493117	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.923[CEU]; 1.0[CHB]; 1.0[JPT]
rs7224199	3_prime_UTR_variant; downstream_gene_variant	0.961[CEU]; 0.954[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs7221154	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 0.954[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs6505158	downstream_gene_variant; intron_variant	0.961[CEU]; 0.954[TSI]
rs4294864	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.856[CHB]; 0.85[JPT]
rs12450441	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs7225686	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.889[CEU]
rs9908901	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs9898353	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7221743	intron_variant; synonymous_variant	0.961[CEU]; 0.954[TSI]
rs9902340	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.924[CEU]; 0.808[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs9904336	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.96[CEU]
rs9900974	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.889[CEU]
rs12103671	intron_variant	0.889[CEU]
rs4350617	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.961[CEU]; 0.977[TSI]; 0.931[CHB]; 0.956[CHD]; 0.85[JPT]
rs11080114	intron_variant	0.961[CEU]; 0.954[TSI]
rs7212292	intron_variant; upstream_gene_variant	0.889[CEU]
rs9900911	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs9905950	intron_variant; non_coding_transcript_variant	0.887[CEU]; 0.93[CHB]; 0.84[JPT]
rs7211246	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.959[CEU]; 1.0[CHB]; 1.0[JPT]
rs4328498	intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs4547389	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.889[CEU]
rs9890886	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]
rs7223786	intron_variant; NMD_transcript_variant	0.961[CEU]; 0.954[TSI]
rs4429345	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4356528	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs7220151	intron_variant; NMD_transcript_variant	0.961[CEU]
rs7222685	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs6505162	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.81[CEU]; 0.931[CHB]; 0.956[CHD]; 0.85[JPT]
rs11080118	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.924[CEU]; 0.806[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4074170	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant; synonymous_variant; upstream_gene_variant	0.961[CEU]
rs4533341	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 0.977[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs8065261	intron_variant; non_coding_transcript_variant	0.961[CEU]; 0.977[TSI]; 0.931[CHB]; 0.956[CHD]
rs4343336	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[TSI]; 1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs12941382	intron_variant; upstream_gene_variant	0.887[CEU]
rs7213517	downstream_gene_variant; intron_variant	0.889[CEU]
rs12602065	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]
rs4075623	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.961[CEU]; 0.954[TSI]
rs7218379	downstream_gene_variant; intron_variant	0.889[CEU]
rs4325622	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]

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

Reference	Statistical Result	Description	Result Category
Ikeda, M., 2006	allelic P-value = 0.557, genotypic P-value = 0.781, Power calculation GRR=1.49	No associations of 'tagging' marker with SCZ was found.	Negative

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