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Large-scale studies

Data Summary

Published Variant
- SNP: 1391
- CNV: 398
- Others: 173
Published Gene: 359
Published Region: 128
Pathway by PBA: 8
Study: 361

Detail ...

SNP Report

Basic Info

Name	rs11080121 dbSNP Ensembl
Location	Chr17:28528842(Fwd)
Variant Alleles	T/C
Ancestral Allele	T
Functional Annotation	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant.
Consequence to Transcript	NMD_transcript_variant(ENST00000579221) intron_variant(ENST00000394821; ENST00000578609; ENST00000401766; ENST00000261707; ENST00000579221) nc_transcript_variant(ENST00000578609) upstream_gene_variant(ENST00000581633)
No. of Studies	1 (significant: 1; non-significant: 0; trend: 0)
Source	Literature-origin

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result of Statistical Analysis
Ilott NE, 2010			QTDT AT P-value=0.14, X²=2.16, df=1, QTDT AW P-va...... QTDT AT P-value=0.14, X²=2.16, df=1, QTDT AW P-value=0.1, X²=2.71, df=1 at age 2; QTDT AT P-value=0.23, X²=0.12, df=1, QTDT AW P-value=0.03, X²=4.77, df=1 at age 3 More...	modest, nominally significant associations in the AW test at...... modest, nominally significant associations in the AW test at age 3 More...	Significant

SNP related genes (count: 1)

Literature-origin genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (significant/non-significant/trend)
SLC6A4	solute carrier family 6 (neurotransmitter transporter, serotonin), member 4	17q11.2	25(13/12/0)

Genes from other sources (count: 0)

SNPs in LD with rs11080121 (count: 84) View in gBrowse (chr17:28330280..28550732 )

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: 6)

rs_ID	Functional Annotation	#studies(significant/non-significant/trend)	r²[population]

rs1042173	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant	1(0/1/0)	0.961[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs3813034	3_prime_UTR_variant; downstream_gene_variant	4(0/4/0)	0.961[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs4583306	intron_variant; upstream_gene_variant	1(1/0/0)	0.851[CEU]; 0.92[JPT]
rs1979572	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; nc_transcript_variant; non_coding_exon_variant; synonymous_variant	1(1/0/0)	0.924[CEU]; 1.0[CHB]; 1.0[JPT]
rs4325622	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(1/0/0)	0.962[CEU]; 1.0[CHB]; 1.0[JPT]
rs140701	intron_variant; upstream_gene_variant	3(1/2/0)	0.81[CEU]; 0.92[JPT]

LD-proxies (count: 78)

rs_ID	Functional Annotation	r²[population]
rs9908901	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.924[CEU]; 1.0[CHB]; 1.0[JPT]
rs9904336	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.92[CEU]
rs8074028	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.921[CEU]; 1.0[CHB]; 1.0[JPT]
rs7211246	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.919[CEU]; 1.0[CHB]; 1.0[JPT]
rs4239227	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.921[CEU]
rs9890205	NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.921[CEU]
rs11080118	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.883[CEU]; 1.0[CHB]; 1.0[JPT]
rs7222685	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7218379	downstream_gene_variant; intron_variant	0.846[CEU]
rs4074170	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; synonymous_variant; upstream_gene_variant	0.924[CEU]
rs8082175	intron_variant; nc_transcript_variant	0.921[CEU]; 0.931[CHB]; 0.92[JPT]
rs4294864	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.924[CEU]; 0.858[CHB]; 0.92[JPT]
rs12450441	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.96[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs2054846	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs4343336	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9303628	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.883[CEU]; 1.0[CHB]; 1.0[JPT]
rs6505158	downstream_gene_variant; intron_variant	0.921[CEU]
rs8080343	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.919[CEU]; 1.0[CHB]; 0.915[JPT]
rs11080115	intron_variant	0.846[CEU]
rs7220151	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.924[CEU]
rs3794808	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.848[CEU]; 0.92[JPT]
rs7207021	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.921[CEU]
rs7219456	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.846[CEU]
rs7213076	downstream_gene_variant; intron_variant; nc_transcript_variant	0.843[CEU]; 0.931[CHB]; 0.833[JPT]
rs12449783	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[JPT]
rs7225686	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.846[CEU]
rs4575590	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.921[CEU]
rs9906340	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.921[CEU]
rs4528633	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.846[CEU]
rs4547389	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.846[CEU]
rs9890886	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.921[CEU]
rs9896012	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.883[CEU]; 1.0[CHB]; 1.0[JPT]
rs4328498	NMD_transcript_variant; intron_variant	0.921[CEU]
rs4350617	downstream_gene_variant; intron_variant; nc_transcript_variant	0.921[CEU]; 0.931[CHB]; 0.92[JPT]
rs8071742	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.921[CEU]
rs12103671	intron_variant	0.846[CEU]
rs10853136	downstream_gene_variant; intron_variant	0.851[CEU]
rs7213517	downstream_gene_variant; intron_variant	0.846[CEU]
rs9896062	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.921[CEU]
rs7212497	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.921[CEU]
rs9902340	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.883[CEU]; 1.0[CHB]; 1.0[JPT]
rs7223786	NMD_transcript_variant; intron_variant	0.921[CEU]
rs4075623	NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.921[CEU]
rs7221743	intron_variant; synonymous_variant	0.921[CEU]
rs1906451	downstream_gene_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs9902453	NMD_transcript_variant; intron_variant	0.921[CEU]
rs17825877	downstream_gene_variant	0.96[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs8065059	downstream_gene_variant; intron_variant; nc_transcript_variant	0.921[CEU]; 0.931[CHB]; 0.833[JPT]
rs7216631	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.896[JPT]
rs7220004	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.846[CEU]
rs9905950	intron_variant; nc_transcript_variant	0.814[CEU]; 0.931[CHB]; 0.915[JPT]
rs4427857	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.852[CEU]; 1.0[CHB]; 1.0[JPT]
rs8065261	intron_variant; nc_transcript_variant	0.921[CEU]; 0.931[CHB]; 0.833[JPT]
rs7217961	downstream_gene_variant; intron_variant	0.846[CEU]
rs2020939	intron_variant	0.851[CEU]
rs4795529	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.846[CEU]; 0.931[CHB]; 0.92[JPT]
rs4533341	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs12948898	intron_variant; upstream_gene_variant	0.846[CEU]
rs6505162	5_prime_UTR_variant; NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.931[CHB]; 0.92[JPT]; 0.943[YRI]
rs4470197	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.922[CEU]; 1.0[CHB]; 1.0[JPT]
rs12602065	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.962[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9900974	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.846[CEU]
rs11653805	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.843[CEU]
rs4356528	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7221154	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.919[CEU]; 1.0[CHB]; 1.0[JPT]
rs4493117	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.849[CEU]; 1.0[CHB]; 1.0[JPT]
rs12941382	intron_variant; upstream_gene_variant	0.843[CEU]
rs2054847	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.855[CEU]; 0.859[CHB]; 0.92[JPT]
rs4465650	NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.921[CEU]
rs7217638	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.921[CEU]
rs4581755	intron_variant; nc_transcript_variant	0.921[CEU]; 0.931[CHB]; 0.92[JPT]
rs11080114	intron_variant	0.921[CEU]
rs4429345	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9912741	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.921[CEU]
rs9900911	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.921[CEU]
rs9898353	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.924[CEU]; 1.0[CHB]; 1.0[JPT]
rs7212292	intron_variant; upstream_gene_variant	0.818[CEU]
rs7224199	3_prime_UTR_variant; downstream_gene_variant	0.921[CEU]; 1.0[CHB]; 1.0[JPT]