ADHDgene Database

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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	rs1979572 dbSNP Ensembl
Location	Chr17:28511978(Fwd)
Variant Alleles	G/A
Ancestral Allele	A
Functional Annotation	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; nc_transcript_variant; non_coding_exon_variant; synonymous_variant.
Consequence to Transcript	3_prime_UTR_variant(ENST00000394826; ENST00000475652) NMD_transcript_variant(ENST00000475652; ENST00000394826) downstream_gene_variant(ENST00000580103; ENST00000577289) nc_transcript_variant(ENST00000540900) non_coding_exon_variant(ENST00000540900) synonymous_variant(ENST00000247026)
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
Nyman ES, 2007			Logistic regression for single markers: adjusted for sex: P-...... Logistic regression for single markers: adjusted for sex: P-value=0.0258, OR=0.54, 95%CI=0.32-0.93 for 12vs.11; Males: P-value=0.0264, OR=0.43, 95%CI=0.20-0.91 for 12vs.22 More...	nominally associated, but the results were considered inconc...... nominally associated, but the results were considered inconclusive because the effect was seen only for heterozygotes, and no risk (or protective) allele could be identified. More...	Significant

SNP related genes (count: 2)

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: 1)

Approved Symbol	Approved Name	Location
NSRP1	nuclear speckle splicing regulatory protein 1	17q11.2

SNPs in LD with rs1979572 (count: 86) View in gBrowse (chr17:28320473..28538715 )

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]

rs3813034	3_prime_UTR_variant; downstream_gene_variant	4(0/4/0)	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs4325622	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(1/0/0)	0.928[CEU]; 1.0[CHB]; 1.0[JPT]
rs1042173	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant	1(0/1/0)	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs11080121	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1(1/0/0)	0.924[CEU]; 1.0[CHB]; 1.0[JPT]
rs140701	intron_variant; upstream_gene_variant	3(1/2/0)	0.92[JPT]
rs4583306	intron_variant; upstream_gene_variant	1(1/0/0)	0.921[JPT]

LD-proxies (count: 80)

rs_ID	Functional Annotation	r²[population]
rs4294864	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.891[CEU]; 0.843[CHB]; 0.851[JPT]
rs4528633	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.925[CEU]
rs7211246	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9906340	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.923[CEU]
rs7225686	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.925[CEU]
rs9902340	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.962[CEU]; 1.0[CHB]; 1.0[JPT]
rs9905950	intron_variant; nc_transcript_variant	0.891[CEU]; 0.924[CHB]; 0.842[JPT]
rs12450441	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]; 1.0[CHB]; 1.0[JPT]
rs4795529	downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.925[CEU]; 0.924[CHB]; 0.85[JPT]
rs7212292	intron_variant; upstream_gene_variant	0.895[CEU]
rs10853136	downstream_gene_variant; intron_variant	0.907[CEU]
rs12103671	intron_variant	0.925[CEU]
rs7216631	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CHB]; 0.896[JPT]
rs6505162	5_prime_UTR_variant; NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.81[CEU]; 0.924[CHB]; 0.85[JPT]
rs8074028	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs4547389	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]
rs1906451	downstream_gene_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7221743	intron_variant; synonymous_variant	0.923[CEU]
rs4075623	NMD_transcript_variant; intron_variant; nc_transcript_variant; non_coding_exon_variant; upstream_gene_variant	0.923[CEU]
rs7222685	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.927[CEU]; 1.0[CHB]; 1.0[JPT]
rs4328498	NMD_transcript_variant; intron_variant	0.923[CEU]
rs12948898	intron_variant; upstream_gene_variant	0.925[CEU]
rs12941382	intron_variant; upstream_gene_variant	0.923[CEU]
rs4356528	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs8082175	intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]; 0.85[JPT]
rs7217961	downstream_gene_variant; intron_variant	0.925[CEU]
rs4350617	downstream_gene_variant; intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]; 0.85[JPT]
rs9896012	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.962[CEU]; 1.0[CHB]; 1.0[JPT]
rs4581755	intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]; 0.85[JPT]
rs7218379	downstream_gene_variant; intron_variant	0.925[CEU]
rs9890886	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.923[CEU]
rs11080115	intron_variant	0.925[CEU]
rs2054846	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs8080343	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[CEU]; 1.0[CHB]; 0.915[JPT]; 0.963[YRI]
rs6505158	downstream_gene_variant; intron_variant	0.923[CEU]
rs7224199	3_prime_UTR_variant; downstream_gene_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9904336	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.887[CEU]
rs9900911	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.923[CEU]
rs7207021	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.923[CEU]
rs4427857	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.929[CEU]; 1.0[CHB]; 1.0[JPT]
rs4575590	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.887[CEU]
rs9890205	NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.923[CEU]
rs7223786	NMD_transcript_variant; intron_variant	0.923[CEU]
rs11080118	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.962[CEU]; 1.0[CHB]; 1.0[JPT]
rs7217638	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.923[CEU]
rs7219456	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]
rs12602065	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	0.928[CEU]; 1.0[CHB]; 1.0[JPT]
rs17825877	downstream_gene_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs7220004	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]
rs4074170	3_prime_UTR_variant; NMD_transcript_variant; downstream_gene_variant; synonymous_variant; upstream_gene_variant	0.891[CEU]
rs4470197	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9896062	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.923[CEU]
rs4239227	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.923[CEU]
rs11653805	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.923[CEU]
rs8071742	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.923[CEU]
rs7213517	downstream_gene_variant; intron_variant	0.925[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]
rs9303628	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.962[CEU]; 1.0[CHB]; 1.0[JPT]
rs7225462	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]
rs4343336	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs8065059	downstream_gene_variant; intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]
rs9912741	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.923[CEU]
rs3794808	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.92[JPT]
rs9900974	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.925[CEU]
rs4533341	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.961[CEU]; 1.0[CHB]; 1.0[JPT]
rs8065261	intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]
rs2054847	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	0.844[CHB]; 0.921[JPT]
rs4465650	NMD_transcript_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.923[CEU]
rs9908901	NMD_transcript_variant; downstream_gene_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs7221154	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs7213076	downstream_gene_variant; intron_variant; nc_transcript_variant	0.923[CEU]; 0.924[CHB]
rs12449783	NMD_transcript_variant; intron_variant; nc_transcript_variant; upstream_gene_variant	1.0[JPT]
rs7212497	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.923[CEU]
rs9898353	NMD_transcript_variant; intron_variant; nc_transcript_variant	1.0[CEU]; 1.0[CHB]; 1.0[JPT]; 1.0[YRI]
rs9902453	NMD_transcript_variant; intron_variant	0.923[CEU]
rs4493117	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.927[CEU]; 1.0[CHB]; 1.0[JPT]
rs11080114	intron_variant	0.923[CEU]
rs7220151	NMD_transcript_variant; intron_variant; upstream_gene_variant	0.927[CEU]
rs12150261	NMD_transcript_variant; intron_variant; nc_transcript_variant	0.923[CEU]
rs12939344	NMD_transcript_variant; downstream_gene_variant; intron_variant	0.925[CEU]