Variant report

Variant	rs3808667
Chromosome Location	chr9:17782325-17782326
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10122224	0.82[CEU][hapmap]
rs10122834	0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10738488	0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10738489	0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10756912	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10810847	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs10810851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12377594	0.91[EUR][1000 genomes]
rs1886589	0.80[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2182091	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2209424	0.96[CEU][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs2209428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2209431	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2209432	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2224954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2224955	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2296367	0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2383046	0.88[JPT][hapmap]
rs3808664	0.81[CEU][hapmap]
rs3808670	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808673	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3808675	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs3808681	0.82[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4302941	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4348595	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4961591	0.82[JPT][hapmap]
rs7029798	0.81[CEU][hapmap]
rs7036431	0.96[EUR][1000 genomes]
rs7041545	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7860861	0.82[CEU][hapmap]
rs9298783	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9298784	0.82[CEU][hapmap]
rs9406711	0.82[CEU][hapmap]
rs9407874	0.82[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892675	chr9:17694823-17790526	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1034673	chr9:17739006-17916606	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1023089	chr9:17748811-17919574	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3808667	CNTLN	cis	cerebellum	SCAN
rs3808667	SH3GL2	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17764600-17782800	Weak transcription	Gastric	stomach
2	chr9:17776800-17786200	Weak transcription	Fetal Brain Male	brain
3	chr9:17778800-17784000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:17780200-17787200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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