Variant report

Variant	rs1049430
Chromosome Location	chr9:17796668-17796669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10122224	0.88[CEU][hapmap]
rs10738488	0.81[JPT][hapmap]
rs10756918	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10810852	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10810853	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10810854	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10963281	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10963285	0.84[ASN][1000 genomes]
rs10963286	0.82[ASN][1000 genomes]
rs11792712	0.86[ASN][1000 genomes]
rs12552903	0.80[ASN][1000 genomes]
rs12555445	0.80[ASN][1000 genomes]
rs12555732	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13288654	0.85[ASN][1000 genomes]
rs2182082	0.81[YRI][hapmap]
rs2274216	0.81[YRI][hapmap]
rs2296367	0.82[CEU][hapmap]
rs3736897	0.84[CEU][hapmap]
rs3808664	0.88[CEU][hapmap]
rs3808675	0.82[CEU][hapmap]
rs4284124	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4302936	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4373621	0.82[EUR][1000 genomes]
rs4510955	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4523358	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4961449	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4961450	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4961451	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4961596	0.86[ASN][1000 genomes]
rs4961597	0.84[ASN][1000 genomes]
rs4961599	0.80[ASN][1000 genomes]
rs6475174	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6475177	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6475178	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6475181	0.86[EUR][1000 genomes]
rs7018795	0.81[EUR][1000 genomes]
rs7023218	0.80[ASN][1000 genomes]
rs7026318	0.80[ASN][1000 genomes]
rs7028412	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7029727	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7029798	0.87[CEU][hapmap]
rs7032367	0.83[AMR][1000 genomes]
rs7036989	0.96[CEU][hapmap]
rs7039352	0.80[ASN][1000 genomes]
rs72691895	0.80[ASN][1000 genomes]
rs7847005	0.86[ASN][1000 genomes]
rs7850617	0.83[ASN][1000 genomes]
rs7857826	0.86[EUR][1000 genomes]
rs7860861	0.88[CEU][hapmap]
rs7861909	0.84[ASN][1000 genomes]
rs7863227	0.80[ASN][1000 genomes]
rs7863603	0.80[ASN][1000 genomes]
rs7869721	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9298784	0.88[CEU][hapmap]
rs9406711	0.88[CEU][hapmap]
rs9407874	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
rs1049430	CNTLN	cis	cerebellum	SCAN
rs1049430	SH3GL2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17784800-17799400	Weak transcription	Hela-S3	cervix
2	chr9:17787000-17800400	Weak transcription	Fetal Brain Female	brain
3	chr9:17788600-17805400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:17794200-17799400	Weak transcription	Fetal Brain Male	brain
5	chr9:17795000-17797200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:17796000-17812000	Weak transcription	Aorta	Aorta
7	chr9:17796200-17798200	Weak transcription	Brain Germinal Matrix	brain

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