Variant report

Variant	rs4961598
Chromosome Location	chr9:17810983-17810984
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:33352554..33353197-chr9:17810608..17811353,2	MCF-7	breast:
2	chr9:17810623..17811776-chr9:18207859..18208526,4	MCF-7	breast:
3	chr9:17810712..17811652-chr9:18207926..18208828,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10120630	0.89[AMR][1000 genomes]
rs1049430	0.94[JPT][hapmap]
rs10756915	0.89[AMR][1000 genomes]
rs10963282	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963283	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10963285	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10963286	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11791520	0.83[AMR][1000 genomes]
rs11791576	0.84[AMR][1000 genomes]
rs11792712	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12552903	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12555445	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12555732	0.81[ASN][1000 genomes]
rs13288654	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34349189	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35956180	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36003385	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141716	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs4265281	0.90[AMR][1000 genomes]
rs4961451	0.81[ASN][1000 genomes]
rs4961596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4961597	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4961599	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7023218	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026318	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7039352	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7040307	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72691895	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7847005	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850617	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7861909	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7863227	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7863603	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7863806	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869721	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv824867	chr9:17810486-17828870	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv8422	chr9:17810758-17829560	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2761507	chr9:17810983-17901307	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4961598	CNTLN	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17796000-17812000	Weak transcription	Aorta	Aorta
2	chr9:17808400-17812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:17810600-17811800	Enhancers	Hela-S3	cervix
4	chr9:17810600-17812600	Enhancers	Fetal Brain Male	brain
5	chr9:17810800-17811000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:17810800-17811000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:17810800-17811000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr9:17810800-17811000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:17810800-17811000	Enhancers	Brain Angular Gyrus	brain
10	chr9:17810800-17811000	Enhancers	Brain Anterior Caudate	brain
11	chr9:17810800-17811000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
12	chr9:17810800-17811000	Bivalent Enhancer	Fetal Lung	lung
13	chr9:17810800-17811000	Bivalent Enhancer	HUVEC	blood vessel
14	chr9:17810800-17811000	Bivalent Enhancer	Osteobl	bone
15	chr9:17810800-17811200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:17810800-17811200	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr9:17810800-17811200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr9:17810800-17811200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:17810800-17811200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:17810800-17811200	Enhancers	Fetal Brain Female	brain
21	chr9:17810800-17811200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:17810800-17812400	Enhancers	Duodenum Smooth Muscle	Duodenum

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