Variant report

Variant	rs7869721
Chromosome Location	chr9:17825216-17825217
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10122224	0.88[CEU][hapmap]
rs1049430	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756917	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10756918	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810853	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10810854	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10963281	0.81[AMR][1000 genomes]
rs10963282	0.80[ASN][1000 genomes]
rs10963283	0.80[ASN][1000 genomes]
rs10963285	0.90[ASN][1000 genomes]
rs10963286	0.84[ASN][1000 genomes]
rs11792712	0.80[ASN][1000 genomes]
rs12552903	0.96[ASN][1000 genomes]
rs12555445	0.96[ASN][1000 genomes]
rs12555732	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13288654	0.91[ASN][1000 genomes]
rs2209432	0.83[MEX][hapmap]
rs2296367	0.82[CEU][hapmap]
rs34349189	0.84[ASN][1000 genomes]
rs35956180	0.95[ASN][1000 genomes]
rs3736897	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs3808664	0.88[CEU][hapmap]
rs3808675	0.82[CEU][hapmap]
rs4284124	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4302936	0.81[AMR][1000 genomes]
rs4373621	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4391525	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4510955	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4523358	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4599896	0.87[EUR][1000 genomes]
rs4961449	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4961450	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961451	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961596	0.87[ASN][1000 genomes]
rs4961597	0.90[ASN][1000 genomes]
rs4961598	0.81[ASN][1000 genomes]
rs4961599	0.99[ASN][1000 genomes]
rs6475174	0.86[AMR][1000 genomes]
rs6475177	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6475178	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6475181	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7018795	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7019050	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7023218	0.96[ASN][1000 genomes]
rs7025077	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7026318	0.96[ASN][1000 genomes]
rs7028412	0.80[AMR][1000 genomes]
rs7029727	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7029798	0.87[CEU][hapmap]
rs7036989	0.96[CEU][hapmap]
rs7039352	0.96[ASN][1000 genomes]
rs7041618	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72691895	0.96[ASN][1000 genomes]
rs7847005	0.92[ASN][1000 genomes]
rs7850617	0.96[ASN][1000 genomes]
rs7857826	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7860861	0.88[CEU][hapmap];0.87[MEX][hapmap]
rs7861909	0.95[ASN][1000 genomes]
rs7863227	0.99[ASN][1000 genomes]
rs7863603	0.99[ASN][1000 genomes]
rs7863806	0.97[ASN][1000 genomes]
rs9298784	0.88[CEU][hapmap]
rs9406711	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs9407874	0.88[CEU][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
9	esv2757321	chr9:17811584-17828437	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2759675	chr9:17811584-17828437	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2754695	chr9:17811600-17828400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7869721	CNTLN	cis	cerebellum	SCAN
rs7869721	SH3GL2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17823600-17825800	Enhancers	Fetal Brain Male	brain
2	chr9:17823800-17825600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:17824000-17826000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:17824200-17825600	Enhancers	Fetal Brain Female	brain
5	chr9:17824400-17825400	Enhancers	HSMMtube	muscle
6	chr9:17824400-17825600	Flanking Active TSS	Fetal Heart	heart
7	chr9:17824600-17825600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:17824600-17825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:17824600-17825800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:17824600-17825800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:17824600-17825800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:17824600-17825800	Enhancers	Ovary	ovary
13	chr9:17824800-17825600	Enhancers	Colon Smooth Muscle	Colon
14	chr9:17824800-17829800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:17824800-17830000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:17825000-17825400	Weak transcription	Right Ventricle	heart
17	chr9:17825000-17825600	Enhancers	Aorta	Aorta
18	chr9:17825000-17825600	Enhancers	Stomach Smooth Muscle	stomach
19	chr9:17825000-17829800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:17825000-17829800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:17825000-17829800	Weak transcription	Left Ventricle	heart
22	chr9:17825200-17829800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:17825200-17830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:17825200-17830000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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