Variant report

Variant	rs13290659
Chromosome Location	chr9:17274331-17274332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10810743	0.83[EUR][1000 genomes]
rs10810745	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810746	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10810755	0.81[EUR][1000 genomes]
rs10810759	0.81[EUR][1000 genomes]
rs10810762	0.81[EUR][1000 genomes]
rs10810780	1.00[CEU][hapmap]
rs10962944	0.90[EUR][1000 genomes]
rs10962949	0.91[EUR][1000 genomes]
rs10962956	0.93[EUR][1000 genomes]
rs10962958	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962959	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962993	0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10962994	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10962996	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[MKK][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962998	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962999	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10963000	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10963001	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10963005	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10963015	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10963017	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10963018	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10963019	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10963022	0.87[EUR][1000 genomes]
rs10963025	0.87[EUR][1000 genomes]
rs10963030	0.81[EUR][1000 genomes]
rs10963031	0.81[EUR][1000 genomes]
rs10963036	0.80[EUR][1000 genomes]
rs10963039	0.81[EUR][1000 genomes]
rs10963040	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10963041	0.81[EUR][1000 genomes]
rs10963045	0.80[CEU][hapmap]
rs10963069	0.84[CEU][hapmap]
rs10963073	1.00[CEU][hapmap]
rs10963077	1.00[CEU][hapmap]
rs10963078	1.00[CEU][hapmap]
rs11515075	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11523716	0.92[EUR][1000 genomes]
rs11523726	0.82[EUR][1000 genomes]
rs11789418	0.89[EUR][1000 genomes]
rs11789741	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11789786	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs11791463	0.89[EUR][1000 genomes]
rs11795325	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12156444	1.00[CEU][hapmap]
rs12376505	0.93[EUR][1000 genomes]
rs12376938	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12376973	0.80[EUR][1000 genomes]
rs12377081	0.90[EUR][1000 genomes]
rs12378677	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12379538	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs12379655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551355	0.80[EUR][1000 genomes]
rs12553516	1.00[CEU][hapmap]
rs13283291	1.00[CEU][hapmap]
rs13283891	0.81[EUR][1000 genomes]
rs13285577	1.00[CEU][hapmap]
rs13286311	0.93[EUR][1000 genomes]
rs13286365	1.00[CEU][hapmap]
rs13287407	0.87[EUR][1000 genomes]
rs13289670	0.80[EUR][1000 genomes]
rs13289755	0.89[EUR][1000 genomes]
rs13289968	1.00[CEU][hapmap]
rs13292365	0.91[EUR][1000 genomes]
rs13292380	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13292550	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13301284	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1348278	0.84[JPT][hapmap]
rs1372703	1.00[CEU][hapmap]
rs1442517	1.00[CEU][hapmap]
rs17755748	0.87[EUR][1000 genomes]
rs17828423	0.87[EUR][1000 genomes]
rs17829280	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1889087	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1953106	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2027014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095156	0.90[EUR][1000 genomes]
rs2151342	1.00[CEU][hapmap]
rs2184063	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2383013	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584538	0.95[CEU][hapmap]
rs34189605	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34256131	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs34502029	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597155	0.90[EUR][1000 genomes]
rs34768018	0.92[EUR][1000 genomes]
rs35884270	0.87[EUR][1000 genomes]
rs35968717	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35998538	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36063154	0.80[EUR][1000 genomes]
rs36077273	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3739490	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3808783	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3808791	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3808794	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs3808795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317676	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4375098	0.84[CEU][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405013	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4574939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4626705	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4961438	0.83[JPT][hapmap]
rs4961536	0.82[JPT][hapmap]
rs4961559	0.94[CEU][hapmap];0.84[JPT][hapmap]
rs59833414	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60520802	0.85[AMR][1000 genomes]
rs61565870	0.86[EUR][1000 genomes]
rs62558297	0.90[EUR][1000 genomes]
rs62558300	0.91[EUR][1000 genomes]
rs62558301	0.91[EUR][1000 genomes]
rs62558320	0.89[EUR][1000 genomes]
rs62558354	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7026852	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7028577	1.00[CEU][hapmap]
rs7041744	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7042230	0.90[EUR][1000 genomes]
rs7867175	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs894379	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv892662	chr9:17168867-17329964	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1031269	chr9:17204320-17316969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv892663	chr9:17243746-17329964	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv892664	chr9:17250170-17296630	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv892666	chr9:17256043-17280616	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
17	nsv892667	chr9:17269437-17296630	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv613695	chr9:17273731-17348412	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13290659	CNTLN	cis	Nerve Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:17262600-17280400	Weak transcription	Liver	Liver
3	chr9:17262800-17339800	Weak transcription	Left Ventricle	heart
4	chr9:17268600-17280000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:17270000-17280600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:17271600-17275600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr9:17272600-17275800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:17272800-17274800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr9:17272800-17279800	Weak transcription	Fetal Lung	lung
10	chr9:17272800-17280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:17272800-17280800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:17272800-17293000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:17273200-17301800	Weak transcription	Dnd41	blood
14	chr9:17274200-17278400	Weak transcription	Colon Smooth Muscle	Colon

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