Variant report

Variant	rs3122360
Chromosome Location	chr9:17168226-17168227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10465046	0.82[ASN][1000 genomes]
rs10511633	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10756867	0.84[CHB][hapmap]
rs10962886	0.81[EUR][1000 genomes]
rs10962909	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10962922	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10962923	0.81[ASN][1000 genomes]
rs10962924	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10962939	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1113379	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1113380	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1413418	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1413419	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1576958	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1582029	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1759452	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759453	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759457	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs1759458	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759459	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759460	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759462	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759463	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1759464	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1759465	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs1759616	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1930592	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1930639	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1930641	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2039413	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs2044119	0.84[CHB][hapmap]
rs2104915	0.85[EUR][1000 genomes]
rs2151289	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2210539	0.80[EUR][1000 genomes]
rs2774621	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2774622	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2774623	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2774626	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2774629	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2779763	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779766	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2779767	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779768	0.80[EUR][1000 genomes]
rs2779771	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2779772	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2780204	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2780205	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2815173	0.94[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815174	0.80[EUR][1000 genomes]
rs2815176	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2815177	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815181	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815182	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3119847	0.95[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3119848	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808785	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs3814137	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3814139	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3891457	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs4128606	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4147023	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4621917	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs4961529	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961530	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4961534	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4961551	0.94[CHB][hapmap]
rs585682	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs600041	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs600133	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs601960	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs613966	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs614412	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs614471	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs632176	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs634383	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs634446	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs642582	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs646025	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs647013	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs6475109	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475114	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6475115	0.90[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6475122	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6475125	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6475129	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs6475141	0.84[CHB][hapmap]
rs6475143	0.84[CHB][hapmap]
rs6475144	0.84[CHB][hapmap]
rs654521	0.84[CHB][hapmap]
rs664447	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs673587	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs679666	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs7020918	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap]
rs7021738	0.81[ASN][1000 genomes]
rs7030801	0.86[YRI][hapmap];0.91[AMR][1000 genomes]
rs7031133	0.83[JPT][hapmap]
rs7034768	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7035525	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7043703	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7046327	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7850279	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7862069	0.84[CHB][hapmap]
rs7864296	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870101	0.84[CHB][hapmap]
rs7870682	0.89[CEU][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs870270	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9407787	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9407788	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv892657	chr9:17008137-17223492	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	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
5	nsv1023525	chr9:17121773-17236072	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv892659	chr9:17130360-17236376	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17155400-17169400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:17155600-17169200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:17156000-17169000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:17156000-17171400	Weak transcription	Liver	Liver
5	chr9:17156200-17168800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:17156200-17168800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:17156200-17169000	Weak transcription	Left Ventricle	heart
8	chr9:17156200-17171400	Weak transcription	Ovary	ovary
9	chr9:17156200-17171400	Weak transcription	Pancreas	Pancrea
10	chr9:17156200-17171600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:17156200-17177400	Weak transcription	Fetal Stomach	stomach
12	chr9:17156200-17178200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:17156200-17178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:17156400-17169000	Weak transcription	Fetal Lung	lung
15	chr9:17157800-17169000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:17159800-17195600	Weak transcription	Aorta	Aorta
17	chr9:17165400-17169000	Weak transcription	Brain Germinal Matrix	brain
18	chr9:17166000-17169200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:17167000-17170000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:17168000-17169000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:17168000-17171400	Weak transcription	Dnd41	blood
22	chr9:17168000-17172800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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