Variant report

Variant	rs859238
Chromosome Location	chr17:15801125-15801126
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11654524	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11655374	0.84[ASN][1000 genomes]
rs11656489	0.84[ASN][1000 genomes]
rs11656518	0.84[ASN][1000 genomes]
rs11658370	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11658454	0.88[ASN][1000 genomes]
rs11658871	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11870637	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12051835	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12603728	0.88[ASN][1000 genomes]
rs12603863	0.88[ASN][1000 genomes]
rs1558409	0.83[ASN][1000 genomes]
rs1613538	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1639393	0.88[ASN][1000 genomes]
rs1639394	0.93[ASN][1000 genomes]
rs17776817	0.82[ASN][1000 genomes]
rs1797453	0.93[ASN][1000 genomes]
rs1797460	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797462	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1889021	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1974626	0.83[ASN][1000 genomes]
rs2429742	0.93[ASN][1000 genomes]
rs2535598	0.93[ASN][1000 genomes]
rs2535599	0.93[ASN][1000 genomes]
rs2586557	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779187	0.91[ASN][1000 genomes]
rs2787070	0.83[EUR][1000 genomes]
rs35743185	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744329	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744330	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3859260	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4297751	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4791653	0.90[ASN][1000 genomes]
rs4792704	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4792705	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62071036	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62071037	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62071038	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62072029	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62072030	0.88[ASN][1000 genomes]
rs62072031	0.90[ASN][1000 genomes]
rs62072032	0.88[ASN][1000 genomes]
rs62072033	0.90[ASN][1000 genomes]
rs62072034	0.89[ASN][1000 genomes]
rs62072052	0.84[ASN][1000 genomes]
rs62072161	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072162	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62072168	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62072173	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62072198	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62072201	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62072203	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62072205	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6502475	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs708590	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs708591	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs708593	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214215	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7218000	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7223657	0.85[ASN][1000 genomes]
rs7503620	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8076401	0.89[ASN][1000 genomes]
rs8079686	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080194	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs859226	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859228	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859229	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs859230	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859233	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs859234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859240	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs859247	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859248	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859252	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859253	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859255	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859256	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859257	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9893636	0.87[ASN][1000 genomes]
rs9894474	0.83[ASN][1000 genomes]
rs9901375	0.84[ASN][1000 genomes]
rs9903682	0.84[ASN][1000 genomes]
rs9907878	0.87[ASN][1000 genomes]
rs9912875	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
4	nsv1062951	chr17:15561070-15890644	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1066023	chr17:15607267-16053512	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
8	nsv1061222	chr17:15672934-15999778	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv907706	chr17:15731923-16056442	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	esv1801208	chr17:15789804-15807280	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1810041	chr17:15789804-15807280	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv1826171	chr17:15789804-15807280	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv1829876	chr17:15789804-15807280	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	esv1811790	chr17:15790320-15807280	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15796000-15811600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:15797200-15812600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:15799400-15804800	Weak transcription	Pancreas	Pancrea
4	chr17:15800400-15801600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:15800600-15801200	Enhancers	GM12878-XiMat	blood
6	chr17:15800800-15801200	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr17:15800800-15801200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr17:15800800-15801200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr17:15800800-15801200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:15800800-15801200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr17:15800800-15801200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr17:15800800-15801400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:15800800-15801400	Active TSS	Primary T cells fromperipheralblood	blood
14	chr17:15800800-15801400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr17:15800800-15801400	Flanking Active TSS	Dnd41	blood
16	chr17:15800800-15801400	Active TSS	NHLF	lung
17	chr17:15800800-15801600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:15800800-15801600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:15800800-15801600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr17:15800800-15801600	Active TSS	Thymus	Thymus
21	chr17:15801000-15801200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr17:15801000-15801200	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr17:15801000-15801200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:15801000-15801200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:15801000-15801200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:15801000-15801200	Active TSS	Osteobl	bone
27	chr17:15801000-15801400	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr17:15801000-15801400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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