Variant report

Variant	rs12359569
Chromosome Location	chr10:28558058-28558059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28550629..28558294-chr10:28588558..28593348,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10763652	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs10763653	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10763654	0.83[CEU][hapmap]
rs10763655	0.83[CEU][hapmap]
rs10826426	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10826427	0.85[ASN][1000 genomes]
rs10826428	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10826429	0.85[ASN][1000 genomes]
rs10826430	0.84[ASN][1000 genomes]
rs10826431	0.88[ASN][1000 genomes]
rs10826432	0.81[CEU][hapmap]
rs10826438	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826439	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006921	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs11006924	0.85[ASN][1000 genomes]
rs11006930	0.85[ASN][1000 genomes]
rs11006931	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11006940	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs11006941	0.84[CEU][hapmap]
rs11006942	0.88[CEU][hapmap]
rs11006953	0.96[ASN][1000 genomes]
rs11006972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006974	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006979	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006980	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11006982	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11813709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11814117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098410	0.81[EUR][1000 genomes]
rs12243871	0.85[ASN][1000 genomes]
rs12243947	0.85[ASN][1000 genomes]
rs12247867	0.85[ASN][1000 genomes]
rs12258617	0.85[ASN][1000 genomes]
rs12258912	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263084	0.84[ASN][1000 genomes]
rs12263807	0.85[ASN][1000 genomes]
rs12264931	0.85[ASN][1000 genomes]
rs12355677	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12356457	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12357214	0.85[ASN][1000 genomes]
rs12357236	0.85[ASN][1000 genomes]
rs12357685	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12358399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359994	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928633	0.88[CEU][hapmap]
rs1840877	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1840879	0.85[ASN][1000 genomes]
rs3847384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41406248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55654850	0.88[ASN][1000 genomes]
rs58057536	0.88[ASN][1000 genomes]
rs61845919	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845921	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845936	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6481511	0.84[ASN][1000 genomes]
rs6481513	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6481514	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7070142	0.84[ASN][1000 genomes]
rs7070175	0.86[CEU][hapmap]
rs7071331	0.83[ASN][1000 genomes]
rs7072480	0.94[CEU][hapmap]
rs7072588	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7072854	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7078842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081371	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7084650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084702	0.85[ASN][1000 genomes]
rs7084878	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7085924	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7086267	0.85[ASN][1000 genomes]
rs7086807	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090735	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7091031	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092706	0.88[ASN][1000 genomes]
rs7094807	0.84[ASN][1000 genomes]
rs7097351	0.85[ASN][1000 genomes]
rs7100582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7100983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101006	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73608074	0.85[ASN][1000 genomes]
rs74129034	0.87[AFR][1000 genomes]
rs7893685	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7893733	0.84[ASN][1000 genomes]
rs7893878	0.84[ASN][1000 genomes]
rs7893935	0.83[ASN][1000 genomes]
rs7911615	0.88[CEU][hapmap]
rs7923023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9664773	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv525448	chr10:28337570-28563732	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv6199	chr10:28555515-28563204	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 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	chr10:28550400-28582600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:28550600-28562400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr10:28550600-28562600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:28550600-28563600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr10:28551400-28563600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr10:28552800-28558200	Weak transcription	NHEK	skin
7	chr10:28552800-28559000	Weak transcription	Aorta	Aorta
8	chr10:28553000-28559200	Weak transcription	Fetal Stomach	stomach
9	chr10:28553000-28570800	Weak transcription	Esophagus	oesophagus
10	chr10:28553200-28568400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr10:28553400-28569600	Weak transcription	Pancreas	Pancrea
12	chr10:28553600-28558200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr10:28553800-28563400	Weak transcription	HepG2	liver
14	chr10:28556000-28562200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:28556000-28563400	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:28556200-28563400	Weak transcription	Primary T cells from cord blood	blood
17	chr10:28556200-28563400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr10:28556200-28570800	Weak transcription	Primary B cells from cord blood	blood
19	chr10:28556400-28563800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:28556400-28571000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:28557600-28567800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr10:28557800-28568000	Weak transcription	Monocytes-CD14+_RO01746	blood

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