Variant report

Variant	rs55654850
Chromosome Location	chr10:28518885-28518886
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28518323..28520452-chr10:28523797..28525301,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10763652	0.86[ASN][1000 genomes]
rs10763653	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826426	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826427	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826428	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826429	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10826431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10826438	0.88[ASN][1000 genomes]
rs10826439	0.88[ASN][1000 genomes]
rs11006921	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006924	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006930	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006931	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006940	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006941	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11006942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11006953	0.84[ASN][1000 genomes]
rs11006972	0.87[ASN][1000 genomes]
rs11006974	0.88[ASN][1000 genomes]
rs11006975	0.88[ASN][1000 genomes]
rs11006976	0.88[ASN][1000 genomes]
rs11006977	0.88[ASN][1000 genomes]
rs11006979	0.88[ASN][1000 genomes]
rs11006980	0.87[ASN][1000 genomes]
rs11006981	0.87[ASN][1000 genomes]
rs11006982	0.87[ASN][1000 genomes]
rs11813709	0.88[ASN][1000 genomes]
rs11814117	0.88[ASN][1000 genomes]
rs12243871	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12243947	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12247867	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12258617	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12258912	0.88[ASN][1000 genomes]
rs12263084	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12263807	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12264931	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12355677	0.87[ASN][1000 genomes]
rs12356457	0.87[ASN][1000 genomes]
rs12357214	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12357236	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12357685	0.87[ASN][1000 genomes]
rs12358399	0.88[ASN][1000 genomes]
rs12359569	0.88[ASN][1000 genomes]
rs12359994	0.88[ASN][1000 genomes]
rs1418758	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16928633	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1840877	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1840878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1840879	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34130351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3847384	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs41406248	0.90[ASN][1000 genomes]
rs58057536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845919	0.88[ASN][1000 genomes]
rs61845921	0.88[ASN][1000 genomes]
rs61845936	0.88[ASN][1000 genomes]
rs6481511	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6481512	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6481513	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6481514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070142	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7070175	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7071331	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072173	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7072854	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7078842	0.88[ASN][1000 genomes]
rs7081371	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7084650	0.88[ASN][1000 genomes]
rs7084702	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7084878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7085924	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7086267	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7086807	0.88[ASN][1000 genomes]
rs7086943	0.88[ASN][1000 genomes]
rs7091031	0.88[ASN][1000 genomes]
rs7091331	0.88[ASN][1000 genomes]
rs7092706	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094807	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7097351	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100582	0.88[ASN][1000 genomes]
rs7100619	0.87[ASN][1000 genomes]
rs7100983	0.88[ASN][1000 genomes]
rs7101006	0.88[ASN][1000 genomes]
rs73608074	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74129028	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7893685	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7893733	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7893878	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7893935	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7896797	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7911615	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7923023	0.87[ASN][1000 genomes]
rs9664773	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9665710	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	nsv831817	chr10:28369836-28539930	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28467600-28525600	Weak transcription	Aorta	Aorta
2	chr10:28487600-28529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:28491200-28523200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr10:28498200-28531200	Weak transcription	Primary B cells from cord blood	blood
5	chr10:28498200-28537000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:28502000-28531600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:28502400-28523000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr10:28502400-28525000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:28507200-28528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:28507400-28522000	Weak transcription	Primary T cells from cord blood	blood
11	chr10:28507400-28525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr10:28507400-28530600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr10:28507600-28531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:28509800-28524000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr10:28510200-28523200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:28510800-28530400	Weak transcription	HSMMtube	muscle
17	chr10:28511000-28528800	Weak transcription	Fetal Heart	heart
18	chr10:28515600-28528000	Weak transcription	Gastric	stomach
19	chr10:28516000-28523000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:28516600-28527400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:28516800-28530400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr10:28517600-28521200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr10:28518400-28531000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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