Variant report

Variant	rs12258617
Chromosome Location	chr10:28506171-28506172
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:28505448..28507000-chr10:28508709..28511532,2	K562	blood:
2	chr10:28503327..28506252-chr10:28507179..28508857,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10763652	0.89[ASN][1000 genomes]
rs10763653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826426	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826429	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10826431	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10826432	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10826438	0.85[ASN][1000 genomes]
rs10826439	0.85[ASN][1000 genomes]
rs11006921	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006940	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006941	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11006942	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11006953	0.81[ASN][1000 genomes]
rs11006972	0.84[ASN][1000 genomes]
rs11006974	0.85[ASN][1000 genomes]
rs11006975	0.85[ASN][1000 genomes]
rs11006976	0.85[ASN][1000 genomes]
rs11006977	0.85[ASN][1000 genomes]
rs11006979	0.85[ASN][1000 genomes]
rs11006980	0.84[ASN][1000 genomes]
rs11006981	0.84[ASN][1000 genomes]
rs11006982	0.84[ASN][1000 genomes]
rs11813709	0.85[ASN][1000 genomes]
rs11814117	0.85[ASN][1000 genomes]
rs12243871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258912	0.85[ASN][1000 genomes]
rs12263084	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12263807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355677	0.84[ASN][1000 genomes]
rs12356457	0.84[ASN][1000 genomes]
rs12357214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357685	0.84[ASN][1000 genomes]
rs12358399	0.85[ASN][1000 genomes]
rs12359569	0.85[ASN][1000 genomes]
rs12359994	0.85[ASN][1000 genomes]
rs1418758	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16928633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1840877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1840879	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34130351	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3847384	0.85[ASN][1000 genomes]
rs41406248	0.87[ASN][1000 genomes]
rs55654850	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58057536	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61845919	0.85[ASN][1000 genomes]
rs61845921	0.85[ASN][1000 genomes]
rs61845936	0.85[ASN][1000 genomes]
rs6481511	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6481512	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6481513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6481514	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7070142	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7070175	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7071331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7072173	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7072854	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7078842	0.85[ASN][1000 genomes]
rs7081371	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084650	0.85[ASN][1000 genomes]
rs7084702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7086267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086807	0.85[ASN][1000 genomes]
rs7086943	0.85[ASN][1000 genomes]
rs7091031	0.85[ASN][1000 genomes]
rs7091331	0.85[ASN][1000 genomes]
rs7092706	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7094807	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100582	0.85[ASN][1000 genomes]
rs7100619	0.84[ASN][1000 genomes]
rs7100983	0.85[ASN][1000 genomes]
rs7101006	0.85[ASN][1000 genomes]
rs73608074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74129028	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7893685	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7893733	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7893878	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7893935	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7896797	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7911615	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7923023	0.84[ASN][1000 genomes]
rs9664773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9665710	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv1042524	chr10:28290149-28506812	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv6188	chr10:28489076-28514068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3494702	chr10:28502096-28512894	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3494704	chr10:28502496-28512794	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3494700	chr10:28502799-28512747	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3314296	chr10:28502956-28512061	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3314308	chr10:28502956-28512061	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3514591	chr10:28503047-28511888	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3494699	chr10:28503097-28511918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3494701	chr10:28503107-28511884	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3494705	chr10:28503162-28511857	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3514592	chr10:28503162-28511857	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3494703	chr10:28503269-28511812	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv498723	chr10:28503272-28511810	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3494706	chr10:28503273-28511810	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv14688	chr10:28504295-28511827	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:47 , 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	chr10:28492200-28506800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr10:28492600-28506400	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:28492600-28507200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:28497400-28506600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:28498000-28506600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:28498200-28506600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:28498200-28531200	Weak transcription	Primary B cells from cord blood	blood
11	chr10:28498200-28537000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:28499000-28506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:28499000-28507000	Weak transcription	Ovary	ovary
14	chr10:28500400-28506800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:28501800-28506200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr10:28502000-28506400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:28502000-28531600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:28502400-28506600	Weak transcription	Primary T cells from cord blood	blood
19	chr10:28502400-28523000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr10:28502400-28525000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:28502600-28506600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:28502600-28507000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr10:28503400-28506200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr10:28503400-28506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:28503800-28515600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr10:28504200-28506600	Enhancers	Hela-S3	cervix
27	chr10:28504200-28506800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:28504400-28506600	Enhancers	HSMM	muscle
29	chr10:28504600-28509400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr10:28505000-28506600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr10:28505000-28506600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr10:28505000-28506800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:28505000-28506800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:28505200-28506200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr10:28505200-28506200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:28505200-28506200	Weak transcription	Psoas Muscle	Psoas
37	chr10:28505200-28506800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:28505200-28506800	Weak transcription	Lung	lung
39	chr10:28505200-28507000	Weak transcription	Esophagus	oesophagus
40	chr10:28505200-28507000	Weak transcription	Stomach Mucosa	stomach
41	chr10:28505200-28507200	Weak transcription	Gastric	stomach
42	chr10:28505200-28507200	Weak transcription	Pancreas	Pancrea
43	chr10:28505200-28508800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr10:28505200-28512000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:28505600-28506600	Enhancers	HSMMtube	muscle
46	chr10:28505800-28506400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:28506000-28516000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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