Variant report

Variant	rs12783598
Chromosome Location	chr10:89539414-89539415
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	chr10:89539239..89541985-chr10:89576945..89578679,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138138	Chromatin interaction
ENSG00000223820	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10082347	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051441	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10887748	0.89[YRI][hapmap]
rs10887749	0.89[YRI][hapmap]
rs10887750	0.89[YRI][hapmap]
rs10887753	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202526	0.89[YRI][hapmap]
rs11202527	0.89[YRI][hapmap]
rs11202531	0.81[EUR][1000 genomes]
rs11202536	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11202538	0.90[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202557	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202563	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202564	0.85[CEU][hapmap]
rs11202565	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202568	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11202571	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11498630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11812787	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11816798	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11817759	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11818430	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12247482	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12253113	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12413371	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12570131	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12570639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12571331	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12572346	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12572581	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12573160	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12573349	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12762731	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12762914	0.85[AFR][1000 genomes]
rs12764439	0.80[EUR][1000 genomes]
rs12765184	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12765681	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12768487	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12769214	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12769771	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12770433	0.90[EUR][1000 genomes]
rs12770684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771188	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771844	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12772552	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12773536	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12775017	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12775041	0.89[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12776656	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12778199	0.89[CEU][hapmap];1.00[EUR][1000 genomes]
rs12779667	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12779915	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12780234	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12780237	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12781171	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12782128	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12782235	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782454	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096702	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1819162	0.89[CEU][hapmap];1.00[EUR][1000 genomes]
rs1819163	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853167	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1923260	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923261	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923262	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960047	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1993845	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038554	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057358	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2067661	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306157	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34325090	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34466534	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34559481	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34878240	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35254974	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35388513	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35662941	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35814940	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3740278	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3816651	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4443987	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4933461	0.89[YRI][hapmap]
rs4934363	0.89[YRI][hapmap]
rs4934364	0.89[YRI][hapmap]
rs4934366	0.89[YRI][hapmap]
rs4934367	0.89[YRI][hapmap]
rs4934369	0.94[AFR][1000 genomes]
rs6586102	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66863455	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7068497	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7073644	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7090088	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090432	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7096449	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7098653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7480	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7481	0.84[CEU][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7898915	0.85[CEU][hapmap]
rs7901767	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7904344	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7905932	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7908203	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7910692	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913763	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7920554	0.89[YRI][hapmap]
rs7920778	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7920910	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7921017	0.88[YRI][hapmap]
rs7921889	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9651491	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9663978	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9664653	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89463000-89541400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:89473000-89577200	Weak transcription	Gastric	stomach
3	chr10:89476200-89542400	Weak transcription	Pancreas	Pancrea
4	chr10:89495000-89541400	Weak transcription	Right Ventricle	heart
5	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:89495200-89542600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:89495200-89544600	Weak transcription	Brain Substantia Nigra	brain
8	chr10:89495200-89559200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
10	chr10:89498200-89541400	Weak transcription	Aorta	Aorta
11	chr10:89504200-89551800	Weak transcription	Psoas Muscle	Psoas
12	chr10:89507000-89557600	Weak transcription	Lung	lung
13	chr10:89510200-89553800	Weak transcription	Esophagus	oesophagus
14	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
15	chr10:89512800-89560400	Weak transcription	Fetal Brain Male	brain
16	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr10:89514600-89539800	Weak transcription	Fetal Kidney	kidney
18	chr10:89516000-89541200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:89516400-89541400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:89516400-89557800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:89518200-89556600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:89518400-89559000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr10:89520200-89542800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:89520400-89556400	Weak transcription	Brain Germinal Matrix	brain
25	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
26	chr10:89521800-89540400	Weak transcription	Thymus	Thymus
27	chr10:89523200-89553000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:89523400-89562800	Weak transcription	K562	blood
29	chr10:89523800-89562000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:89524600-89560400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:89526000-89549000	Weak transcription	Brain Angular Gyrus	brain
32	chr10:89526200-89549400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:89526600-89541400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:89527400-89539600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr10:89527400-89539600	Weak transcription	Fetal Brain Female	brain
36	chr10:89527400-89541000	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:89527400-89541400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr10:89527400-89542600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:89527400-89553600	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:89527600-89554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:89527600-89554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr10:89527800-89539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:89527800-89547800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:89528600-89541400	Weak transcription	HepG2	liver
46	chr10:89529600-89542600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr10:89529600-89542800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr10:89530800-89541200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr10:89530800-89549800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain

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